Products for DNA Research · 2019. 4. 24. · Company awarded patents for a chemical phosphorylation reagent compatible with DMT-ON purification. 2002 . Company made an agreement

Products for DNA Research2019 Catalog

TABLE OF CONTENTS

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INTRODUCTION 5ABOUT US 5CATALOG 6

STERLING 7QUALITY AND PERFORMANCE ASSURED 7

APPLIED BIOSYSTEMS INSTRUMENTS 8STERLING CE PHOSPHORAMIDITES 8STERLING SOLVENTS/REAGENTS 8STERLING SUPPORTS 9AB 3900 POLYSTYRENE MODIFIER COLUMNS 11

EXPEDITE™ INSTRUMENTS 12STERLING CE PHOSPHORAMIDITES 12STERLING SOLVENTS/REAGENTS 12STERLING SUPPORTS 13

DNA PHOSPHORAMIDITES - SPECIAL PACKAGING 15

MERMADE INSTRUMENTS 16STERLING CE PHOSPHORAMIDITES 16STERLING SOLVENTS/REAGENTS 16STERLING SUPPORTS 17

GE HEALTHCARE LIFE SCIENCES INSTRUMENTS 18STERLING CE PHOSPHORAMIDITES 18STERLING SOLVENTS/REAGENTS 19

DR. OLIGO INSTRUMENTS 20STERLING CE PHOSPHORAMIDITES 20STERLING SOLVENTS/REAGENTS 20STERLING SUPPORTS 21OLIGONUCLEOTIDE PURIFICATION 21

ALTERNATIVE PROTECTING GROUPS 22DEPURINATION RESISTANT CE PHOSPHORAMIDITES 22ULTRAMILD CE PHOSPHORAMIDITES 23ULTRAMILD SUPPORTS 23ULTRAMILD SOLVENTS/REAGENTS 23

ULTRAMILD DNA SYNTHESIS 23

SUPPORTS 24GLEN UNYSUPPORT 24GLEN UNYSUPPORT FC 25UNIVERSAL SUPPORT III 26Q-SUPPORTS 27HIGH LOAD CPG 29

REAGENTS 30ALTERNATIVE SOLVENTS/REAGENTS 30CSOFORNON-AQUEOUSOXIDATION 32UNICAP PHOSPHORAMIDITE 32

BACKBONE MODIFICATION 33SULFURIZING REAGENTS 335’-CEPHOSPHORAMIDITES 345’-SUPPORTS 35METHYL PHOSPHONAMIDITES 36PACE PHOSPHORAMIDITES 37METHYL PHOSPHORAMIDITES 38

Oligo synthesis success. The first time and every time.

TABLE OF CONTENTS TABLE OF CONTENTS

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ULTRAMILD SOLVENTS/REAGENTS 38H-PHOSPHONATEMONOMERS 39H-PHOSPHONATEREAGENTS 39THIOPHOSPHORAMIDITES 40LOCKED ANALOG PHOSPHORAMIDITES 41

OLIGONUCLEOTIDE-DIRECTED MUTAGENESIS 42TRIMER PHOSPHORAMIDITES 42

DUPLEX STABILITY MODIFICATION 46BASESAFFECTINGDUPLEXSTABILITY 46ZIPNUCLEICACIDS(ZNA®) 48CDPI3 MGB™ LABELING 48SELECTIVELYBINDINGCOMPLEMENTARY(SBC)OLIGOS 48UNNATURAL BASE PAIRS 48CAPSFORINCREASEDDUPLEXSTABILITYANDBASE-PAIRINGFIDELITY 49

EPIGENETICS 50DNA METHYLATION 50

PCR/SEQUENCING APPLICATIONS 51DUPLEXEFFECTS 51Tm MODULATION 53CLEANAMP™ MONOMERS 54CHAIN TERMINATORS 55

STRUCTURAL STUDIES 57STRUCTURE/ACTIVITY RELATIONSHIP 57HALOGENATED NUCLEOSIDES 60DNA DAMAGE/REPAIR 61CLICK DNA AND RNA LIGATION 645’-LABELINGOFMicroRNAs 642’-5’LINKEDOLIGONUCLEOTIDES 65MUTAGENESIS 66IN SITU SYNTHESIS OF DNA ANALOGS 67PROBING DNA STRUCTURE WITH FLUORESCENT NUCLEOSIDES 68PHOTO-REGULATIONOFDNAFUNCTION 70INHIBITION OF DNA METHYLTRANSFERASES 71LARGE SCALE SYNTHESIS 71NON-CANONICALSTRUCTURES 72G-QUADRUPLEX 72TRIPLEX-FORMINGOLIGONUCLEOTIDES 72i-MOTIFDNASTRUCTURES 72APTAMER DEVELOPMENT 73

MODIFIERS 74TERMINUS MODIFIERS 74SEQUENCE MODIFIERS 773’-MODIFIERS 79CHEMICAL PHOSPHORYLATION 82ALDEHYDE MODIFICATION 83SPACER MODIFIERS 84DENDRIMERS 85BRANCHING PHOSPHORAMIDITE 85PHOTOCLEAVABLE MONOMERS 86CONJUGATION USING CLICK CHEMISTRY 87OLIGO-CLICKKITS 90COPPER-FREECLICKCHEMISTRY 91SERINOL REAGENTS FOR MODIFICATION AND LABELING 94COT SERINOL PHOSPHORAMIDITE 97DABCYL LABELING 98BIOTIN LABELING 99FLUORESCEIN LABELING 102FLUORESCEINLABELING(SIMA) 105

CYANINE LABELING 106ELITECHGROUP DYES AND QUENCHER 108BLACK HOLE QUENCHER DYES 110BLACKBERRY®QUENCHER(BBQ-650®) 112RHODAMINE(TAMRA)LABELING 113ACRIDINE LABELING 114DNP LABELING 114CHOLESTEROL LABELING 115TOCOPHEROL LABELING 115STEARYL LABELING 115N-ACETYLGALACTOSAMINE(GalNAc)LABELING 116CDPI3 MGB™ LABELING 117PSORALEN LABELING 118EDTA LABELING 118FERROCENE LABELING 119METHYLENE BLUE LABELING 119LABELING WITH METAL CHELATES 120LABELING WITH POLYAROMATIC HYDROCARBONS 120PUROMYCIN CPG 121QUENCHEDAUTOLIGATION(QUAL)PROBES 121LABELINGFORPHOTO-REGULATIONOFOLIGONUCLEOTIDES 122LABELLINGWITHULTRAFASTPHOTOCROSS-LINKER 123

RNA SUPPORTS 125RNA SUPPORTS FOR 3’ MODIFICATION 125

RNA SYNTHESIS 126TOM-PROTECTEDRNAPHOSPHORAMIDITES 126RNA SUPPORTS FOR TOM RNA SYNTHESIS 126TBDMS-PROTECTEDRNAPHOSPHORAMIDITES 128RNAPHOSPHORAMIDITES-SPECIALPACKAGING 128ULTRAMILD TBDMS RNA PHOSPHORAMIDITES 129TBDMS RNA SUPPORTS 129ULTRAMILD SOLVENTS/REAGENTS 130

MINOR RNA BASES 131MINORRNAPHOSPHORAMIDITES(TOMPROTECTED) 131RNASEQUENCEMODIFIER(TOMPROTECTED) 132MINORRNAPHOSPHORAMIDITES(TBDMSPROTECTED) 133MINOR RNA TRIPHOSPHATES 136

2’-OME-RNA SYNTHESIS 1372’-OME-RNAPHOSPHORAMIDITES 137ULTRAMILD2’-OME-RNA 138ULTRAMILD SOLVENTS/REAGENTS 1382’-OME-RNASUPPORTS 139MINOR2’-OME-RNAPHOSPHORAMIDITES 1402’-OME-THIOPHOSPHORAMIDITES 142

2’-F RNA SYNTHESIS 1432’-F-RNAPHOSPHORAMIDITES 143

2’-F ANA SYNTHESIS 1442’-F-ARABINONUCLEICACID(2’-F-ANA) 144

2’-OME-RNA-PACE SYNTHESIS 1452’-OME-RNA-PACEPHOSPHORAMIDITES 145

PURIFICATION 147GLEN-PAK™PURIFICATION 147POLY-PAK™PURIFICATION 149GLENGEL-PAK™DESALTING 150OLIGO-AFFINITYSUPPORT 151

TABLE OF CONTENTS INTRODUCTION

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INDEX 162

GENERAL INFORMATION 172ORDERING 172DISCOUNTS 172TERMS AND CONDITIONS OF SALE 172PATENTS 172

ABOUT US

GlenResearchdevelops,manufacturesandmarketsreagents foroligonucleotidesynthesis,modification, labelingandpurification.Thecompanyservescustomersworldwideinvolvedinbasicresearch,diagnosticsandtherapeutics.AlthoughGlenResearch’soriginalmissionwastoprovidestate-of-the-artreagentstoresearchers,thecompanyalsobeganofferingstandardreagentsforoligonucleotidesynthesisbutwiththeinnovationthateverybatchwasaccompaniedbyaCertificateofAnalysis.Theanalyticaltechniquesandqualitycriteriausedfortheevaluationandacceptanceofthesereagentsweretobecomeanindustrystandardyearslater.ThecompanyisheadquarteredinSterling,Virginia.Aprivatelyheldcompany,GlenResearchwasacquiredbyMaravaiLifeSciencesinDecember2017.

OVER 30 YEARS OF ASSURED QUALITY FOR OLIGO SYNTHESIS

1987 GlenResearchwasincorporatedintheCommonwealthof Virginia

1991Company awarded SBIR grant for the investigationof large scale oligonucleotide synthesis usingH-phosphonatechemistry1993

Glen Research introduced the Sterling line of products, anewstandardofqualityforoligonucleotidesynthesis 1995

GlenResearchnegotiatedanexclusiveagreementtosupply5’-biotinphosphoramiditeworldwide

1996 CompanynegotiatedanexclusivelicensewithGileadSciencestosupplyC5-propynylpyrimidinenucleosidesandG-Clampphosphoramidites 1997

GlenResearchmoves intoacustombuiltbuilding inSterling, Virginia

1999 Company awarded patents for a chemica lphosphorylation reagent compatiblewithDMT-ONpurification 2002

CompanymadeanagreementwithEpochBiosciences,Inc.tosupplytheirproprietarydyesandnucleosidesto the research market2003

Glen Research negotiated an agreementwithGEHealthcareBiosciencesCorp.tosupplyCyanineDyesto the research market 2004

Companyawardedpatentsforatrulyuniversalsupportforoligonucleotidesynthesis-USIII.

2006In collaborationwithBerry&Associates, Inc.,GlenResearch awardedpatents for pyrrolo-C analogues(fluorescentCanalogues). 2008

GlenResearchobtainedalicenseforthesaleofGlenUnySupportfromIonisPharmaceuticals

2013In collaborationwithNelsonBiotechnologies, Inc.,companyawardedpatentforserinolphosphoramiditesand supports 2017

GlenResearchisacquiredbyMaravaiLifeSciences

Excellence Since 1987

CATALOG

WelcometotheGlenResearchCatalogcontainingthemostcompleteselectionofproductsforDNAandRNAresearch.TheTableofContentsatthebeginningandtheIndexattheendoftheCatalogarethemostcomprehensivewehaveproduced.Therearealwayslimitationstoprintedcatalogsinafast-movingtechnologysectorandacompleteandup-to-datecatalogisalsomaintainedonourwebsite.

Allminorbases,modifiersandRNAproductsarepackagedforAppliedBiosystemsinstruments.Wecanprovidevialsandcolumnsforawidevarietyofotherinstruments.Asshowninthetabletotheleft,wecanaccommodatecatalognumbersforunusualproductstofitallpopularinstruments.Thetabletotheleftisreproducedonallrelevantspreadsofthiscatalog.

WeareuniqueinconductingaQCtestforsupportstoshowthelengthofoligothatcanbepreparedbeforeadrop-offincouplingduetostericeffectsbeginstooccur.Thedrop-offpointisrecordedintheCertificateofAnalysisorAnalyticalReport.Unlessotherwisespecified,ourminorbaseandmodificationsupportsare1000ÅCPG,whichresultsinimprovedperformanceandtheabilitytomakemuchlongeroligos.Polystyrenesupportsarealsoavailableforsomeofourmostpopularitems.

Forreasonsofqualityassurance,wedonottransferpowdersoroilsfromstockAppliedBiosystemsvialstovialsforotherinstruments.Powdersmaybehygroscopicandelectrostatic,makingtransferdifficult,andoilshavetobedissolvedandthesolventevaporated.Forbestperformance,itispreferableforthecustomertodissolvetheproductandimmediatelytransferthesolutiontothecorrectinstrumentvial.Consequently,theproductwillbedeliveredinanindustry-standardseptum-cappedvialalongwithacleandryvialfortheappropriateinstrument.

GlenResearch’sdistributorscoveraverysignificantpercentageofcountrieswhereoligonucleotidesynthesisiscommonlypracticed.OurvastselectionofunusualproductsisreallyonlycomprehensivelystockedhereinVirginiaandsomeofourwebviewershaveaskedustosetupadirectshippingchannel.Forthem,weoffertheeGlenprogramwhichisdescribedinthefollowingweblink:http://www.glenresearch.com/Reference/eGlen.html.

Authorized distributorsforGlenResearchproductsarelistedbelow.OthercountriesnotlistedarecoveredbydirectsalesfromourSterling,USAoffice.

UK and Ireland Nordic and Baltic Countries Japan

CambioLtdTelephoneNumber:+44(0)1954210200

FaxNumber:+44(0)1954210300e-mailaddresses:[email protected] and

[email protected]:http://www.cambio.co.uk/

BioNordika ASTelephoneNumber:+4723035800

FaxNumber:+4723035801e-mailaddress:[email protected]:http://www.bionordika.no/

NihonTechnoServiceCo.,Ltd.TelephoneNumber:+81298866811

FaxNumber:+81298700210e-mailaddress:[email protected]:http://www.ntsbio.com/

China Belgium Israel

BeijingLeBoBiotechCo.,LtdTelephoneNumber:+86-10-52405563

FaxNumber:+86-10-58850899emailaddress:[email protected] Website:http://www.lab-bio.com/

EurogentecS.A.TelephoneNumber:+3243727400

FaxNumber:+3243727500e-mailaddress:[email protected]:http://www.eurogentec.com/

EisenbergBros.Ltd.TelephoneNumber:972-3-9777000

FaxNumber:972-3-9777001e-mailaddress:[email protected]

Website:http://www.eisenbros.co.il/

Netherlands Germany France

Eurogentecb.v.TelephoneNumber:+31433520698

FaxNumber:+31433541965e-mailaddress:[email protected]

EurogentecGmbHTelephoneNumber:+492212589455


Eurogentecs.a.TelephoneNumber:+33241733373


Republic of Korea

BosungScientificCo.,Ltd.TelephoneNumber:+82-02-6105-5630

FaxNumber:+82-02-6105-5680emailaddress:[email protected]:https://bosungsci.com/

OTHER INSTRUMENT TYPES

Allminorbases,RNAproductsandmodifiersarepackagedinseptum-cappedvialssuitableforABIandotherinstruments.Ifyouwouldlikeanothertypeofvial/columnaddthefollowingtotheendofthecatalognumber.

MonomersFor Instrument type Add

Expedite EMerMade M

ColumnsFor Instrument type Add

Expedite E AppliedBiosystems3900 A MerMade M

(Please inquire for availability of vials and columns for other instrument types.)

QUALITY AND PERFORMANCE ASSURED

GlenResearchhasdevelopedandimplementedaQualityManagementSystem(QMS)designedtoenhance

customersatisfactionbyfocusingonprocessesforcontinualimprovementandonassuranceofconformityto

customer needs, withfullconsiderationofapplicableregulatoryrequirements.

STERLING PERFORMANCE

The standard of accomplishment for DNA and

RNAsynthesis.EverybatchofSterlingreagentsis

analyzedbytitrationtoconfirmexactformulation.

EverybatchofSterlingmonomers,supportsand

activators is synthesis-tested toensureoptimal

performance.CertificatesofAnalysisprovideyour

guaranteeofSterlingPerformance.

isatrademarkofGlenResearchCorporation.

Glen Research offersthehighestlevelofQualityAssuranceforreagentsforDNAandRNAsynthesis-Sterling

QualityandPerformance.WenowapplytheSterlingcriteriaofqualityandperformancetoallofGlenResearch’s

establishedproducts.

Thecommonmonomersandsupports,whosestructuresareillustratedbelow,areavailableforthevarietyof

synthesizerslistedonthefollowingpages.

STERLING

dA-CE Phosphoramidite dC-CE Phosphoramidite Ac-dC-CE Phosphoramidite dG-CE Phosphoramidite dT-CE Phosphoramidite

STERLING QUALITY

The benchmark for excellence in DNA and

RNA synthesis. All Sterlingmaterialsmust

passstringentpurityand identitytestspriorto

acceptance. Sterlingproductsare formulated,

filtered,andpackagedinoptimalenvironments

using specially cleaned and dried glassware

and columns. Color-coded labeling andpost-

packaging analysis guarantee accuracy and

SterlingQuality.

dT-lcaa-CPGdG-lcaa-CPGAc-dC-lcaa-CPGdC-lcaa-CPGdA-lcaa-CPG

STERLING

O

O P N(iPr)2O CNEt

DMTO

NHBz

N

N

N

N

O

O P N(iPr)2O CNEt

DMTO

NHBz

O N

N

O

O P N(iPr)2O CNEt

DMTO

NHAc

O N

N

O

O P N(iPr)2O CNEt

DMTOiBuHN

O

N

N

N

HN

O

O P N(iPr)2O CNEt

DMTOO

O

N

HNCH 3

ODMTO

OOlcaaCPGCCH 2CH 2CO

NHBz

N

N

N

N

ODMTO

NHBz

O N

N


ODMTO

NHAc

O N

N


ODMTO


iBuHN

O

N

N

N

HN

ODMTO


O

O

N

HNCH 3

STERLING INTRODUCTION

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http://www.glenresearch.com/Reference/eGlen.html

mailto:[email protected]


http://www.cambio.co.uk


http://www.bionordika.no


http://www.ntsbio.com


http://www.lab-bio.com/


http://www.eurogentec.com


http://www.eisenbros.co.il





https://bosungsci.com/

QUALITY ASSURANCE

EverybatchoftheseCEPhosphoramiditesistestedasfollows:

1. HPLCa) Identityisconfirmedbycomparison

withareferencesample.b)PurityisdeterminedbyHPLCtobe

≥98.0%.2. TLC

PurityisverifiedbyTLC.3. 31P NMR

Purityisdeterminedby31P NMR to be≥98%.

4. Coupling Test Couplingefficiencyisdeterminedtobe≥99%.

5. Solution Test A0.1Msolutionisdeterminedtobeclearandfreeofparticulatecontamination.

6. Loss on Drying Volatilecontaminantsaredeterminedtobe≤2%.

dmf-dG-CE Phosphoramidite

O

O P N(iPr)2O CNEt

DMTO

(Me)2NN

O

N

N

N

HN

ABI INSTRUMENTS

1. 60mLseptum-cappedvialsusedon oldest ABI 380, 381 and 391 instruments.200mLoxidizerand450mLdeblockscrew-cappedbottlesalso used on ABI 380, 381 and 391 instruments.

2. Smallscrew-cappedvialsusedonABI392and394instruments.

3. Largerscrew-cappedvialsusedonABI392.394and3400instruments.

4. LargebottlesusedonABI3900instruments.

SEE ALSO

Depurination Resistant dA on page 22

ABBREVIATIONS

Ac2O=AceticAnhydride CE=Cyanoethyl CPG = Controlled Pore Glass DCM = Dichloromethane dmf=dimethylformamidine I2 = Iodine lcaa=longchainalkylamino MeIm=1-Methylimidazole µm=micromole(s) nm=nanomole(s) TCA=TrichloroaceticAcid THF=Tetrahydrofuran

dmf-dG-CPG

O

O

DMTO

(Me)2NN

O

N

N

N

HN

C CH 2CH 2C lcaaO O

CPG

STERLING CE PHOSPHORAMIDITES

GlenResearchCE(β-cyanoethyl)PhosphoramiditesareproducedandpackagedtoensurethehighestperformanceonDNAsynthesizers.EveryGlenResearchproductisaccompaniedbyaCertificateofAnalysisandHPLCtrace,showingtheresultsofourQCtesting.EveryGlenResearchmonomervialisspeciallycleanedtoeliminateparticulatecontaminationandtestedtoensureatightfitonsynthesizers.

Item Catalog No. Pack Price ($)

dA-CEPhosphoramidite 10-1000-02 0.25g 12.50 10-1000-05 0.5g 25.00 10-1000-10 1.0g 50.00 10-1000-20 2.0g 100.00 10-1000-40 4.0g 200.00dC-CEPhosphoramidite 10-1010-02 0.25g 12.50 10-1010-05 0.5g 25.00 10-1010-10 1.0g 50.00 10-1010-20 2.0g 100.00 10-1010-40 4.0g 200.00Ac-dC-CEPhosphoramidite 10-1015-02 0.25g 12.50 10-1015-05 0.5g 25.00 10-1015-10 1.0g 50.00 10-1015-20 2.0g 100.00 10-1015-40 4.0g 200.00dG-CEPhosphoramidite 10-1020-02 0.25g 12.50 10-1020-05 0.5g 25.00 10-1020-10 1.0g 50.00 10-1020-20 2.0g 100.00 10-1020-40 4.0g 200.00dmf-dG-CEPhosphoramidite 10-1029-02 0.25g 12.50 10-1029-05 0.5g 25.00 10-1029-10 1.0g 50.00 10-1029-20 2.0g 100.00 10-1029-40 4.0g 200.00dT-CEPhosphoramidite 10-1030-02 0.25g 12.50 10-1030-05 0.5g 25.00 10-1030-10 1.0g 50.00 10-1030-20 2.0g 100.00 10-1030-40 4.0g 200.00

STERLING SOLVENTS/REAGENTS

Allsolventsandreagentsarepreparedtoourexactingspecificationstoensurethehighestsynthesisefficiencyandarepassedthrougha0.2micronfilterduringpackagingtoeliminateparticulatecontamination.GlenResearchusesfreshlysublimed1H-tetrazoleforpremiumperformanceonAppliedBiosystemssynthesizers.

Item Catalog No. Pack Price ($)ActivatorTetrazoleinAcetonitrile 30-3100-451 45mL 40.00 30-3100-522 200mL 100.00 30-3100-573 450mL 200.00 30-3100-624 2000mL 760.00

DiluentAcetonitrile,anhydrous 40-4050-45 60mL 12.00 40-4050-50 100mL 16.00

STERLING CE PHOSPHORAMIDITES (CONT.)


Cap Mix ATHF/Pyridine/Ac2O 40-4110-451 45mL 16.00 40-4110-522 200mL 30.00 40-4110-573 450mL 72.00 40-4110-624 2000mL 325.00

Cap Mix B16%1-MeIminTHF 40-4220-451 45mL 20.00 (This Cap B solution is identical to the 40-4220-522 200mL 40.00 formulation produced by Applied Biosystems.) 40-4220-624 2000mL 425.00

Oxidizing Solution0.02MI2inTHF/Pyridine/H2O 40-4330-521,2 200mL 30.00 40-4330-573 450mL 72.00 40-4330-624 2000mL 325.00

Deblocking Mix3%TCA/DCM 40-4140-571,2 450mL 36.00 40-4140-623,4 2000mL 144.00

STERLING SUPPORTS

All Glen Research CPG supportsusethestandardlongchainalkylamino(lcaa)linkerbutdifferintheglassporesize,500Å,1000Åor2000Å.The500Åsupportisappropriateforshortersequences,whilethe1000Åsupportsperformbetterinthesynthesisoflonger(>30-mer)DNAsequences.The2000Åsupportisbestforverylong(>150-mer)oligonucleotides.WehaveinstitutedanadditionalQCtestforsupportstoshowthelengthofoligothatcanbepreparedbeforeadrop-offincouplingduetostericeffectsbeginstooccur.Thedrop-offpointisrecordedintheCertificateofAnalysis.AllGlenResearchsupportsarefullyend-cappedtoensurethattheCPGsurfaceistotallyinert,therebyavoidingtheintroductionofimpuritysequencescontainingdeletionsatthe3’-terminus.

Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Pack Price($) dA dC dG dT dA,dC,dG,dT Ac-dC dmf-dG (1columnof) eachbase)

500Å Columns

20-2100-42 20-2110-42 20-2120-42 20-2130-42 20-2140-42 20-2113-42 4x0.2µm 40.0020-2100-41 20-2110-41 20-2120-41 20-2130-41 20-2140-41 20-2113-41 4x1.0µm 60.0020-2100-13 20-2110-13 20-2120-13 20-2130-13 20-2113-13 1x10µm 100.00

1000Å Columns

20-2101-45 20-2111-45 20-2121-45 20-2131-45 20-2141-45 20-2115-45 20-2129-45 4x40nm 40.0020-2101-42 20-2111-42 20-2121-42 20-2131-42 20-2141-42 20-2115-42 20-2129-42 4x0.2µm 40.0020-2101-41 20-2111-41 20-2121-41 20-2131-41 20-2141-41 20-2115-41 20-2129-41 4x1.0µm 60.0020-2101-13 20-2111-13 20-2121-13 20-2131-13 20-2115-13 20-2129-13 1x10µm 100.00

APPLIED BIOSYSTEMS INSTRUMENTS APPLIED BIOSYSTEMS INSTRUMENTS

SEE ALSO

Alternative Solvents on page 30

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AB 3900 1000Å CPG COLUMNS

GlenResearch’sAB39001000ÅCPGcolumnsbringthelowercostofCPGtothisplatformwhilemaintainingthehighsynthesisefficiencyof1000ÅCPG.Ourcolumnsofferthefollowingkeyattributes:

• Noneedtochangeinstrumentsettings• Noneedtochangesoftware

parameters• Easierhandlingpost-synthesis

compared to PS• Highquality1000ÅCPGforoptimal

synthesisresults

BULK CPG LOADING

500Åsupports 35-50µmoles/g 1000Åsupports 25-40µmoles/g

AB 3900 1000Å CPG COLUMNS

GlenResearch’sAB39001000ÅCPGcolumnsbringthelowercostofCPGtothisplatformwhilemaintainingthehighsynthesisefficiencyof1000ÅCPG.Ourcolumnsofferthefollowingkeyattributes:

• Noneedtochangeinstrumentsettings• Noneedtochangesoftware

parameters• Easierhandlingpost-synthesis

compared to PS• Highquality1000ÅCPGforoptimal

synthesisresults

STERLING SUPPORTS (CONT.)

Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Pack Price($) dA dC dG dT dA,dC,dG,dT Ac-dC dmf-dG (1columnof) eachbase)

2000Å Columns

20-2102-42 20-2112-42 20-2122-42 20-2132-42 20-2142-42 4x0.2µm 40.00

Low Volume (LV) Polystyrene Columns

26-2100-45 26-2110-45 26-2120-45 26-2130-45 26-2140-45 4x40nm 48.0026-2100-42 26-2110-42 26-2120-42 26-2130-42 26-2140-42 4x0.2µm 48.00

AB 3900 Polystyrene Columns

26-2600-65 26-2610-65 26-2630-65 26-2629-65200x40nm 825.0026-2600-62 26-2610-62 26-2630-62 26-2629-62200x200nm 825.00

AB 3900 1000Å CPG Columns

20-2101-65 20-2131-65 20-2115-65 20-2129-65200x40nm 600.0020-2101-62 20-2131-62 20-2115-62 20-2129-62200x200nm 650.0020-2101-61 20-2131-61 20-2115-61 20-2129-61200x1.0µm 875.00

500Å Bulk CPG

20-2000-01 20-2010-01 20-2020-01 20-2030-01 20-2013-01 0.1g 9.0020-2000-02 20-2010-02 20-2020-02 20-2030-02 20-2013-02 0.25g 20.0020-2000-10 20-2010-10 20-2020-10 20-2030-10 20-2013-10 1.0g 75.00

1000Å Bulk CPG

20-2001-01 20-2011-01 20-2021-01 20-2031-01 20-2015-01 20-2029-01 0.1g 9.0020-2001-02 20-2011-02 20-2021-02 20-2031-02 20-2015-02 20-2029-02 0.25g 20.0020-2001-10 20-2011-10 20-2021-10 20-2031-10 20-2015-10 20-2029-10 1.0g 75.00

2000Å Bulk CPG

20-2002-01 20-2012-01 20-2022-01 20-2032-01 0.1g 15.0020-2002-02 20-2012-02 20-2022-02 20-2032-02 0.25g 30.0020-2002-10 20-2012-10 20-2022-10 20-2032-10 1.0g 105.00


EmptySynthesisColumns-TWIST40nm,0.2umor1um 20-0030-00 Packof10 60.00EmptySynthesisColumns-TWIST10um/15um 20-0040-00 Packof10 300.00ReplacementFrits-TWIST10um/15um 20-0040-0F Packof20 30.00

Productstructuresareshowninpage5.TWISTisatrademarkofGlenResearchCorporation.

AB 3900 POLYSTYRENE MODIFIER COLUMNS

SomeofourmorepopularminorbaseandmodifiersupportsareavailableonpolystyreneincolumnsfullycompatiblewiththeAppliedBiosystems3900synthesizer.TheseincludeourpopularUniversalSupportIII,whichwillallowDNA,RNAorLNAoligostobeproducedonthe3900withANYbaseatthe3’terminus.Atthesametime,weareoffering1μmolecolumnsofUniversalSupport III forthe3900instrument.Structuresandmorecompletedescriptionsarefoundintherelevantcatalogsectionsforeachitem.AB3900columnscanbepreparedwithvirtuallyanyoftheCPGsupportsinthiscatalog.ItisnolongernecessarytoadjusttheflowusingourAB3900CPGcolumns,asnotedintheboxtotheright.ModifiedCPGcolumnsareonlyavailablein200nmolesize-simpleadd‘A’totheregularcatalognumbertoorder.


Universal Support III PS 200nmolecolumns 26-5110-52 Packof10 100.00 40nmolecolumns(AB3900Format) 26-5110-55 Packof10 100.00

GlenUnySupport™PS 200nmolecolumns 26-5140-52 Packof10 100.00 40nmolecolumns 26-5140-55 Packof10 100.00

3’-PhosphatePS 200nmolecolumns 26-2900-52 Packof10 150.00 40nmolecolumns 26-2900-55 Packof10 150.00

3’-PT-Amino-ModifierC6PS 200nmolecolumns 26-2956-52 Packof10 220.00 40nmolecolumns 26-2956-55 Packof10 220.00

3’-(6-FAM)PS 200nmolecolumns 26-2961-52 Packof10 300.00 40nmolecolumns 26-2961-55 Packof10 300.00

3’-DabcylPS 200nmolecolumns 26-5912-52 Packof10 300.00 40nmolecolumns 26-5912-55 Packof10 300.00

3’-TAMRAPS 200nmolecolumns 26-5910-52 Packof10 300.00 40nmolecolumns 26-5910-55 Packof10 300.00

3’-BiotinTEGPS 200nmolecolumns 26-2955-52 Packof10 300.00 40nmolecolumns 26-2955-55 Packof10 300.00

APPLIED BIOSYSTEMS INSTRUMENTS APPLIED BIOSYSTEMS INSTRUMENTS

SEE ALSO

Universal Supports on page 24 Q-Supports on page 27High Load Supports on page 29

SEE ALSO

Universal Supports on page 24

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QUALITY ASSURANCE




≥98.0%.2. TLC






EXPEDITE INSTRUMENTS

1. ForuseonExpedite8905instruments.

2. ForuseonExpedite8909instruments.

BULK CPG LOADING

500Åsupports 35-50µmoles/g 1000Åsupports 25-40µmoles/g

ABBREVIATIONS

Ac2O=AceticAnhydride CE=Cyanoethyl CPG = Controlled Pore Glass DCM = Dichloromethane dmf=dimethylformamidine I2 = Iodine lcaa=longchainalkylamino MeIm=1-Methylimidazole µm=micromole(s) nm=nanomole(s) TCA=TrichloroaceticAcid THF=Tetrahydrofuran


GlenResearchCE(β-cyanoethyl)PhosphoramiditesareproducedandpackagedtoensurethehighestperformanceonDNAsynthesizers.EveryGlenResearchproductisaccompaniedbyaCertificateofAnalysisandHPLCtrace,showingtheresultsofourQCtesting.EveryGlenResearchmonomervialisspeciallycleanedtoeliminateparticulatecontamination.


dA-CEPhosphoramidite 10-1000-C2 0.25g 12.50 10-1000-C5 0.5g 25.00 10-1000-1C 1.0g 50.00 10-1000-2C 2.0g 100.00

dC-CEPhosphoramidite 10-1010-C2 0.25g 12.50 10-1010-C5 0.5g 25.00 10-1010-1C 1.0g 50.00 10-1010-2C 2.0g 100.00

Ac-dC-CEPhosphoramidite 10-1015-C2 0.25g 12.50 10-1015-C5 0.5g 25.00 10-1015-1C 1.0g 50.00 10-1015-2C 2.0g 100.00

dG-CEPhosphoramidite 10-1020-C2 0.25g 12.50 10-1020-C5 0.5g 25.00 10-1020-1C 1.0g 50.00 10-1020-2C 2.0g 100.00

dmf-dG-CEPhosphoramidite 10-1029-C2 0.25g 12.50 10-1029-C5 0.5g 25.00 10-1029-1C 1.0g 50.00 10-1029-2C 2.0g 100.00

dT-CEPhosphoramidite 10-1030-C2 0.25g 12.50 10-1030-C5 0.5g 25.00 10-1030-1C 1.0g 50.00 10-1030-2C 2.0g 100.00


All solventsandreagentsarepreparedtoourexactingspecificationstoensurethehighestsynthesisefficiencyandarepassedthrougha0.2micronfilterduringpackagingtoeliminateparticulatecontamination.GlenResearchusesfreshlysublimed1H-tetrazoleforpremiumperformanceonExpeditesynthesizers.


ActivatorTetrazoleinAcetonitrile 30-3102-661 60mL 50.00 30-3102-522 200mL 100.00 30-3100-572 450mL 200.00


STERLING SOLVENTS/REAGENTS (CONT.)


Anhydrous WashAcetonitrile,anhydrous 40-4050-531 300mL 40.00 40-4050-572 450mL 50.00

Cap Mix ATHF/Ac2O 40-4012-661 60mL 15.00 40-4012-522 200mL 30.00 40-4012-572 450mL 72.00

Cap Mix B10%1-MeIminTHF/Pyridine 40-4122-661 60mL 20.00 40-4122-522 200mL 40.00 40-4122-572 450mL 96.00

Oxidizing Solution0.02MI2inTHF/H2O/Pyridine 40-4132-661 60mL 20.00 40-4132-522 200mL 40.00 40-4132-572 450mL 96.00

Deblocking Mix3%TCA/DCM 40-4140-681 180mL 18.00 40-4140-712 1L 80.00

STERLING SUPPORTS

All Glen Research supportsusethestandard longchainalkylamino(lcaa) linkerbutdiffer intheglassporesize,500Å,1000Åor2000Å.The500Åsupportisappropriateforshortersequences,whilethe1000Åsupportsperformbetterinthesynthesisoflonger(>30-mer)DNAsequences.The2000Åsupportisbestforverylong(>150-mer)oligonucleotides.WehaveinstitutedanadditionalQCtestforsupportstoshowthelengthofoligothatcanbepreparedbeforeadrop-offincouplingduetostericeffectsbeginstooccur.Thedrop-offpointisrecordedintheCertificateofAnalysis.AllGlenResearchsupportsarefullyend-cappedtoensurethattheCPGsurfaceistotallyinert,therebyavoidingtheintroductionofimpuritysequencescontainingdeletionsatthe3’-terminus.

Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Pack Price($) dA dC dG dT dA,dC,dG,dT Ac-dC dmf-dG (1 column of eachbase)

500Å Columns

20-2200-42 20-2210-42 20-2220-42 20-2230-42 20-2240-42 20-2213-42 4x0.2µm 40.0020-2200-41 20-2210-41 20-2220-41 20-2230-41 20-2240-41 20-2213-41 4x1.0µm 60.0020-2200-14 20-2210-14 20-2220-14 20-2230-14 20-2213-14 1x15µm 150.00

1000Å Columns

20-2201-45 20-2211-45 20-2221-45 20-2231-45 20-2241-45 20-2215-45 20-2229-45 4x40nm 40.0020-2201-42 20-2211-42 20-2221-42 20-2231-42 20-2241-42 20-2215-42 20-2229-42 4x0.2µm 40.0020-2201-41 20-2211-41 20-2221-41 20-2231-41 20-2241-41 20-2215-41 20-2229-41 4x1.0µm 60.0020-2201-14 20-2211-14 20-2221-14 20-2231-14 20-2215-14 20-2229-14 1x15µm 150.00

EXPEDITE™ INSTRUMENTS EXPEDITE™ INSTRUMENTS

SEE ALSO


SEE ALSO


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INSTRUMENT TYPES

Glen Research packages these monomersinavarietyofindustry-standardvialsandbottles.Pleaseprovidetheexactspecificationofthebottlerequiredpriortoreceivingaquotation.

STERLING SUPPORTS (CONT.)

Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Pack Price($) dA dC dG dT dA,dC,dG,dT Ac-dC dmf-dG (1 column of eachbase)

2000Å Columns

20-2202-42 20-2212-42 20-2222-42 20-2232-42 20-2242-42 4x0.2µm 40.00

500Å Bulk CPG

20-2000-01 20-2010-01 20-2020-01 20-2030-01 20-2013-01 0.1g 9.0020-2000-02 20-2010-02 20-2020-02 20-2030-02 20-2013-02 0.25g 20.0020-2000-10 20-2010-10 20-2020-10 20-2030-10 20-2013-10 1.0g 75.00

1000Å Bulk CPG

20-2001-01 20-2011-01 20-2021-01 20-2031-01 20-2015-01 20-2029-01 0.1g 9.0020-2001-02 20-2011-02 20-2021-02 20-2031-02 20-2015-02 20-2029-02 0.25g 20.0020-2001-10 20-2011-10 20-2021-10 20-2031-10 20-2015-10 20-2029-10 1.0g 75.00

2000Å Bulk CPG

20-2002-01 20-2012-01 20-2022-01 20-2032-01 0.1g 15.0020-2002-02 20-2012-02 20-2022-02 20-2032-02 0.25g 30.0020-2002-10 20-2012-10 20-2022-10 20-2032-10 1.0g 105.00


EmptySynthesisColumns,40nm,0.2umExpediteStyle 20-0021-02 Packof10 48.00EmptySynthesisColumns,1umExpediteStyle 20-0021-01 Packof10 48.00ReplacementFilters-Expedite 20-0021-0F Packof20 20.00

EmptySynthesisColumns-TWIST10um/15um 20-0040-00 Packof10 300.00ReplacementFrits-TWIST10um/15um 20-0040-0F Packof20 30.00

Productstructuresareshowninpage5.TWISTisatrademarkofGlenResearchCorporation.ExpediteisatrademarkofAppliedBiosystems.

DNA PHOSPHORAMIDITES - SPECIAL PACKAGING

WeofferourhighqualityDNAphosphoramidites specificallypackaged forhigh throughputand large-scale synthesiscustomers.Thesecustomersnormallyrequirehighqualitymaterialsproducedundertheguidelinesofavalidatedqualitymanagementsystemwhilestillbeingpricedaggressively.TheseproductsincludetheusualGlenResearchcertificationandguaranteesandtheyareavailableinlargerpacksorinbulk.ThecorecatalognumbersforregularDNAphosphoramiditesareshownbelow.Fortheseproducts,pleaserequestaquote.


dA-CEPhosphoramidite 10-1000-SPdC-CEPhosphoramidite 10-1010-SPAc-dC-CEPhosphoramidite 10-1015-SPdG-CEPhosphoramidite 10-1020-SPdmf-dG-CEPhosphoramidite 10-1029-SPdT-CEPhosphoramidite 10-1030-SP

EXPEDITE™ INSTRUMENTS DNA PHOSPHORAMIDITES - SPECIAL PACKAGING

SEE ALSO

Universal Supports on page 24 Q-Supports on page 27High Load Supports on page 29

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QUALITY ASSURANCE




≥98.0%.2. TLC






ABBREVIATIONS

Ac2O=AceticAnhydride CE=Cyanoethyl CPG = Controlled Pore Glass DCM = Dichloromethane dmf=dimethylformamidine I2 = Iodine MeIm=1-Methylimidazole TCA=TrichloroaceticAcid THF=Tetrahydrofuran


MerMadesynthesizersbelongtoafamilyofsynthesizers,includingthecolumn-basedMerMade4,MerMade6and12instrumentsand theparallel array synthesizers,MerMade192andMerMade192E,manufacturedbyBioAutomationCorporation.Theirwebsitecanbefoundat:http://www.BioAutomation.com.Phosphoramiditemonomersarepackagedin30mLand240mLamberbottlesfordissolvingataconcentrationof1g/20mLandareconnecteddirectlytotheinstrument.SomeinstrumentsmayalsobeconfiguredtoacceptAppliedBiosystemsserumvials,asshownonpage6.


dA-CEPhosphoramidite 10-1000-02M 0.25g 12.50 10-1000-05M 0.5g 25.00 10-1000-10M 1.0g 50.00 10-1000-5S 5.0g 250.00 10-1000-1S 10.0g 500.00dC-CEPhosphoramidite 10-1010-02M 0.25g 12.50 10-1010-05M 0.5g 25.00 10-1010-10M 1.0g 50.00 10-1010-5S 5.0g 250.00 10-1010-1S 10.0g 500.00Ac-dC-CEPhosphoramidite 10-1015-02M 0.25g 12.50 10-1015-05M 0.5g 25.00 10-1015-10M 1.0g 50.00 10-1015-5S 5.0g 250.00 10-1015-1S 10.0g 500.00dG-CEPhosphoramidite 10-1020-02M 0.25g 12.50 10-1020-05M 0.5g 25.00 10-1020-10M 1.0g 50.00 10-1020-5S 5.0g 250.00 10-1020-1S 10.0g 500.00dmf-dG-CEPhosphoramidite 10-1029-02M 0.25g 12.50 10-1029-05M 0.5g 25.00 10-1029-10M 1.0g 50.00 10-1029-5S 5.0g 250.00 10-1029-1S 10.0g 500.00dT-CEPhosphoramidite 10-1030-02M 0.25g 12.50 10-1030-05M 0.5g 25.00 10-1030-10M 1.0g 50.00 10-1030-5S 5.0g 250.00 10-1030-1S 10.0g 500.00


All solventsandreagentsarepreparedtoourexactingspecificationstoensurethehighestsynthesisefficiencyandarepassedthrougha0.2micronfilterduringpackagingtoeliminateparticulatecontamination.Parallelsynthesizerstypicallyuse5-ethylthio-1H-tetrazole(ETT)asactivatortominimizethechanceofcrystallization.ETTisusedataconcentrationof0.25Minacetonitrile,whichisfarbelowthelevelatwhichcrystallizationmayoccur.


Activator0.25M5-Ethylthio-1H-TetrazoleinAcetonitrile 30-3140-57 450mL 200.00 30-3140-61 960mL 365.00 30-3140-62 2000mL 760.00



DiluentAcetonitrile,anhydrous 40-4050-50 100mL 16.00

Cap Mix ATHF/2,6-Lutidine/Ac2O 40-4010-57 450mL 72.00 40-4010-61 960mL 154.00 40-4010-62 2000mL 325.00

Cap Mix B16%1-MeIminTHF 40-4220-57 450mL 96.00 40-4220-61 960mL 204.00 40-4220-62 2000mL 425.00

Ozidizing Solution0.02MI2inTHF/Pyridine/H2O 40-4330-57 450mL 72.00 40-4330-61 960mL 154.00 40-4330-62 2000mL 325.00

Deblocking Mix3%DichloroaceticacidinDCM 40-4040-57 450mL 36.00 40-4040-61 960mL 75.00 40-4040-62 2000mL 144.003%TCA/DCM 40-4140-57 450mL 36.00 40-4140-61 960mL 75.00 40-4140-62 2000mL 144.00

STERLING SUPPORTS

Columnscontaining1000ÅCPGareavailableinpacksof200tofitMerMadeplates.Regular500Åor1000Åsupports, listed onpage8,mayalsobeusedtofillthewellsofregular96wellplates.However,thisrequireseachplatetobepreparedwitheachnucleosideaccuratelyinallwells.Auniversalsupportclearlyremovestheneedforfourspecificsupportsandmakespreparingplatesstraightforward.GlenUnySupport™40nmolefrits,asdescribedonpage22,canalsobeused.

Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Pack Price($) dA dC dG dT Ac-dC dmf-dG

Mermade 1000Å Columns20-2001-65 20-2021-65 20-2031-65 20-2015-65 20-2029-65 200x50nm 750.0020-2001-62 20-2021-62 20-2031-62 20-2015-62 20-2029-62 200x200nm 750.0020-2001-61 20-2021-61 20-2031-61 20-2015-61 20-2029-61 48x1.0µm 300.00


Glen UnySupport™ 1000 1µmolecolumns 20-5141-91 Packof96 375.00 200nmolecolumns 20-5141-92 Packof96 250.00 40nmolecolumns 20-5141-95 Packof96 250.00

Empty MerMade Columns EmptyMerMadeColumns(50nm) 20-0050-05 Packof48 200.00 EmptyMerMadeColumns(200nmand1µm) 20-0050-02 Packof48 200.00

MERMADE INSTRUMENTS MERMADE INSTRUMENTS

SEE ALSO


SEE ALSO


SEE ALSO

Universal Supports on page 24Q-Supports on page 27High Load Supports on page 29

SEE ALSO

Alternative Activators on page 30

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http://www.BioAutomation.com

QUALITY ASSURANCE




≥98.0%.2. TLC






ABBREVIATIONS

Ac2O=AceticAnhydride CE=Cyanoethyl

CPG = Controlled Pore Glass DCA=DichloroaceticAcid

DCM = Dichloromethane I2 = Iodine MeIm=1-Methylimidazole

µm=micromole(s)

* CapMixBisatwopartformulationthatiscombinedimmediatelybeforeshipment.


GlenResearchCE(β-cyanoethyl)PhosphoramiditesareproducedandpackagedtoensurethehighestperformanceonDNAsynthesizers.EveryGlenResearchproductisaccompaniedbyaCertificateofAnalysisandHPLCtrace,showingtheresultsofourQCtesting.EveryGlenResearchmonomervialisspeciallycleanedtoeliminateparticulatecontamination.


ÄKTA oligopilotdA-CEPhosphoramidite 10-1000-20 2.0g 100.00 10-1000-50 5.0g 250.00

dC-CEPhosphoramidite 10-1010-20 2.0g 100.00 10-1010-50 5.0g 250.00

Ac-dC-CEPhosphoramidite 10-1015-20 2.0g 100.00 10-1015-50 5.0g 250.00

dG-CEPhosphoramidite 10-1020-20 2.0g 100.00 10-1020-50 5.0g 250.00

dmf-dG-CEPhosphoramidite 10-1029-20 2.0g 100.00 10-1029-50 5.0g 250.00

dT-CEPhosphoramidite 10-1030-20 2.0g 100.00 10-1030-50 5.0g 250.00


All solventsandreagentsarepreparedtoourexactingspecificationstoensurethehighestsynthesisefficiencyandarepassedthrougha0.2micronfilterduringpackagingtoeliminateparticulatecontamination.



ÄKTA oligopilot

Activator0.40MTetrazoleinAcetonitrile 30-3105-71 1L 380.00

Cap Mix AAcetonitrile/MeIm 40-4015-71 1L 145.00

Cap Mix B*Acetonitrile/Ac2O/Lutidine 40-4028-71 1L 190.00

Oxidizing Solution0.05MI2inPyridine/H2O 40-4035-71 1L 225.00

Deblocking Mix3%DichloroaceticacidinDCM 40-4040-71 1L 80.003%TCA/DCM 40-4140-71 1L 80.003%DCAinToluene 40-4240-71 1L 145.00

GE HEALTHCARE LIFE SCIENCES INSTRUMENTS GE HEALTHCARE LIFE SCIENCES INSTRUMENTS

SEE ALSO


SEE ALSO


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QUALITY ASSURANCE




≥98.0%.2. TLC






ABBREVIATIONS

Ac2O=AceticAnhydride CE=Cyanoethyl CPG = Controlled Pore Glass DCM = Dichloromethane dmf=dimethylformamidine I2 = Iodine MeIm=1-Methylimidazole TCA=TrichloroaceticAcid THF=Tetrahydrofuran


Dr.Oligosynthesizersbelongtoafamilyofsynthesizers,includingtheparallelarraysynthesizers,Dr.Oligo96,Dr.Oligo192,Dr.Oligo384andDr.Oligo768,manufacturedbyBiolytic®LabPerformance,Inc.inFremont,CA.Theirwebsitecanbefoundat:http://www.biolytic.com.Phosphoramiditemonomersarepackagedin30mLand240mLamberbottlesfordissolvingataconcentrationof1g/20mLandareconnecteddirectlytotheinstrument.SomeinstrumentsmayalsobeconfiguredtoacceptAppliedBiosystemsserumvials,asshownonpage6.


dA-CEPhosphoramidite 10-1000-02M 0.25g 12.50 10-1000-05M 0.5g 25.00 10-1000-10M 1.0g 50.00 10-1000-5S 5.0g 250.00 10-1000-1S 10.0g 500.00

dC-CEPhosphoramidite 10-1010-02M 0.25g 12.50 10-1010-05M 0.5g 25.00 10-1010-10M 1.0g 50.00 10-1010-5S 5.0g 250.00 10-1010-1S 10.0g 500.00

Ac-dC-CEPhosphoramidite 10-1015-02M 0.25g 12.50 10-1015-05M 0.5g 25.00 10-1015-10M 1.0g 50.00 10-1015-5S 5.0g 250.00 10-1015-1S 10.0g 500.00

dG-CEPhosphoramidite 10-1020-02M 0.25g 12.50 10-1020-05M 0.5g 25.00 10-1020-10M 1.0g 50.00 10-1020-5S 5.0g 250.00 10-1020-1S 10.0g 500.00

dmf-dG-CEPhosphoramidite 10-1029-02M 0.25g 12.50 10-1029-05M 0.5g 25.00 10-1029-10M 1.0g 50.00 10-1029-5S 5.0g 250.00 10-1029-1S 10.0g 500.00

dT-CEPhosphoramidite 10-1030-02M 0.25g 12.50 10-1030-05M 0.5g 25.00 10-1030-10M 1.0g 50.00 10-1030-5S 5.0g 250.00 10-1030-1S 10.0g 500.00


All solventsandreagentsarepreparedtoourexactingspecificationstoensurethehighestsynthesisefficiencyandarepassedthrougha0.2micronfilterduringpackagingtoeliminateparticulatecontamination.Parallelsynthesizerstypicallyuse5-ethylthio-1H-tetrazole(ETT)asactivatortominimizethechanceofcrystallization.ETTisusedataconcentrationof0.25Minacetonitrile,whichisfarbelowthelevelatwhichcrystallizationmayoccur.


Activator0.25M5-Ethylthio-1H-TetrazoleinAcetonitrile 30-3140-57 450mL 200.00 30-3140-62 2000mL 760.00



DiluentAcetonitrile,anhydrous 40-4050-50 100mL 16.00

Cap Mix ATHF/2,6-Lutidine/Ac2O 40-4010-57 450mL 72.00 40-4010-62 2000mL 325.00

Cap Mix B16%1-MeIminTHF 40-4220-57 450mL 96.00 40-4220-62 2000mL 425.00

Oxidizing Solution0.02MI2inTHF/Pyridine/H2O 40-4330-57 450mL 72.00 40-4330-62 2000mL 325.00

Deblocking Mix3%DichloroaceticacidinDCM 40-4040-57 450mL 36.00 40-4040-62 2000mL 144.003%TCA/DCM 40-4140-57 450mL 36.00 40-4140-62 2000mL 144.00

STERLING SUPPORTS

Dr.Oligoinstrumentsaredesignedforflexibityintheuseofsupportsandcolumns.TheycanusefrittedplateswithlooseCPG(page8)andAB3900stylepolystyreneandCPGcolumns.GlenUnySupport™40nmolefritscanalsobeused.Dr.Oligoinstrumentsaredesignedforflexibityintheuseofsupportsandcolumns.TheycanusefrittedplateswithlooseCPG(page8)andAB3900stylepolystyreneandCPGcolumns.GlenUnySupport™40nmolefritscanalsobeused.

Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Pack Price($) dA dC dG dT Ac-dC dmf-dG

AB 3900 Polystyrene Columns26-2600-65 26-2610-65 26-2630-65 26-2629-65 200x40nm 825.0026-2600-62 26-2610-62 26-2630-62 26-2629-62 200x200nm 825.00

AB 3900 1000Å CPG Columns20-2101-65 20-2131-65 20-2115-65 20-2129-65 200x40nm 600.0020-2101-62 20-2131-62 20-2115-62 20-2129-62 200x200nm 650.0020-2101-61 20-2131-61 20-2115-61 20-2129-61 200x1.0µm 875.00

OLIGONUCLEOTIDE PURIFICATION

BiolyticLabs.alsoofferstheinnovativeDr.OligoProcessorforhighthroughputpurificationofoligonucleotidesusingGlen-Pak™DNAPurificationCartridges:https://www.biolytic.com/p-6814-dr-oligo-processor-fully-automated.aspx.

DR. OLIGO INSTRUMENTS DR. OLIGO INSTRUMENTS

SEE ALSO


SEE ALSO


SEE ALSO

Alternative Activators on page 30

SEE ALSO

Universal Supports on page 24 Q-Supports on page 27High Load Supports on page 29Glen-Pak™ DNA on page 147

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https://www.biolytic.com/p-6814-dr-oligo-processor-fully-automated.aspx

DEPURINATION RESISTANT CE PHOSPHORAMIDITES

Depurination isdefinedasthecleavageof theglycosidicbondattachingapurinebasetothesugarmoiety. Electronwithdrawingacylprotectinggroupslikebenzoylandisobutyrylonthepurineaminogroup(s)destabilizetheglycosidicbond,whereaselectrondonatingformamidineprotectinggroupsstabilizetheglycosidicbond.Theconsequenceofdepurinationduringoligonucleotidesynthesisisthelossofthepurinebasetoformaninternucleotidelinkagecontainingtheabasicsugaratthatposition.Thissiteisstableduringfurthersynthesiscyclesbut,upondeprotectionwithbasicreagents,theoligonucleotideiscleavedatthatpositionleadingtotwoshorterfragments.Thefragmenttowardsthe5’terminusstillcontainstheDMTgroup.IfDMT-ONpurificationisbeingused,thedepurinatedfragmentsareco-purifiedalongwiththefulllengthproductastruncatedoligonucleotides.

ThemostcommonlyuseddA-CEPhosphoramiditecontainingbenzoylprotectinggroupssufferssubstantialdegradationbydepurinationafterexcessiveexposuretoTCA.Atthesametime,twodepurinationresistantdAmonomers,protectedwithdiethylformamidine (def)anddimethylacetamidine (dma),areessentiallystable todepurinationduring thesameexposuretoTCA.

BothnewdepurinationresistantdAmonomers(defanddmaprotected),wererapidlydeprotectedinammoniumhydroxideandarefullycompatiblewithregulardeprotectionstrategies.Def-protected-dAwasrapidlydeprotectedwithAMAat65°in20minutes,whichmakesitfullycompatiblewithregularAMAdeprotection.Incontrast,thedma-protected-dArequired80minuteswithAMAat65°forcompletedeprotection.

Dmf-dGisalsoadepurinationresistantCEPhosphoramiditewiththeisobutyrylgroupoftheoriginalmonomerreplacedwithdimethylformamidine(dmf).

Althoughdepurinationdoesoccurinregularoligonucleotidesynthesis,thedegradationisatanextremelylowlevel.Howeverincertainothercircumstances,depurinationmaybecomemoresignificant,suchassynthesisoflongoligos,chip-basedsynthesis,andlarge-scalesynthesis


def-dA-CEPhosphoramidite 10-1504-02 0.25g 15.00 10-1504-05 0.5g 30.00 10-1504-10 1.0g 60.00

dma-dA-CEPhosphoramidite 10-1505 Please inquire.

dmf-dG-CEPhosphoramidite 10-1029-02 0.25g 12.50 10-1029-05 0.5g 25.00 10-1029-10 1.0g 50.00 10-1029-20 2.0g 100.00 10-1029-40 4.0g 200.00

def-dA dma-dA

N

N N

N

N

ODMTO

O P N(iPr)2

O CNEt

N(Me)2

Me

N

N N

N

N

ODMTO

O P N(iPr)2

O CNEt

N(Et)2

dmf-dG

O

O P N(iPr)2O CNEt

DMTO

(Me)2NN

O

N

N

N

HN


All minor bases, RNA products andmodifiers are packaged in septum-capped vials suitable forABI andotherinstruments. If youwould like anothertypeofvial/columnaddthefollowingtotheendofthecatalognumber.


Expedite EMerMade M




ULTRAMILD CE PHOSPHORAMIDITES

AnalternativeprotectingschemeforthenormalCEphosphoramiditesshouldallowUltraMILDdeprotectionandshouldnotreactwithawidervarietyoftagsandlabels.Asetofmonomersusingphenoxyacetyl(Pac)protecteddAand4-isopropyl-phenoxyacetyl(iPr-Pac)protecteddG,alongwithacetylprotecteddC,metthedesiredcriteriaforUltraMILDdeprotection.

Werecommendtheuseofphenoxyaceticanhydride(Pac2O)inCapA.ThismodificationremovesthepossibilityofexchangeoftheiPr-PacprotectinggrouponthedGwithacetatefromtheaceticanhydridecappingmix.Cleavageanddeprotectioncanbecarriedoutin2hoursatroomtemperaturewithammoniumhydroxideor4hourswith0.05Mpotassiumcarbonateinmethanol.


Pac-dA-CEPhosphoramidite 10-1601-02 0.25g 15.00 10-1601-05 0.5g 30.00 10-1601-10 1.0g 60.00

Ac-dC-CEPhosphoramidite 10-1015-02 0.25g 12.50 10-1015-05 0.5g 25.00 10-1015-10 1.0g 50.00

iPr-Pac-dG-CEPhosphoramidite 10-1621-02 0.25g 15.00 10-1621-05 0.5g 30.00 10-1621-10 1.0g 60.00

ULTRAMILD SUPPORTS

Item Catalog No. Catalog No. Catalog No. Pack Price($) Pac-dA Ac-dC iPr-Pac-dG

UltraMildCPG(Bulk) 20-2601-01 Listed 20-2621-01 0.1g 18.00 20-2601-02 on 20-2621-02 0.25g 40.00 20-2601-10 Page8 20-2621-10 1.0g 150.00ABIColumns 20-2701-45 20-2115-45 20-2721-45 4X40nm 40.00 20-2701-42 20-2115-42 20-2721-42 4X0.2µm 40.00 20-2701-41 20-2115-41 20-2721-41 4X1µm 60.00 20-2701-13 20-2115-13 20-2721-13 10µm 100.00ExpediteColumns 20-2801-45 20-2215-45 20-2821-45 4X40nm 40.00 20-2801-42 20-2215-42 20-2821-42 4X0.2µm 40.00 20-2801-41 20-2215-41 20-2821-41 4X1µm 60.00 20-2801-14 20-2215-14 20-2821-14 15µm 150.00

ULTRAMILD SOLVENTS/REAGENTS


Cap Mix ATHF/Pyridine/Pac2O 40-4210-52 200mL 140.00 (Applied Biosystems) 40-4210-57 450mL 300.00 THF/Pac2O 40-4212-52 200mL 140.00 (Expedite) 40-4212-57 450mL 300.00

Deprotection Solution0.05MPotassiumCarbonateinMethanol 60-4600-30 30mL 30.00

ULTRAMILD DNA SYNTHESIS




Expedite EMerMade M




Pac-dA Ac-dC

iPr-Pac-dG

O

O P N(iPr)2O CNEt

DMTO

NHAc

O N

N

O

O P N(iPr)2O CNEt

DMTON

N

N

N

NHAcOPh

O

O P N(iPr)2O CNEt

DMTOiPrPhOAcHN

O

N

N

N

HN

ALTERNATIVE PROTECTING GROUPS

SEE ALSO

Universal Support III on page 26

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REFERENCES

(1)A.P.Guzaev,andM.Manoharan,J Am Chem Soc, 2003, 125,2380-2381.

(2)R.K.Kumar,A.P.Guzaev,C.Rentel,andV.T.Ravikumar,Tetrahedron, 2006, 62, 4528.

ELIMINATION CONDITIONS

Reagent Conditions

Ammoniumhydroxide 80°C/2h 55°C/8h

Ammoniumhydroxide/ 80°C/0.5h40%Methylamine(AMA) 65°C/1h 55°C/8h MethylamineGas 65°C/0.5h/30psi PotassiumCarbonate RT/17h in Methanol

t-Butylamine/Water(1:3v/v) 60°C/4h

Glen UnySupport

GLEN UNYSUPPORT

Arecentdevelopmenthasbeentheuseofasupportbasedonamoleculewhichis“conformationallypreorganized”toacceleratethedephosphorylationreaction.1,2Byusingarigidbicyclicmoleculeonthesupport,therateofeliminationismarkedlyfasterthantheoriginalUniversalSupport.ThestructureofGlenUnySupport™isshownbelow.TheN-phenylversion,developedatIsisPharmaceuticalsasUnyLinker™,isavailablefromseveralcompaniesforlargescaleoligosynthesis.GlenUnySupportistheN-methylversion,whichispreferredforhighthroughputoligonucleotidesynthesissincemethylamineratherthananilineisformedondeprotection.WearehappytoofferGlenUnySupportinavarietyofpopularformatsunderlicensefromIonisPharmaceuticals.

Item Catalog No. Pack Price($)

Bulk SupportsGlenUnySupport 20-5040-01 0.1g 11.00 (500ÅCPG) 20-5040-02 0.25g 25.00 20-5040-10 1.0g 95.00

GlenUnySupport 20-5041-01 0.1g 11.00 (1000ÅCPG) 20-5041-02 0.25g 25.00

20-5041-10 1.0g 95.00

HighLoadGlenUnySupport 25-5040-01 0.1g 15.00 25-5040-02 0.25g 30.00 25-5040-10 1.0g 115.00

GlenUnySupportPS 26-5040-01 0.1g 16.00 26-5040-02 0.25g 35.00 26-5040-10 1.0g 125.00

ColumnsThe1000Åcolumnsandfritsbelowareroutinelystocked.

ABI Format (not LV) 1µmolecolumns 20-5141-41 Packof4 60.00 0.2µmolecolumns 20-5141-42 Packof4 40.00 40nmolecolumns 20-5141-45 Packof4 40.00 10µmolecolumn(TWISTFormat) 20-5141-13 Packof1 100.00 40nmolefrits 20-5441-95 Packof96 150.00

Female-FemaleLuerAdapterfor40nmolefrits 20-0060-00 Packof10 20.00

AB 3900 FormatGlenUnySupportPS 200nmolecolumns 26-5140-52 Packof10 100.00 40nmolecolumns 26-5140-55 Packof10 100.00

Expedite Format 1µmolecolumns 20-5241-41 Packof4 60.00 0.2µmolecolumns 20-5241-42 Packof4 40.00 40nmolecolumns 20-5241-45 Packof4 40.00 15µmolecolumn(TWISTFormat) 20-5241-14 Packof1 150.00

96 Well Format (MerMade, etc.) 1µmolecolumns 20-5141-91 Packof96 375.00 200 nmolecolumns 20-5141-92 Packof96 250.00 40nmolecolumns 20-5141-95 Packof96 250.00

INTELLECTUAL PROPERTY

ThisproductiscoveredbyUSPatent7,202,264ownedbyIonisPharmaceuticals,Inc..

NH

O

O

O

O ODMT

N

O

O

Me




Expedite EMerMade M




GLEN UNYSUPPORT FC

TheextendedtimerequiredtocleavethesuccinatelinkageoftheoriginalGlenUnySupportcanbeproblematical,especiallyinhigh-throughputproductionofoligos,duetotheoutgassingofammoniaand/ormethylamine.ThisreductioninconcentrationofgascannecessitatetheevaporationofthecleavagesolutionandadditionoffreshAmmoniumHydroxide:MethylAmine1:1(AMA)orammoniumhydroxide(NH4OH)toensurecompletedeprotectionanddephosphorylationoftheproductoligos.UsingadiglycolatelinkageinGlenUnySupportFCinsteadofthesuccinateinGlenUnySupport,asignificantincreaseintherateofcleavagehasbeenachieved.Theminimumcleavagetimesforbothversionsareasfollows: AMA NH4OHGlenUnySupport 10min. 40min.GlenUnySupportFC 2min. 5min.

WiththecleavagetimeofGlenUnySupportFCreducedtolessthan5minutes,thereisminimallossofvolatilegasand,therefore,noneedtoevaporatethecleavagesolutionandreplenishwithfreshAMAorammoniumhydroxidesolutions.

WeofferGlenUnySupportFCattachedto1000ÅCPGinavarietyofformatssuitedtohighthroughputsynthesis,aswellasinbulkformoreroutineuse.


Bulk SupportGlenUnySupportFC 22-5041-01 0.1g 11.00 (1000ÅCPG) 22-5041-02 0.25g 25.00 22-5041-10 1.0g 95.00

ABI Format (not LV) 1µmolecolumns 22-5141-41 Packof4 60.00 0.2µmolecolumns 22-5141-42 Packof4 40.00 40nmolecolumns 22-5141-45 Packof4 40.00 10µmolecolumn(TWISTFormat) 22-5141-13 Packof1 100.00

AB 3900 FormatGlenUnySupportCPG 200nmolecolumns 22-5141-52 Packof10 100.00 40nmolecolumns 22-5141-55 Packof10 100.00

Expedite Format 1µmolecolumns 22-5241-41 Packof4 60.00 0.2µmolecolumns 22-5241-42 Packof4 40.00 40nmolecolumns 22-5241-45 Packof4 40.00 15µmolecolumn(TWISTFormat) 22-5241-14 Packof1 150.00

96 Well Format (MerMade, etc.) 1µmolecolumns 22-5141-91 Packof96 375.00 200nmolecolumns 22-5141-92 Packof96 250.00 40nmolecolumns 22-5141-95 Packof96 250.00

SUPPORTS

ELIMINATION CONDITIONS

Reagent Conditions

Ammoniumhydroxide 80°C/2h 55°C/8h

Ammoniumhydroxide/ 80°C/0.5h40%Methylamine(AMA) 65°C/1h 55°C/8h MethylamineGas 65°C/0.5h/30psi PotassiumCarbonate RT/17h in Methanol

t-Butylamine/Water(1:3v/v) 60°C/4h


ThisproductiscoveredbyUSPatent7,202,264ownedbyIonisPharmaceuticals,Inc..

Glen UnySupport FC

O

O

O ODMT

N

O

O

MeO

HN

O

SUPPORTS

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SUPPORTS

UNIVERSAL SUPPORT III

Thekeystepintheuseofanyuniversalsupportinoligonucleotidesynthesisisthedephosphorylationofthe3’-phosphategrouptoformthedesired3’-hydroxylgroup.Azhayev1,2hasexcelledintheinvestigationofneighboringgroupassistanceinthedephosphorylationreaction.AmidegroupsmaybeconsideredtobeweakN-Hacidsandcandisplaybasicpropertiesinammoniumhydroxideoraqueousmethylamine.Intheoriginalwork1,2,(±)-3-amino-1,2-propanediolwasusedtoformanoveluniversalsupport(1).Asuccinatelinkerattachesthe3-aminogrouptothesupportandthe2-OHisprotectedwithabase-labilegrouptosetupanamideassistedeliminationinmildlybasicconditions.Inthisway,thedephosphorylationreactionwouldeliminatethedesired3’-OHoligonucleotideintosolutionandtheproductofanyß-eliminationcompetingsidereactionwouldremainboundtothesupport.Afurtherimprovementhasbeenachievedbyusingacarbamategrouptoconnecttheuniversallinkertothesupport,asinourproductUniversalSupportIII(2).UsingUniversalSupportIII,anoligoyieldof>80%canbeachievedonpolymericsupports,withpurityequivalenttothesameoligopreparednormally.

ConditionsforCleavageandDeprotectionareoutlinedinthetableopposite. UniversalSupport IIIhasbeenshowntogenerateoligonucleotideswiththesameefficacyinpolymeraseextensionreactionsasregularoligos.Despitethemildeliminationreaction,oligonucleotidesupto75merinlengthcanbepreparedroutinelywithoutlossofoligoduringthesynthesiscycles.ThissupportisalsousedfortheproductionofsiRNAoligos.


Bulk SupportUniversalSupportIIIPS 26-5010-01 0.1g 16.00 26-5010-02 0.25g 35.00 26-5010-10 1.0g 125.00

ABI Format (not LV) Universal Support III PS 1µmolecolumns 26-5110-41 Packof4 60.00 0.2µmolecolumns 26-5110-42 Packof4 40.00 40nmolecolumns 26-5110-45 Packof4 40.00

10µmolecolumn(TWISTFormat) 26-5110-13 Packof1 100.00

Expedite Format 1µmolecolumns 26-5210-41 Packof4 60.00 0.2µmolecolumns 26-5210-42 Packof4 40.00 40nmolecolumns 26-5210-45 Packof4 40.00

15µmolecolumn(TWISTFormat) 26-5210-14 Packof1 150.00

96 Well Format (MerMade, etc.)Universal Support III PS 1µmolecolumns 26-5110-91 Packof96 375.00 200nmolecolumns 26-5110-92 Packof96 250.00 40nmolecolumns 26-5110-95 Packof96 250.00

AB 3900 FormatUniversal Support III PS 200nmolecolumns 26-5110-52 Packof10 100.00 40nmolecolumns 26-5110-55 Packof10 100.00Universal Support (1)

CLEAVAGE AND DEPROTECTION

1. Cleavage ForstandardandUltraFastdeprotection

protocols, cleave the oligo from the support using 2M ammonia in methanol at room temperature for30minutes.(Onlyforoligonucleotidesgreaterthan50 nucleotides in length, rinse the supportwithafurthervolumeofwater.Combinethetwowashesandevaporatetodryness.)

2. Deprotection Standard Add 1 volume of 30% ammonium

hydroxide, seal and deprotect usingtheconditionsappropriateforremovalof the protecting groups on the nucleobases.

UltraFast Add 1 volume of AMA (ammonium

hydroxide/40%aqueousmethylamine1:1)sealanddeprotectat65°Cfor10minutes.

UltraMild Using Ammonium Hydroxide Add1volumeofammoniumhydroxide,

seal and leave at room temperature for 8hours.

UltraMild Cleavage and Deprotection Using Potassium Carbonate in Methanol Cleave the oligo from the support

using50mMpotassiumcarbonate inmethanol at room temperature for 30 minutes. Seal and leaveovernight atroomtemperature.

O

ODMTO

HNO

NHO

CHCl 2

O


ThisproductiscoveredbyUSPatentNo.:6,770,754andEuropeanPatentNo.:1404695.

DTMO

HNHN

O

CHCl2

O

OUniversal Support III (2)

REFERENCES

(1)A.V.Azhayev,Tetrahedron, 1999, 55, 787-800.

(2)A.V.AzhayevandM.Antopolsky,Tetrahedron, 2001, 57, 4977-4986.

Q/SUCCINATE COMPARISON

Q-Support Succinate (2 minutes (60 minutes cleavage) cleavage)

132 ODU* 125 ODU*

*Average crude yield from eight 1µmole columns deprotected normally.

REFERENCE

(1)R.T.PonandS.Y.Yu,Tetrahedron Lett, 1997, 38, 3327-3330.

SUPPORTS

Q-SUPPORTS

Oligonucleotidesareroutinelypreparedonsupportstowhichthefirstnucleosideisattachedviaasuccinatelinkage.Overtheyears,thesuccinatelinkagehasdemonstratedstabilityduringthesynthesisprocessbuthassufficientlabilitytobecleavedquicklyinthedeprotectionstep.However,ifthecleavagestepiscarriedoutwithammoniumhydroxidemanuallyoronthesynthesizer,itconsumesonehourofprecioustimewhilereleasingonlyabout80%oftheoligonucleotide.Thisstepis,therefore,abottleneckintheproductivityofmanysynthesisgroups.

Isitpossibletofindareplacementtothesuccinategroupwhichoffersgoodstabilitytothesynthesisreagentswhileofferingamuchfastercleavagestep?Theoxalategrouphasbeenshowntobeverylabileduringcleavagebutitsstabilitytothenormalsynthesisreagentsisnotgood,requiringchangesforsuccessfuluse.Inapracticalbutelegantstudy1 of various bifunctional carboxylic acids,RichardPon’s group identifiedhydroquinone-O,O’-diaceticacidas themost satisfactoryalternativetothesuccinategroup.Nucleosideswiththis linkerarm(Q-linker)areattachedtosupportswiththesameeaseasthesuccinyllinkerarm.

Thecleavagetimeinammoniumhydroxideatroomtemperaturewasfoundtobe2minutes,butwhataboutthestabilityduringsynthesis? Howsignificantwasprematurecleavageofoligonucleotideonthesynthesizerbecauseof thebasicreagentsinthecappingmixesandoxidizer?PonshowedthattheQ-linkerisstabletothecappingreagentsbutveryslightlylabiletotheoxidizer(8%cleavageinovernightexposurewhichwouldcorrespondtoabout2,000normalsynthesiscycles).

Wetestedthesignificanceofprematurecleavagebypreparingsixteen20meroligonucleotidesona0.2µmolescale,eightwithsuccinateandeightwithQ-linkers.Thesuccinatesupportedoligoswerecleavedfor1houratroomtemperature,whilethoseontheQ-supportwerecleavedfor2minutes.Bothsetswerethendeprotectednormallywithammoniumhydroxide. TheQ-supportsactuallygave5%betteryieldsofproductthanthesuccinatesupports. Oligopuritieswereequivalentinbothsets.

TheQ-linkerisabsolutelycompatiblewithallhydrolyticcleavageprocedures,butespeciallymildprocedureslikepotassiumcarbonateinmethanol.PonalsoshowedthatitispreferableforRNAsupports,improvingthecleavagetimefor2’-silylprotectednucleosidesupportsfrom2hours(60-65%cleavage)to5minutes(95%cleavage).

WeareofferingQ-linkersofthefourregularnucleosideson500ÅCPGin0.2and1µmolescales.




Expedite EMerMade M




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Q-SUPPORTS (CONT.)

Catalog No. Catalog No. Catalog No. Catalog No. Catalog No. Pack Price($) dA dC Ac-dC dmf-dG dT

500Å Bulk Support21-2000-01 21-2010-01 21-2013-01 21-2029-01 21-2030-01 0.1g 11.0021-2000-02 21-2010-02 21-2013-02 21-2029-02 21-2030-02 0.25g 25.0021-2000-10 21-2010-10 21-2013-10 21-2029-10 21-2030-10 1.0g 95.00

ABI Format (not LV)21-2100-41 21-2110-41 21-2113-41 21-2129-41 21-2130-41 4X1µm 60.0021-2100-42 21-2110-42 21-2113-42 21-2129-42 21-2130-42 4X0.2µm 40.00

Expedite Format21-2200-41 21-2210-41 21-2213-41 21-2229-41 21-2230-41 4X1µm 60.0021-2200-42 21-2210-42 21-2213-42 21-2229-42 21-2230-42 4X0.2µm 40.00

dA-Q dC-Q

dmf-dG-Q dT-Q

SUPPORTS

Ac-dC-Q

OO

DMTOO

OO O

O

NH

NHBz

N

N

N

N

OO

DMTOO

OO O

O

NH

NHBz

O N

N

O

ODMTO

NHAc

O N

N

O

O

O OO

NH

NH

OOO

O

O

Me2NN

O

N

N

N

HN

ODMTO

O O

ODMTO

O

OO O

O

NH

O

O

N

HNCH 3

SUPPORTS

HIGH LOAD CPG

Ourhigh loading support isbasedoncontrolledpore silicaand it retains theusual500Åpores. The spacer is alsoconventional.Theonlysignificantdifferenceistheloadingwhichisintherange80-130µmoles/gorabout2.5timestheloadingofnormal500ÅCPG.TypicalloadingsforourhighloadCPGareinthe100-120µmoles/grange.Asaconsequenceofthehighloading,thissupportshouldnotbeusedforsequenceslongerthan40mers.Thishighloadingsupportisavailableincolumnsformostsynthesizers.The2.5µmolecolumnisidenticaltoourstandard1µmolecolumn(withtheexceptionoftheloading).Itshouldbeusedonoccasionswhengreaterthan1µmoleisdesiredbutwhena10or15µmolesynthesisistoohigh.Itshouldberunusingthe1µmolecycle.The25µmolecolumnisidenticaltothe10µmolecolumnusedonAppliedBiosystemssynthesizers.Itisrunusingthe10µmolecycle.The35µmolecolumnisusedasanalternativetothe15µmoleExpeditecolumn.Againnochangestothestandardcyclearerecommended.Thesupportisofcourseavailableinbulkforuseonlarge-scalesynthesizers.Awordofcautionisinorder.Whenusingacolumnwithahigherloadthanrecommendedbytheinstrumentmanufacturer,thereisamuchsmallermarginforerror.Allreagentsmustbefreshandanhydrousdiluentandactivatormustbeused.Shouldyoudecidetopreparehigher-loadingcolumns,ensurethatthemolarexcessofmonomertosupportnucleosideisatleast5Xandpreferably10X.

Item Catalog No. Catalog No. Catalog No. Catalog No. Pack Price($) dA dC dG dT

Columns (ABI) 25-2100-46 25-2110-46 25-2120-46 25-2130-46 4X2.5µm 75.00 25-2100-17 25-2110-17 25-2120-17 25-2130-17 1X25µm 125.00

(Expedite) 25-2200-46 25-2210-46 25-2220-46 25-2230-46 4X2.5µm 75.00 25-2200-18 25-2210-18 25-2220-18 25-2230-18 1X35µm 185.00

Bulk

25-2000-02 25-2010-02 25-2020-02 25-2030-02 0.25g 25.00 25-2000-10 25-2010-10 25-2020-10 25-2030-10 1.0g 90.00

dT-CPGdG-CPGdC-CPGdA-CPG

ODMTO


NHBz

N

N

N

N

ODMTO

NHBz

O N

N


ODMTO


iBuHN

O

N

N

N

HN

ODMTO


O

O

N

HNCH 3




Expedite EMerMade M




SEE ALSO

Glen UnySupport on page 24

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REAGENTS

5-Ethylthio-1H-tetrazole

ALTERNATIVE SOLVENTS/REAGENTS

GlenResearchoffersalternative solventsand reagents in suitablebottlesand formulations foruseonvariousDNAsynthesizers.Allsolventsandreagentsarepreparedtoourexactingspecificationstoensurethehighestcouplingefficienciesandarepassedthrougha0.2micronfilterduringpackagingtoeliminateparticulatecontamination.GlenResearchofferstheactivatorsbelowinpowderformforlaterdissolutioninanhydrousacetonitrileorasapreparedsolution.


Activator5-Ethylthio-1H-tetrazole(ETT) 30-3040-10 1g 35.00 (Dissolve 1g in 31mL anhydrous 30-3040-20 2g 60.00 acetonitrile for a 0.25M solution) 30-3040-25 25g 500.00

0.25M5-Ethylthio-1H-tetrazoleinAcetonitrile 30-3140-45 45mL 40.00 (Applied Biosystems) 30-3140-52 200mL 100.00 30-3140-57 450mL 200.00 30-3140-62 2L 760.00 (Expedite) 30-3142-52 200mL 100.00 30-3140-57 450mL 200.00

4,5-Dicyanoimidazole(DCI),crystalline 30-3050-10 1g 35.00 (Dissolve 1g in 34mL anhydrous 30-3050-25 25g 500.00 acetonitrile for a 0.25M solution) 0.25MDCIinAcetonitrile 30-3150-45 45mL 40.00 (Applied Biosystems) 30-3150-52 200mL 100.00 30-3150-57 450mL 200.00 30-3150-62 2L 760.00 (Expedite) 30-3152-52 200mL 100.00 30-3150-57 450mL 200.00

5-Benzylthio-1H-tetrazole(BTT) 30-3070-10 1g 35.00 (Dissolve 1g in 21.3mL anhydrous 30-3070-20 2g 60.00 acetonitrile for a 0.25M solution) 30-3070-25 25g 500.00

0.25M5-Benzylthio-1H-tetrazoleinAcetonitrile 30-3170-45 45mL 40.00 (Applied Biosystems) 30-3170-52 200mL 100.00 30-3170-57 450mL 200.00 30-3170-62 2L 760.00 (Expedite) 30-3172-52 200mL 100.00 30-3170-57 450mL 200.00

Saccharin1-Methylimidazole(SMI) 30-3080-10 1g 35.00 (Dissolve 1g in 31mL anhydrous 30-3080-20 2g 60.00 acetonitrile for a 0.2M solution) 30-3080-25 25g 500.00

0.2MSaccharin1-Methylimidazole(SMI)inAcetonitrile 30-3180-45 45mL 40.00 (Applied Biosystems) 30-3180-52 200mL 100.00 30-3180-57 450mL 200.00 30-3180-62 2L 760.00 (Expedite) 30-3182-52 200mL 100.00 30-3180-57 450mL 200.00

ABBREVIATIONS

Ac2O=AceticAnhydride DCA=DichloroaceticAcid DCM = Dichloromethane DMAP=Dimethylaminopyridine I2 = Iodine MeIm=1-Methylimidazole TCA=TrichloroaceticAcid THF=Tetrahydrofuran

DCI

NN

NN

HCH 3CH 2S

N

NH

CN

CN

N

NN

N

H

PhCH2S

5-Benzylthio-1H-tetrazole

NS

O O

O-

H+N

N

Saccharin 1-Methylimidazole


SMI is sold under license from Avecia BiotechnologyInc.

ALTERNATIVE SOLVENTS/REAGENTS (CONT.)


Cap Mix ATHF/Lutidine/Ac2O 40-4010-52 200mL 30.00 40-4010-57 450mL 72.00 40-4010-62 2L 325.00

THF/Ac2O(9:1) 40-4012-62 2L 275.00

Cap Mix B6.5%DMAPinTHF 40-4020-52 200mL 42.00 (Cap B solutions containing DMAP are preferred by some researchers for preparing long oligos.)

10%MeIminTHF 40-4120-52 200mL 30.00 40-4120-57 450mL 72.00 40-4120-62 2L 325.00

10%MeIminTHF/Pyridine(8:1) 40-4122-62 2L 325.00

Oxidizing Solution0.02MI2inTHF/Pyridine/H2O 40-4132-62 2L 325.00

Deblocking Mix3%DCA/DCM 40-4040-57 450mL 36.00 (DCA solutions are more mildly acidic than 40-4040-62 2L 144.00 the TCA equivalents, possibly causing less depurination of dA sites.)

2.5%DCA/DCM 40-4042-57 450mL 36.00 40-4042-62 2L 144.00

REAGENTS

30 31

STER

LIN

GBA

CKBO

NE

MO

DIF

IERS

MIN

OR

BASE

SM

OD

IFIC

ATIO

N/L

ABEL

ING

RNA

AND

2’-O

Me-

RNA

MIS

CELL

ANEO

US

30 31

STER

LIN

G

REAGENTS


This capping reagent is supplied under license.

OO

OCNEtON(iPr)2P

UniCap Phosphoramidite

ON

CH3H3C

SO O

CSO

SEE ALSO

0.1M CSO in PACE Chemistry on page 37

CSO FOR NON-AQUEOUS OXIDATION

Iodine-basedoxidizershavebeenthestandardforDNAandRNAsynthesissincetheadventofautomatedsynthesizers.Theyarefastandefficientoxidizers,typicallyrequiringlessthan30secondsforcompleteoxidationofphosphitetriesterstophosphatetriesters.However,whileiodine-basedoxidizersworkwellformostapplications,therearesomecircumstanceswherenon-aqueousoxidizersmaybeadvantageous,especiallywherethebasesorlinkagesbeingproducedaresensitivetothepresenceofwaterand/oriodineduringsynthesis.

Theuseof(1S)-(+)-(10-camphorsulfonyl)-oxaziridine(CSO)hasbeeninvestigatedasanon-aqueousoxidizerinDNAsynthesis.Forexample,wefoundthata0.5MsolutionofCSOinacetonitrileworkedwellasanoxidizerforthesynthesisofoligoscontainingmultipleincorporationsof7-deaza-dG,comparedwithiodineoxidationwhichcausedsubstantialdegradation.CSOhasalsoworkedwellinthesynthesisofalongpoly-dIoligo,whichcouldnotbepreparedusingiodineoxidationduetothesensitivityofthebase.

CSOhasbeenusedforsynthesizingoligosthatincorporatethephosphonoacetatemodification.Asolutionof0.1MCSOisrecommendedfortheoxidationofPACEmodificationsasthephosphoniteinternucleotidelinkageismoreeasilyoxidizedthanthephosphiteinternucleotidelinkage.WhensynthesizingDNA-phosphonoacetatechimericoligos,a0.5MCSOsolutionisrecommended.


0.5MCSOinAnhydrousAcetonitrile(ABI) 40-4632-52 200mL 250.000.5MCSOinAnhydrousAcetonitrile(Expedite) 40-4632-52E 200mL 250.000.5MCSOinAnhydrousAcetonitrile 40-4632-57 450mL 560.00 (A minimum oxidation time of 3 minutes is required on small scales.)

UNICAP PHOSPHORAMIDITE

Thephosphoramiditeofdiethyleneglycolmonoethylether,UniCap,isthebasisforanalternativecappingreagent.TouseUniCapasacappingamiditeontheExpedite8909orABsynthesizers,diluteittothestandardamiditeconcentrationandplacethevialinposition5ontheinstrument.Cyclescanbemodifiedbyaddingcouplingstepsforamiditereservoir5afterthelastcolumncouplingstep.Thestandardcappingstepscanbeleftoutofthecycle.UniCapPhosphoramiditewasoriginallydevelopedforoligosynthesisonthesurfaceofchipsandisthecappingreagentofchoiceforthisapplication.

Item Catalog No. Pack Price ($) UniCapPhosphoramidite 10-4410-02 0.25g 50.00 10-4410-05 0.5g 100.00 10-4410-10 1.0g 200.00 10-4410-20 2.0g 400.00

BACKBONE MODIFICATION

SULFURIZING REAGENTS

GlenResearch’sSulfurizingReagentsareusedtopreparephosphorothioatelinkagesusingCEphosphoramiditechemistry.Eachreagentexhibitsthefollowingattributes:1)Reliablysoluble,makingthemsafetouseonautomatedsynthesizers.2)Reactionisfast(30seconds),makingtheprocessconvenientonsmallscalesandreadilyamenabletoscale-up.3)Processisefficient,withbetterthan96%ofthelinkagesbeingphosphorothioateandtheremainderbeingphosphodiester.

SulfurizingReagentII(3-((Dimethylamino-methylidene)amino)-3H-1,2,4-dithiazole-3-thione,DDTT)exhibitsallthepropertiesofBeaucageReagentwhileaddingstabilityinsolutiononthesynthesizerANDofferingstrongabilitytosulfurizeRNAlinkages.SulfurizingReagentIIisavailableinpowderformandasastablesolution.


SulfurizingReagentII(DDTT) 40-4037-10 1g 50.00 (Dissolveataconcentrationof1g/100mL 40-4037-20 2g 100.00 toformanapproximate0.05Msolution)

0.05MSulfurizingReagentIIinpyridine/acetonitrile 40-4137-51 100mL 100.00 40-4137-52 200mL 200.00 40-4137-57 450mL 450.00

SS

N SN N

Sulfurizing Reagent II

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5’-CE PHOSPHORAMIDITES

GlenResearch5’-CE(ß-cyanoethyl)Phosphoramiditesaredesignedfortheproductionof5’-5’or3’-3’linkages,usefulinantisense studies,or to synthesizeoligonucleotidesegments in theopposite sense fromnormal synthesis (Reverse Synthesis),forstructuralstudies.ThesemonomersarepackagedinABI-stylevials(seenotebox).


dA-5’-CEPhosphoramidite 10-0001-02 0.25g 75.00 10-0001-05 0.5g 150.00 10-0001-10 1.0g 300.00

dC-5’-CEPhosphoramidite 10-0101-02 0.25g 75.00 10-0101-05 0.5g 150.00 10-0101-10 1.0g 300.00

dmf-dG-5’-CEPhosphoramidite 10-9201-02 0.25g 75.00 10-9201-05 0.5g 150.00 10-9201-10 1.0g 300.00

dT-5’-CEPhosphoramidite 10-0301-02 0.25g 75.00 10-0301-05 0.5g 150.00 10-0301-10 1.0g 300.00

dA-5’-CE Phosphoramidite dC-5’-CE Phosphoramidite dT-5’-CE Phosphoramidite

P(iPr)2NOCNEt

O

ODMT

O

NHBz

N

N

N

N

P(iPr)2NOCNEt

O

ODMT

O

NHBz

N

NOP(iPr)2NOCNEt

O

CH 3HN

N

O

O

ODMT

O

Dmf-dG-5’-CE Phosphoramidite

HN

N

N

O

N

O

ODMT

N(Me)2N

OPN(iPr)2

OCNEt




Expedite EMerMade M




dG-5’-CPG dT-5’-CPG

OO

ODMT

NHBz

N

N

N

N

CPG -lcaa-succinyl

5’-SUPPORTS

Thefollowingsupportsareusedtoproduceoligonucleotideswithnucleaseresistant3’-3’linkagesatthe3’terminus(byattachingregular3’-CEphosphoramidites)ortoproduceoligonucleotidesectionsintheoppositesense(byattaching5’-CEphosphoramidites).ABI-stylecolumnsaresuppliedunlessotherwiserequested(seenotebox).


dA-5’-CPG 20-0002-01 0.1g 50.00 20-0002-10 1.0g 375.001µmolecolumns 20-0012-41 Packof4 100.000.2µmolecolumns 20-0012-42 Packof4 75.0010µmolecolumn(ABI) 20-0012-13 Packof1 225.0015µmolecolumn(Expedite) 20-0012-14 Packof1 300.00

dC-5’-CPG 20-0102-01 0.1g 50.00 20-0102-10 1.0g 375.001µmolecolumns 20-0112-41 Packof4 100.000.2µmolecolumns 20-0112-42 Packof4 75.0010µmolecolumn(ABI) 20-0112-13 Packof1 225.0015µmolecolumn(Expedite) 20-0112-14 Packof1 300.00

dG-5’-CPG 20-0202-01 0.1g 50.00 20-0202-10 1.0g 375.001µmolecolumns 20-0212-41 Packof4 100.000.2µmolecolumns 20-0212-42 Packof4 75.0010µmolecolumn(ABI) 20-0212-13 Packof1 225.0015µmolecolumn(Expedite) 20-0212-14 Packof1 300.00

dT-5’-CPG 20-0302-01 0.1g 50.00 20-0302-10 1.0g 375.001µmolecolumns 20-0312-41 Packof4 100.000.2µmolecolumns 20-0312-42 Packof4 75.0010µmolecolumn(ABI) 20-0312-13 Packof1 225.0015µmolecolumn(Expedite) 20-0312-14 Packof1 300.00

OO

ODMT

O N

N

NHBz

CPG -lcaa-succinylO

O

ODMT

iBuHN

O

N

N

N

HN

CPG -lcaa-succinylO

O

ODMT

O

O

N

HNCH 3

CPG -lcaa-succinyl

dA-5’-CPG dC-5’-CPG

BACKBONE MODIFICATION BACKBONE MODIFICATION

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dA-Me Phosphonamidite dT-Me PhosphonamiditedG-Me PhosphonamiditeAc-dC-Me Phosphonamidite

REFERENCE

(1)M.P.Reddy,F.Farooqui,andN.B.Hanna,TetrahedronLett.,1996,37,8691-8694.

METHYL PHOSPHONAMIDITES

MethylPhosphonamiditesmaybeusedinDNAsynthesizersfollowingconventionalCEPhosphoramiditeprotocolstoproduceoligonucleotidescontainingoneormoremethylphosphonatelinkages.However,deprotectionandpurificationtechniquesdifferandadescriptionoftheproceduresisincludedintheTechnicalBulletin.WealsoofferthedCmonomerwithacetylbaseprotection.1Thisprotectinggroupisremovedwithammoniumhydroxideduringthecleavagestep,eliminatingmodificationatthedCsitesduringthedeprotectionstepusingethylenediamineinethanol.


dA-MePhosphonamidite 10-1100-02 0.25g 50.00 10-1100-05 0.5g 100.00

Ac-dC-MePhosphonamidite 10-1115-02 0.25g 50.00 10-1115-05 0.5g 100.00

dG-MePhosphonamidite 10-1120-02 0.25g 50.00 10-1120-05 0.5g 100.00

dT-MePhosphonamidite 10-1130-02 0.25g 50.00 10-1130-05 0.5g 100.00

O

O P N(iPr)2CH 3

DMTO

N

N

N

N

NHBz

O

O P N(iPr)2CH 3

DMTO

NHAc

O N

N

O

O P N(iPr)2CH 3

DMTO

HN

N

N

N

O

iBuHN

O

O P N(iPr)2CH 3

DMTO

HN

N

O

O

CH 3




Expedite EMerMade M




PACE PHOSPHORAMIDITES

Phosphonoacetate (PACE)modifiedoligonucleotides showgreatpotentialasbiologicalmodifiers inawidevarietyofresearchapplications.PACEmonomersarepartofafamilyofPhosphonocarboxylatemonomers.Themonomerscanbeeasilyincorporatedintocomplexoligonucleotidesandarecompatiblewithawidevarietyofothersugarorheterobasemodifications.PACEDNAcanbeconjugatedthroughthecarboxylicacidfunctionalgroup.TheyhavebeenshowntobeactiveinsiRNAduplexesandacceleratetheinitialrateofcleavagebyRNaseH-1whenincorporatedwithphosphorothioates.However,themostinterestingobservationtodateisthattheyexhibitanunprecedentedenhancementinpenetrationofculturedcells.

PACEmonomersarefullysolubleinacetonitrileatarecommendedconcentrationof0.1MandarecompatiblewithstandardDNAsynthesizers.Asanoptimalcycle,werecommendusingDCIasanactivator(30-3150-XX)anda15minutecouplingtime.Followingcoupling,capusingUnicap(10-4410-XX)witharegularcouplingtimeandthenoxidizeusing0.5MCSOfor3minutes.Alternatively,a33minutecouplingtimeusing0.45Mtetrazole,oxidationusinglow-wateriodine(40-4032-XX)followedbycappingwith6.5%DMAPasCapBwillgiveacceptableresults.Fordeprotection,pre-treatthesynthesiscolumnwith1.5%DBUinanhydrousacetonitrilefor60minutesatroomtemperaturetoremove1,1-dimethyl-2-cyanoethylprotectinggroups.Rinsethecolumnwithacetonitrile,dryunderargonandcompletethedeprotectionwith40%aqueousmethylaminefor2hoursatroomtemperature.


dA-PACEPhosphoramidite 10-1140-02 0.25g 100.00 10-1140-05 0.5g 200.00 10-1140-10 1.0g 400.00

Ac-dC-PACEPhosphoramidite 10-1150-02 0.25g 100.00 10-1150-05 0.5g 200.00 10-1150-10 1.0g 400.00

dG-PACEPhosphoramidite 10-1160-02 0.25g 100.00 10-1160-05 0.5g 200.00 10-1160-10 1.0g 400.00

dT-PACEPhosphoramidite 10-1170-02 0.25g 100.00 10-1170-05 0.5g 200.00 10-1170-10 1.0g 400.00

dA-PACE Phosphoramidite dT-PACE PhosphoramiditedG-PACE PhosphoramiditeAc-dC-PACE Phosphoramidite

N

N N

N

NHBz

ODMTO

O P N(iPr)2

OCN

O

ODMTON

N

NHAc

O

O P N(iPr)2

OCN

O

HN

N

N

O

N

ODMTO

O P N(iPr)2

iBuHN

OCN

O

OCN

O

ODTMO

N

HN

O

O

CH3

O P N(iPr)2


Theseproductsarecoveredbypatents,US 6,693,187 and 7,067,641, and patentspendingownedbyMetasenseTechnologies.Purchaseofalloranyof these products includes a limited licensetousetheproductssolelyforthemanufactureofoligonucleotidesforresearchuseonly.Thislicensespecificallyexcludestheuseoftheproductoroligonucleotidescontainingtheproductfor:(a)therapeuticordiagnosticapplications(includingkits,pools,librariesandotherproducts or services that incorporate oligonucleotidescontainingtheproduct),(b)anyinvivotoxicity/safetystudyinsupportofaninvestigationalnewdrugapplication(orforeigncounterpart),or(c)resale(includingsaleofkits,pools,librariesandotherproducts or services that incorporate theproductoroligonucleotidescontainingtheproduct).Ifsuchactivitieshavecommercialapplication,aseparatelicenseisrequiredfromMetasenseTechnologies.Neithertheproductnoranyproductcreatedthroughitsusemaybeusedinhumanclinicaltrials.

Asimpleagreementmustbesignedbeforeend-usersandcustomoligoservicesmaypurchasetheseproductsforuseasdefinedabove.

http://www.glenresearch.com/Reference/PACE.pdf


SEE ALSO

DCI on page 30UniCap on page 320.5M CSO on page 322’-OMe-PACE on page 145


36 37

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https://www.glenresearch.com/media/productattach//p/a/pace.pdf

METHYL PHOSPHORAMIDITES

Formanyyears,GlenResearchhassuppliedmethylphosphoramiditesinadditiontoß-cyanoethyl(CE)phosphoramiditesforthefewsituationswherethemore labilecyanoethylgroupisnotanadvantage. Someofourcustomers,probablyrememberingthatthemethylgroupwasremovedspecificallywiththiophenol,havetriedtousethesemonomerstopreparetheinteresting,uncharged,andnuclease-resistantmethylphosphotriesterlinkage.Unfortunately,thislinkageislabiletoammoniumhydroxideandtheregularphosphodiesterlinkageisformed(alongwithasmallamountofchainscission).WeofferUltraMildmethylphosphoramiditesforthisapplication.Oligosproducedfromthesemonomerscanbedeprotectedwithpotassiumcarbonateinmethanoltoproducemethylphosphotriesterlinkages.Sincetheselinkagesarediastereomericanduncharged,theoligosmaybehardtohandle.Consequently,itislikelythatchimeraswillbeproducedusingthesemonomersalongwiththeregularUltraMildCEphosphoramidites.IfmanydGresiduesareincludedintheoligonucleotide,werecommendtheuseofphenoxyaceticanhydride(Pac2O)inCapA.Thismodificationremovesthepossibilityofexchangeoftheisopropyl-phenoxyacetate(iPr-Pac)protectinggrouponthedGwithacetatefromtheaceticanhydridecappingmix.


Pac-dA-MePhosphoramidite 10-1301-02 0.25g 25.00 10-1301-05 0.5g 50.00 10-1301-10 1.0g 100.00

Ac-dC-MePhosphoramidite 10-1315-02 0.25g 25.00 10-1315-05 0.5g 50.00 10-1315-10 1.0g 100.00

iPr-Pac-dG-MePhosphoramidite 10-1321-02 0.25g 25.00 10-1321-05 0.5g 50.00 10-1321-10 1.0g 100.00

dT-MePhosphoramidite 10-1330-02 0.25g 25.00 10-1330-05 0.5g 50.00 10-1330-10 1.0g 100.00






Pac-dA-Me Phosphoramidite dT-Me PhosphoramiditeiPr-Pac-dG-Me PhosphoramiditeAc-dC-Me Phosphoramidite

O

O P N(iPr)2O

DMTO

CH 3

N

N

N

N

NHAcOPh

O

O P N(iPr)2O

DMTO

CH 3

NHAc

O N

N

O

O P N(iPr)2O CH 3

DMTO

HN

N

N

N

O

iPr-PhOAcHN

O

O P N(iPr)2O CH 3

DMTO

CH 3

O

O

N

HN

dA-H-Phosphonate dC-H-Phosphonate dG-H-Phosphonate dT-H-Phosphonate

H-PHOSPHONATE MONOMERS

Glen ResearchH-PhosphonatesareanalyzedbyHPLCandaresynthesis-tested.H-Phosphonatesareespeciallyusefulforthepreparationofmodifiedinternucleotidelinkageswhichareunattainablebyphosphoramiditechemistry.Themostpopularapplicationisthepreparationofradiolabeledphosphorothioates,sincethesulfurizationreactioniscarriedoutoffthesynthesizer.ThesemonomersarepackagedinABI-stylevials(seenotebox).


dA-H-Phosphonate,TEASalt 10-1200-02 0.25g 40.00 10-1200-05 0.5g 80.00

dC-H-Phosphonate,DBUSalt 10-1210-02 0.25g 40.00 10-1210-05 0.5g 80.00

dG-H-Phosphonate,TEASalt 10-1220-02 0.25g 40.00 10-1220-05 0.5g 80.00

dT-H-Phosphonate,TEASalt 10-1230-02 0.25g 40.00 10-1230-05 0.5g 80.00

H-PHOSPHONATE REAGENTS

OurH-Phosphonatesolventsandreagentshavebeendiscontinued.H-Phosphonatereagentsareeasilypreparedusinghighpurityproductsandtheformulationsshownbelow.


1-AdamantanecarbonylchlorideisavailablefromAldrich,CatalogNo.117722.Diluteto0.1M. (Activator for monomers and capping reagent)

Acetonitrile/Pyridine(50:50),anhydrous (Monomer Diluent)

Acetonitrile/Pyridine(95:5),anhydrous (Activator Diluent)

1%IsopropylPhosphiteinAcetonitrile/Pyridine(50:50) (Capping Reagent)

Acetonitrile/Pyridine(50:50) (Neutralizer and Wash Solvent)

4%I2inPyridine/H2O/THF(10:10:80)THF/H2O/TEA(80:10:10) (Both reagents are required for oxidation of H-phosphonate linkages)


O

O

P

DMTO

HOO- TEA+

NHBz

N

N

N

N

O

O

P

DMTO

HO

NHBz

O N

N

O- DBU+

O

O

P

DMTO

HN

N

O

O

CH 3

HOO- TEA+

O

O

P

DMTO

HOO- TEA+

iBuHN

O

N

N

N

HN




Expedite EMerMade M




ABBREVIATIONS

I2 = Iodine TEA=Triethylamine THF=Tetrahydrofuran

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REFERENCES

(1)J.Nielsen,W.K.D.Brill,andM.H.Caruthers, Tetrahedron Letters, 1988, 29,2911-2914.

(2)L.Cummins,D.Graff,G.Beaton,W.S.Marshall,andM.H.Caruthers,Biochemistry, 1996, 35,8734-41.

(3)X.Yang,andD.G.Gorenstein,Curr Drug Targets, 2004, 5,705-15.

(4)W.S.Marshall,andM.H.Caruthers,Science, 1993, 259,1564-70.

(5)J.L.Tonkinson,etal.,Antisense Research and Development, 1994, 4,269-278.

(6)X.Yang,etal.,Bioorg Med Chem Lett, 1999, 9,3357-62.

(7)X.Yang,etal.,Ann N Y Acad Sci, 2006, 1082,116-9.

(8)X.Yang,etal.,Nucleic Acids Res, 2002, 30,e132.


THIOPHOSPHORAMIDITES

Replacingtwonon-bridgingoxygenatomswithsulfuratomsinaDNAphosphodiesterlinkagecreatesaphosphorodithioate(PS2)linkage.1LikenaturalDNA,thephosphorodithioatelinkageisachiralatphosphorus.ThisanalogiscompletelyresistanttonucleasedegradationandformscomplexeswithDNAandRNAwithsomewhatreducedstabilities.2Moreover,ithasbeenfoundthatPS2-ODNsbindproteinswithahigheraffinitythantheirphosphodiesteranalogues2-6suggestingthatPS2-ODNsmayhaveadditionalutilityintheformofsulfur-modifiedphosphateesteraptamers(thioaptamers)3,6-8fortherapeuticanddiagnosticapplications.ThiophosphoramiditesarenowcommerciallyavailableafterrecentworkatAMBiotechnologies(http://www.thioaptamer.com/).

1)Thiophosphoramidites(ThioPAs)arenotsolubleinanhydrousacetonitrilediluent.Rather,10%DCM(v/v)inacetonitrileisanidealdiluentforallfourofthethioPAsforafinalamiditeconcentrationof0.15M.

2)ThioPAsaresomewhatlessstablethannormalDNAphosphoramiditesinanhydrousacetonitrilecontaining10%DCM;however,thecouplingefficiencyofallfourthioPAsisnotreducedaftertwodaysinsolutionatroomtemperature.

3)Aftersynthesis,thethioPAbottleonthesynthesizershouldbereplacedwithonecontainingacetonitrilediluentandthesynthesizerlineflushedwithacetonitrile.

Atypicalcycleforthesolid-phasesynthesisofaPS2linkageisdifferentfromastandardcycleforthesynthesisofnormalphosphatelinkages.Aftercoupling,theresultingthiophosphitetriesteristhensulfurizedwithDDTT.CappingiscarriedoutAFTERsulfurization.

Uponcompletionoftheautomatedsynthesis,deprotectioniscarriedoutusingaconcentratedammonia:ethanol(3:1,v:v)mixcontaining20mMDTTat55°Cfor15-16h.


dA-Thiophosphoramidite 10-1700-90 100µmole 150.00 10-1700-02 0.25g 360.00

dC-Thiophosphoramidite 10-1710-90 100µmole 150.00 10-1710-02 0.25g 360.00

dG-Thiophosphoramidite 10-1720-90 100µmole 150.00 10-1720-02 0.25g 360.00

dT-Thiophosphoramidite 10-1730-90 100µmole 150.00 10-1730-02 0.25g 360.00

dA-Thiophosphoramidite dC-Thiophosphoramidite dG-Thiophosphoramidite dT-Thiophosphoramidite

N

N N

N

NHBz

ODMTO

O

PN SCH2CH2S C

O

ODMTO

O

PN SCH2CH2S C

O

N

N

NHBz

O

ODMTO

O

PN SCH2CH2S C

O

HN

N

N

O

NiBuHN

ODMTO

O

PN SCH2CH2S C

O

N

HN

O

O

CH3




Expedite EMerMade M




SEE ALSO

2’-OMe-RNA Thiophosphoramidites on page 168

LOCKED ANALOG PHOSPHORAMIDITES

LockedNucleicAcid(LNA)wasfirstdescribedbyWengelandco-workersin19981asanovelclassofconformationallyrestrictedoligonucleotideanalogues.LNAisabicyclicnucleicacidwherearibonucleosideislinkedbetweenthe2’-oxygenandthe4’-carbonatomswithamethyleneunit.OligonucleotidescontainingLNAexhibitunprecedentedthermalstabilitiestowardscomplementaryDNAandRNA2,whichallowsexcellentmismatchdiscrimination.Infact,thehighbindingaffinityofLNAoligosallowsfortheuseofshortprobesin,forexample,SNPgenotyping3,allelespecificPCRandmRNAsamplepreparation.LNAisrecommendedforuseinanyhybridizationassaythatrequireshighspecificityand/orreproducibility,e.g.,duallabelledprobes,in situhybridizationprobes,molecularbeaconsandPCRprimers.Furthermore,LNAoffersthepossibilitytoadjustTmvaluesofprimersandprobesinmultiplexassays.LNAcanbemixedwithDNAandRNA,aswellasothernucleicacidanalogues,modifiersandlabels.LNAoligonucleotidesarewatersoluble,andcanbeseparatedbygelelectrophoresisandprecipitatedbyethanol.

GlenResearchispleasedtoofferthesehighlyusefulreagents-LockedAnalog(LA)Phosphoramidites-astoolsforthistechnology.


Bz-A-LA-CEPhosphoramidite 10-2000-05 0.5g 75.00 10-2000-10 1.0g 150.00

5-Me-Bz-C-LA-CEPhosphoramidite 10-2011-05 0.5g 75.00 10-2011-10 1.0g 150.00

dmf-G-LA-CEPhosphoramidite 10-2029-05 0.5g 75.00 10-2029-10 1.0g 150.00

T-LA-CEPhosphoramidite 10-2030-05 0.5g 75.00 10-2030-10 1.0g 150.00


Bz-A-LNA 5-Me-Bz-C-LNA dmf-G-LNA T-LNA

N

N N

N

NHBz

ODMTO

O

P

O

N(iPr)2

O CNEt

ODMTO

O

P

O

N(iPr)2

O CNEt

N

N

O

NHBz

CH3

ODMTO

O

P

O

N(iPr)2

O CNEt

HN

N

N

O

NN(Me)2N

ODMTO

O

P

O

N(iPr)2

O CNEt

N

HN

O

O

CH3

REFERENCES

(1a)A.A.Koshkin,S.K.Singh,P.Nielsen,V.K.Rajwanshi,R.Kumar,M.Meldgaard,C.E.Olsen,andJ.Wengel,Tetrahedron,1998, 54,3607-3630.

(1b)S.K.Singh,P.Nielsen,A.A.Koshkin,andJ.Wengel,Chem. Comm., 1998, (4),455-456.

(2) L.KværnøandJ.Wengel,Chem. Comm., 1999,(7),657-658.

(3)P.Mouritzen,A.T.Nielsen,H.M.Pfundheller,Y.Choleva,L.Kongsbak,andS.Møller,Expert Review of Molecular Diagnostics, 2003, 3(1),27-38.

40 41

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BON

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OD

IFIE

RS

http://www.thioaptamer.com/

TRIMER PHOSPHORAMIDITES

Trimer phosphoramidites1-4haveproventobeextremelyvaluablebecausetheyallowcodon-basedmutagenesis,whichcircumventsthecommonproblemsofcodon-bias,frame-shiftmutations,andtheintroductionofnonsenseorstopcodons.5

Thisisaccomplishedbyintroducingamixtureofall20aminoacidcodons(orsubsetthereof)atanylocationwithinthesequencedtobemutated.Thisleadstotheproductionofclonallibrariesofexceptionaldiversitywithorder-of-magnitudeincreasesinaminoacidsequencevariancewhileeithermaintainingauniformaminoaciddistribution6oronethatisbiasedtowardadesiredsetofaminoacids.7

However,difficultiesarisewhentryingto introducemutations inmultipledistal regionsofagenesimultaneously.Thesynthesisoflongoligonucleotidesisrequired,whichinevitablyleadstolowersequencefidelityduetodeletionmutants,depurinationeventsand,toalesserextent,mutationsarisingfromdeaminationofcytidine,forexample.

Anelegant solution to thisproblem is theuseofAntisenseTrimerPhosphoramidites. These trimers are the reversecomplementof the cannonical ‘sense’ codons.When theseantisensecodonsareput into thenoncoding strandofatemplateDNAandamplifiedbyPCR,theywillcodeforthesensecodonintheoppositestrandofDNA.ThisallowsthepowerfultechniqueofPCRAssembly8togeneratenotonlykilobase-sizedgenesfromshort50meroligonucleotides,buttosimultaneouslymutatemultipledistalregionsofthatgene,asshowninFigure1.

ThesenseandtheircorrespondingantisensecodonsarelistedinTable1.Conveniently,manyofourexistingsensetrimerscanactasantisensecodons.Forexample,AAC,whichcodesforasparagine,hastheanticodonGTT,whichisthesensecodonforvaline.However,someoftheexistingtrimers,whiletheycanactasanantisensecodon,arenotgoodchoicesforuse.Forexample,TGG,whichcodesfortryptophan,couldbeusedasanantisensecodonforprolinebecauseCCAisoneofproline’ssynonymouscodons.However,CCAhasarelativelylowCodonAdaptationIndex(CAI)value9inE.coli,whichcouldlimitproteinexpressioninthatcommonlyusedorganism.Forthisreason,theanticodonCGGwaschosenforoptimalexpressioninE.coli,asweretheothernewantisensecodonsshowninboldinTable1.

IncludedinTable1arethereactionfactors(RFs)foreachofthesenseandantisensetrimers.Thereactionfactoriscriticalsincethetrimerswill likelybemixedandtheyexhibitdifferentratesofreactionwhencouplingduringoligonucleotidesynthesis.AnexamplewheretheRFisusedtocompensatefordifferingratesofcouplingfollows.TheRFforAACis1.0andforTACis1.6.Therefore,1.6equivalentsofTACareneededforevery1.0equivalentofAACforequalcouplingrates.Sotoobtain25umolesoftrimermixthatyields,onaverage,a1:1ratioofAAC/TACatthemutationsite,9.6umolesofAACwouldbeaddedto15.4umolesofTAC.

Allofthetrimersareavailableindividuallysotheresearcherscanpreparecustomtrimermixes.Twopre-madecatalogtrimermixesareavailable:13-1991-xx,forincorporatingall20aminoacidcodonsequallyintoasequenceand13-1992-xx,forincorporating19aminoacidcodons(-Cys).Foracustomtrimermixofaparticularsubsetofcodonsoratrimermixthatrepresentsasetoftrimersthatisbiasedtowardaparticularcodonorcodons,[email protected] foraquotationandprojecteddeliverydate.

Thereisaconcernthatthesequenceofthetrimershastobeverified.Forexample,CATcodingforhistidine,hastobedifferentiatedfromTAC,codingfortyrosine.ThesetwotrimershavevirtuallyidenticallipophilicityandtheiridentitycannotbeclearlyconfirmedbyHPLC.Thisproblemhasbeensolved4usingHPLCelectrospraymassspectrometricanalysisofthetrimers,whichprovidesdataconfirmingmolecularweightandsequence.

REFERENCES

(1)A.L.Kayushin,M.D.Korosteleva,A.I.Miroshnikov,W.Kosch,D.Zubov,andN.Piel, Nucleic Acids Research, 1996, 24, 3748-3755.

(2)A.Kayushin,etal.,Nucleos Nucleot, 1999, 18,1531-1533.

(3)A.Kayushin,M.Korosteleva,andA.Miroshnikov, Nucleos Nucleot Nucleic Acids, 2000, 19,1967-1976.

(4)T.Mauriala,S.Auriola,A.Azhayev,A.Kayushin,M.Korosteleva,andA.Miroshnikov, J Pharm Biomed Anal, 2004, 34,199-206.

(5)C.Neylon,Nucleic Acids Res, 2004, 32, 1448-59.

(6)L.R.Krumpe,K.M.Schumacher,J.B.McMahon,L.Makowski,andT.Mori,BMC Biotechnol, 2007, 7,65-72.

(7)F.A.Fellouse,etal.,J Mol Biol, 2007, 373,924-40.

(8)W.P.Stemmer,A.Crameri,K.D.Ha,T.M.Brennan,andH.L.Heyneker,Gene, 1995, 164,49-53.

(9)P.M.Sharp,andW.H.Li,Nucleic Acids Res, 1987, 15,1281-95.

DMTO O P O O P OO O

OClPh OClPh

OCEPB1 B2 B3

General Structure of Trimer Phosphoramidites,

where B=Abz, Cbz, Gibu, T

OLIGONUCLEOTIDE-DIRECTED MUTAGENESIS

Figure 1: Simultaneous Mutation of Multiple Distal Regions of Gene

TABLE 1: RF of Trimer Phosphoramidites

Sense codons Reaction Antisense codons Reaction(5'->3') Factor (RF) (5’->3’) Factor (RF)

AAA(Lys) 1.10 TTT 1.70AAC(Asn) 1.00 GTT 1.90ACT(Thr) 1.60 GGT 1.10ATC(Ile) 1.50 GAT 1.40ATG(Met) 1.30 CAT 1.30CAG(Gln) 2.00 CTG 1.20CAT(His) 1.30 ATG 1.30CCG(Pro) 1.80 CGG 0.80CGT(Arg) 1.40 GCG 0.60CTG(Leu) 1.20 CAG 2.00GAA(Glu) 1.40 TTC 1.30GAC(Asp) 1.60 ATC 1.50GCT(Ala) 1.50 TGC 1.50GGT(Gly) 1.10 ACC 0.90GTT(Val) 1.90 AAC 1.00TAC(Tyr) 1.60 GTA 1.50TCT(Ser) 1.30 AGA 1.40TGC(Cys) 1.50 GCA 1.00TGG(Trp) 1.10 CCA 1.10TTC(Phe) 1.30 GAA 1.40

OO

Cl

ClO

O

O P N(iPr)2O CNEt

O

OP

O

OOP

O

DMTO O

HN

N

O

O

CH 3

N

NO

NHBz

NHBz

N

N

N

N

ATC Trimer

Pool of Oligos

PCR


42 43

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[email protected]



Sense TrimersAAATrimerPhosphoramidite 13-1000-95 50µm 385.00 (Lys) 13-1000-90 100µm 770.00

AACTrimerPhosphoramidite 13-1001-95 50µm 385.00 (Asn) 13-1001-90 100µm 770.00

ACTTrimerPhosphoramidite 13-1013-95 50µm 385.00 (Thr) 13-1013-90 100µm 770.00

ATCTrimerPhosphoramidite 13-1031-95 50µm 385.00 (Ile) 13-1031-90 100µm 770.00

ATGTrimerPhosphoramidite 13-1032-95 50µm 385.00 (Met) 13-1032-90 100µm 770.00

CAGTrimerPhosphoramidite 13-1102-95 50µm 385.00 (Gln) 13-1102-90 100µm 770.00

CATTrimerPhosphoramidite 13-1103-95 50µm 385.00 (His) 13-1103-90 100µm 770.00

CCGTrimerPhosphoramidite 13-1112-95 50µm 385.00 (Pro) 13-1112-90 100µm 770.00

CGTTrimerPhosphoramidite 13-1123-95 50µm 385.00 (Arg) 13-1123-90 100µm 770.00

CTGTrimerPhosphoramidite 13-1132-95 50µm 385.00 (Leu) 13-1132-90 100µm 770.00

GAATrimerPhosphoramidite 13-1200-95 50µm 385.00 (Glu) 13-1200-90 100µm 770.00

GACTrimerPhosphoramidite 13-1201-95 50µm 385.00 (Asp) 13-1201-90 100µm 770.00

GCTTrimerPhosphoramidite 13-1213-95 50µm 385.00 (Ala) 13-1213-90 100µm 770.00

GGTTrimerPhosphoramidite 13-1223-95 50µm 385.00 (Gly) 13-1223-90 100µm 770.00

GTTTrimerPhosphoramidite 13-1233-95 50µm 385.00 (Val) 13-1233-90 100µm 770.00

TACTrimerPhosphoramidite 13-1301-95 50µm 385.00 (Tyr) 13-1301-90 100µm 770.00

TCTTrimerPhosphoramidite 13-1313-95 50µm 385.00 (Ser) 13-1313-90 100µm 770.00

TGCTrimerPhosphoramidite 13-1321-95 50µm 385.00 (Cys) 13-1321-90 100µm 770.00

TGGTrimerPhosphoramidite 13-1322-95 50µm 385.00 (Trp) 13-1322-90 100µm 770.00

TTCTrimerPhosphoramidite 13-1331-95 50µm 385.00 (Phe) 13-1331-90 100µm 770.00

TrimerPhosphoramiditeMix1 13-1991-95 50µm 570.00 (Mixofabove20trimers) 13-1991-90 100µm 1140.00

TrimerPhosphoramiditeMix2 13-1992-95 50µm 570.00 (Mixofabove20trimerslessTGC-Cys) 13-1992-90 100µm 1140.00




Expedite EMerMade M






Antisense TrimersAACTrimerPhosphoramidite 13-1001-95 50µm 385.00 (Anti Val) 13-1001-90 100µm 770.00

ACCTrimerPhosphoramidite 13-1011-95 50µm 385.00 (Anti Gly) 13-1011-90 100µm 770.00

AGATrimerPhosphoramidite 13-1020-95 50µm 385.00 (Anti Ser) 13-1020-90 100µm 770.00

ATCTrimerPhosphoramidite 13-1031-95 50µm 385.00 (Anti Asp) 13-1031-90 100µm 770.00

ATGTrimerPhosphoramidite 13-1032-95 50µm 385.00 (Anti His) 13-1032-90 100µm 770.00

CAGTrimerPhosphoramidite 13-1102-95 50µm 385.00 (Anti Leu) 13-1102-90 100µm 770.00

CATTrimerPhosphoramidite 13-1103-95 50µm 385.00 (Anti Met) 13-1103-90 100µm 770.00

CCATrimerPhosphoramidite 13-1110-95 50µm 385.00 (Anti Trp) 13-1110-90 100µm 770.00

CGGTrimerPhosphoramidite 13-1122-95 50µm 385.00 (Anti Pro) 13-1122-90 100µm 770.00

GAATrimerPhosphoramidite 13-1200-95 50µm 385.00 (Anti Phe) 13-1200-90 100µm 770.00

GATTrimerPhosphoramidite 13-1203-95 50µm 385.00 (Anti Ile) 13-1203-90 100µm 770.00

GCATrimerPhosphoramidite 13-1210-95 50µm 385.00 (Anti Cys) 13-1210-90 100µm 770.00

GCGTrimerPhosphoramidite 13-1212-95 50µm 385.00 (Anti Arg) 13-1212-90 100µm 770.00

GGTTrimerPhosphoramidite 13-1223-95 50µm 385.00 (Anti Thr) 13-1223-90 100µm 770.00

GTATrimerPhosphoramidite 13-1230-95 50µm 385.00 (Anti Tyr) 13-1230-90 100µm 770.00

TGCTrimerPhosphoramidite 13-1321-95 50µm 385.00 (Anti Ala) 13-1321-90 100µm 770.00

TTCTrimerPhosphoramidite 13-1331-95 50µm 385.00 (Anti Glu) 13-1331-90 100µm 770.00

TTTTrimerPhosphoramidite 13-1333-95 50µm 385.00 (Anti Lys) 13-1333-90 100µm 770.00

44 45

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5-Me-dC

BASES AFFECTING DUPLEX STABILITY

SubstitutionofC-5propynyl-dC(pdC)fordCandC-5propynyl-dU(pdU)fordTareeffectivestrategiestoenhancebasepairing.Usingthesebasesubstitutions,duplexstabilityandmeltingtemperaturesareraisedbythefollowingamounts:C-5propynyl-C2.8°persubstitution;C-5propynyl-U1.7°persubstitution.AP-dC(G-clamp)substitutesfordCandisanotherveryimportantmodifiednucleosidethatenhanceshybridizationby7-21°persubstitutiondependinguponthesequenceandlocationoftheAP-dC.Theabilityofthesemodifiedbasestoenhancebindingwhilemaintainingspecificityhasprovenusefulinantisenseresearchandinthesynthesisofhighaffinityprobes.AP-dCisalsoafluorescentnucleosideandshouldfindusesinDNAstructuralresearch.


pdC-CEPhosphoramidite 10-1014-90 100µmole 85.00 10-1014-02 0.25g 245.00 10-1014-05 0.5g 490.00

pdU-CEPhosphoramidite 10-1054-90 100µmole 65.00 10-1054-02 0.25g 195.00 10-1054-05 0.5g 390.00

AP-dC-CEPhosphoramidite 10-1097-95 50µmole 230.00 (G-Clamp) 10-1097-90 100µmole 460.00 10-1097-02 0.25g 1175.00

C-5methylpyrimidinenucleosidesareknown to stabilizeduplexes relative to thenon-methylatedbases. Therefore,enhancedbindingcanbeachievedusing5-methyl-dCinplaceofdC,duplexmeltingtemperaturebeingincreasedby1.3°.Ac-5-Me-dC-CEPhosphoramiditeisfullycompatiblewithAMAdeprotectionandnoneoftheN4-Metransaminationmutantisobservedondeprotection.


5-Me-dC-CEPhosphoramidite 10-1060-90 100µmole 50.00 10-1060-02 0.25g 120.00

Ac-5-Me-dC-CEPhosphoramidite 10-1560-90 100µmole 50.00 10-1560-02 0.25g 120.00

O

O P N(iPr)2O CNEt

DMTO

CH 3

NHBz

O N

N

O

O P N(iPr)2O CNEt

DMTON

HN

O

O

CH 3

O

O P N(iPr)2O CNEt

DMTON

N

O

CH 3

NN(iBu)2

pdC pdU

ONHF3C

OHN

DMTO

O P N(iPr)2O CNEt

N

NO

O

O

AP-dC

ODMTON

N

NHAc

O

O P N(iPr)2

O CNEt

CH3

Ac-5-Me-dC

DUPLEX STABILITY MODIFICATION

BASES AFFECTING DUPLEX STABILITY (CONT.)

ThesimplestapproachtothedesignofhighaffinityprimersandprobesistosubstituteAsiteswith2-amino-A,sincethe2-amino-A-TbasepairisequivalentinstrengthtotheG-Tbasepair.2-Amino-AalsodestabilizesA-Gwobblemismatches,thusincreasingspecificity.In1998,weintroduceda2-amino-dAmonomerwhichexhibitsfastandeffectivedeprotectioninammoniumhydroxideanditisstabilizedtodepurinationduringsynthesis.Wenowrecommendtheuseof0.5MCSOinanhydrousacetonitrile (40-4632-xx) forbest resultswithmultipleadditionsof2-amino-dA. This isbecause thebisformamidineprotected2-amino-dA leads to significant strand scissionwhen standard iodineoxidation isusedduringsynthesis.Forthisreason,wehavealsoaddedPac-2-Amino-dA,amonomerwithoptimizedprotectiontomeetthefollowingcriteria:stableduringoligonucleotidesynthesis,oxidation,anddetritylation;labiletowardscommondeprotectionconditions(NH3, AMA, MeNH2);andthenucleobaseprotectinggroupsarecleavedunderfairlymildconditions.


2-Amino-dA-CEPhosphoramidite 10-1085-95 50µmole 70.00 (2,6-diaminopurine) 10-1085-90 100µmole 125.00 10-1085-02 0.25g 250.00

Pac-2-Amino-dA-CEPhosphoramidite 10-1585-95 50µmole 70.00 (2,6-diaminopurine) 10-1585-90 100µmole 125.00 10-1585-02 0.25g 250.00

SequenceswithhighGCcontentmaycontainmismatchesandstillhybridizebecauseofthehighstabilityoftheG-Cbasepair.TheN4-ethylanalogueofdC(N4-Et-dC)hybridizesspecificallytonaturaldGbutthestabilityofthebasepairisreducedtoaboutthelevelofanATbasepair.

CouplingN6-Me-dA(10-1003)andN4-Et-dC(10-1068)with1H-tetrazoleleadstoatraceofbranchingatthesecondaryaminepositions,whileDCIleadstoaround15%branching.IncollaborationwithBerryandAssociates,theacetylprotectedmonomerswereprepared. Acetylprotectionwaschosen since itwouldblockbranching reactions. OligonucleotidessynthesizedusingthesemonomersprovedtobecompatiblewithallpopulardeprotectionstrategiesfromUltraMildtoUltraFast.WhentheacetylprotectedmonomerswerecomparedwiththeunprotectedmonomersusingDCIasactivator,branchingwasreducedfrom15%tozero.


N4-Et-dC-CEPhosphoramidite 10-1068-95 50µmole 125.00 10-1068-90 100µmole 225.00 10-1068-02 0.25g 675.00

N4-Ac-N4-Et-dC-CEPhosphoramidite 10-1513-95 50µmole 125.00 10-1513-90 100µmole 225.00 10-1513-02 0.25g 675.00

N6-Me-dA-CEPhosphoramidite 10-1003-90 100µmole 162.50 10-1003-02 0.25g 495.00

N6-Ac-N6-Me-dA-CEPhosphoramidite 10-1503-90 100µmole 162.50 10-1503-02 0.25g 495.00

N4-Et-dC

Et

O

O P N(iPr)2O CNEt

DMTO

N

NO

NH

ODMTON

N

NAc

O

O P N(iPr)2

O CNEt

Et

N4-Ac-N4-Et-dC N6-Me-dA

O

O P N(iPr)2O CNEt

DMTO

NHMe

N

N

N

NN

N N

N

NAc

ODMTO

O P N(iPr)2

O CNEt

Me

N6-Ac-N6-Me-dA2-Amino-dA

O

O P N(iPr)2O CNEt

DMTO

N

N

N

N

N

N

N(iBu)2

(iBu)2N

ODMTO

O P N(iPr)2

O CNEt

N

N N

N

N

PhOAcHN

N(nBu)2

Pac-2-Amino-dA




Expedite EMerMade M





SEE ALSO

0.5M CSO on page 32N6-Me-dA on page 62

46 47

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”Sperminephosphoramidite”synthonisthesubjectmatterofU.S.DivisionalPatentApplicationNo.14/745,871,EuropeanPatentNo.1973927andforeignequivalentsforwhichPolyplus-transfectionistheco-owner.Productissoldforresearchpurposesonly.Productshallnotbeusedtomanufactureoligospermine-oligonucleotideconjugatesforuseindiagnostics,clinicalorcommercialapplicationsincludinguseinhumans.Thereisnoimpliedlicensetomanufactureoligospermine-oligonucleotideconjugatesfordiagnostic,clinical,orcommercialapplications,includingbutnotlimitedtocontractresearch.PleasecontactPolyplus-transfectionatlicensing@polyplus-transfection.comtoobtainalicenseforsuchuse.

ZNA®isaregisteredtrademarkofPolyplus-transfectionSA.


ZIP NUCLEIC ACIDS (ZNA®)

Sperminephosphoramiditeisusedtoproduceoligospermine-oligonucleotideconjugates-ZipNucleicAcids(ZNA®)Oligos.Thenamereflectsthepresumedmodeofaction.Theconjugatesarebelievedtousetheoligosperminetoseekoutandmovealong(scan)oligonucleotidestrandsuntiltheprobecomplementarysequenceislocated.Theoligosperminethenperformsthefunctionofstabilizingtheformedduplexbyreducingelectrostaticrepulsion,therebyleadingtosignificantlyincreasedbindingaffinities. ZNA®Oligoshave founduse in the followingapplications:MultiplexPCR;PCRofAT-richRegions;RTqPCR;DetectionofMicroRNA;ImprovedSNPDiscrimination;andAntisenseandAntigeneEffects.Sperminephosphoramiditeissimpletouseinoligonucleotidesynthesisandcanbeaddedmultipletimesatthe3’or5’terminus.Deprotectionandisolationarealsostraightforward. HPLCanalysisoftheconjugatesrequireshighpHtosuppresstheionizationofthespermineresidues.


SperminePhosphoramidite 10-1939-95 50µmole 145.00 10-1939-90 100µmole 270.00 10-1939-02 0.25g 525.00

CDPI3 MGB™ LABELING

Syntheticoligonucleotideswithcovalently-attachedCDPI3haveenhancedDNAaffinityandimprovedthehybridizationpropertiesofsequence-specificDNAprobes.ShortCDPI3-oligonucleotideshybridizewithsingle-strandedDNAtogivemorestableDNAduplexesthanunmodifiedODNsofsimilarlength.ThesimplestapproachtoMGBprobedesignistouseanMGBsupport,addaquenchermoleculeasthefirstadditionandcompletethesynthesiswitha5’-fluorophore.Alternatively,afluorophoresupportcouldbeusedwiththe5’terminuscontainingaquenchermoleculefollowedbyafinalMGBadditionatthe5’terminus.GlenResearchoffers5’-CDPI3 MGB™ Phosphoramidite and 3’-CDPI3MGB™CPG.

SELECTIVELY BINDING COMPLEMENTARY (SBC) OLIGOS

SBColigosexhibithighaffinity fornaturaloligonucleotidesbut theyshow littleaffinity forotherSBColigosevenofacomplementarysequence.OligosinwhichAhasbeenreplacedwith2-amino-AandTwith2-thio-TrepresentanexcellentexampleofSBColigos.While2-amino-AformsaverystablebasepairwithTcontainingthreehydrogenbonds,thestabilityofthebasepairwith2-thio-Tisgreatlydiminished.However,2-thio-TbasepairsperfectlywellwithA.Asanexample,SBC20mersannealedagainstaDNA20mertargetexhibitedTmvalues10°ChigherthanthecorrespondingDNA-DNAhybrid,whereastheSBC-SBChybridyieldedTmvalues30°Clower.

UNNATURAL BASE PAIRS

UnnaturalbasepairsdisplayuniqueabilitiesinduplexDNAandinnucleicacidandproteinbiosyntheses.AstandardWatsonandCrickbasepairisformedbetweeniso-Candiso-G,butthehydrogenbondingpatternisquitedifferentfromthenaturalbasepairsA-TandC-G.Iso-basescan,therefore,increasespecificityofnucleicacidhydridizationwhenintroducedasathirdbasepair.Ithasalsobeendemonstratedthatiso-bases5-Me-iso-dCandiso-dGcanfunctionasdegeneratepyrimidineandpurinebases,respectively.Iso-dGfurtherfunctionedasadegeneratebaseoppositeB(C,T,andG)ambiguoussites.

DMTONTFA

NTFA

TFAN

TFAN

O P N(iPr)2

O CNEtSpermine Phosphoramidite


CAPS FOR INCREASED DUPLEX STABILITY AND BASE-PAIRING FIDELITY

Newcapstructuresallowforthepreparationofhybridizationprobeswithincreasedaffinityforcomplementarysequences.ThemonomersusedtopreparecappedoligonucleotidesarephosphoramiditesthatcanbereadilyintroducedviaautomatedDNAsynthesisattheendofsolidphasesyntheses.ThecapsfavortheformationofstableWatson-Crickduplexesbystackingontheterminalbasepair(Figures1and2).

Meltingpointincreasesofover10°Cpermodificationcanberealizedforshortduplexes.1,2ThecapsfitcanonicalWatson-Crickbasepairsanddonotstackwellonmismatchedbasepairs.Thisleadstoincreasedbasepairingselectivityattheterminalandthepenultimatepositionofoligonucleotidesfeaturingthecaps.Basepairingfidelityisusuallylowatthetermini,wherefrayingoccursfrequentlyintheabsenceofcaps.Thebeneficialeffectsofthecapsarealsorealizedwhenlongertargetstrandsarebound,sothereisnoneedforbluntendsfortheduplexesformed.1,2Thecaps,whenattachedtothe5’terminusofanoligonucleotide,alsofacilitatepurificationastheirlipophilicityleadstoprolongedretentiononreversedphasecolumnsorcartridges.Finally,cappingofterminimaydiscouragethedegradationofoligonucleotidesbyexonucleases.

3’-UaqCapCPG,aUridinesupportmodifiedwitha2’-anthraquinoneresidue,isthemosteffectiveoligonucleotidecapknowntodate.3,4ForshorthybridduplexesbetweenDNAprobesandRNAtargetstrands,theincreaseinTmisupto18°CandthemodificationiseffectiveinincreasingtheTmofDNA:DNA,RNA:RNA,andDNA:RNAhybridduplexes.3’-UaqCapalsoincreasesprobespecificitybydepressingthemeltingpointofterminalmismatches.


5’-TrimethoxystilbeneCapPhosphoramidite 10-1986-90 100µmole 195.00 10-1986-02 0.25g 495.00

5’-PyreneCapPhosphoramidite 10-1987-90 100µmole 195.00 10-1987-02 0.25g 495.00

3’-UaqCapCPG 20-2980-01 0.1g 180.00 20-2980-10 1.0g 1500.00 1µmolecolumns 20-2980-41 Packof4 300.00 0.2µmolecolumns 20-2980-42 Packof4 150.00 10µmolecolumn(ABI) 20-2980-13 Packof1 750.00 15µmolecolumn(Expedite) 20-2980-14 Packof1 1125.00

REFERENCES

(1)Dogan,Z.;Paulini,R.;RojasStütz,J.A.;Narayanan,S.;Richert,C.J. Amer. Chem. Soc. 2004, 126,4762-4763.

(2)Narayanan,S.;Gall,J.;Richert,C.Nucleic Acids Res. 2004, 32,2901-2911.

(3)A.Patra,C.Richert,J. Amer. Chem. Soc., 2009, 131,12671-12681.

(4)C.Ahlborn,K.Siegmund,C.Richert,J. Amer. Chem. Soc., 2007, 129,15218-15232.

NH

O

CNEtON(iPr)2PO

MeOOMe

MeO

N

CNEtON(iPr)2PO

5’-Trimethoxystilbene Cap 5’-Pyrene Cap

cap

Unmodified DNA:fraying and wobbling

at the terminus

Duplex with cap-bearing probe

FIGURE 1: STACKING OF CAP ON 5’ TERMINAL BASE PAIR

O

PO2

N

NH

O

O

HO

O

O

O

HN

OO B

OH or OH

O

chain

terminal base

Uaq cap

Cap

capped duplex

ODMT-O N

NH

O

O

O

O

O

O

HNO

HNO

Uaq controlled pore glass oligonucleotide

FIGURE 2: STACKING OF Uaq CAP ON 3’ TERMINAL BASE PAIR

ODMTO

N

HN

O

O

OHN

O

OO

succinyl-CPG3’-Uaq Cap CPG




Expedite EMerMade M




SEE ALSO

CDPI3 MGB™ Labeling on page 1172-Amino-dA on page 47Pac-2-Amino-dA on page 472-Thio-dT on page 58dmf-5-Me-isodC on page 53dmf-isodG on page 53

48 49

MIN

OR

BASE

S

mailto:licensing%40polyplus-transfection.com?subject=

mailto:licensing%40polyplus-transfection.com?subject=

EPIGENETICS

DNA METHYLATION

Oneofthefastestgrowingfieldsinbiologyandcancerresearchisepigenetics.Whiletheunderlyinggeneticcodedefineswhichproteinsandgeneproductsaresynthesized,itisepigeneticcontrolthatdefineswhenandwheretheyareexpressed.ThisdynamiccontrolofgeneexpressionisessentialforXchromosomeinactivation,embryogenesis,cellulardifferentiationandappearsintegraltomemoryformationandsynapticplasticity.

In2009,tworeports1,2describedthediscoveryof5-hydroxymethyl-2’-deoxyCytidine(hmdC),anoveldCmodificationinPurkinjeneuronsandembryonicstemcells.Later,athirdreportfoundthismodificationtobestronglyenrichedinbraintissuesassociatedwithhighercognitive functions.3ThisdCmodification isgeneratedby theactionofa-ketoglutaratedependentteneleventranslocation(TET)enzymes,whichoxidizes5-Me-dCtohmdC.Thisfindingstimulateddiscussionaboutactivedemethylationpathwaysthatcouldoccur,e.g.,viabaseexcisionrepair(BER),withthehelpofspecializedDNAglycosylases.Alternatively,onecouldenvisionaprocessinwhichthehydroxymethylgroupofhmdCisfurtheroxidizedto5-formyl-dC(fdC)or5-carboxy-dC(cadC)followedbyeliminationofeitherformicacidorcarbondioxide4,5.

GlenResearchhas supported this research since its inceptionbyproviding thebuildingblocks for the synthesis ofoligonucleotidescontainingallthenewdCderivatives-hmdC,fdCandcadC.ThefirstgenerationhmdCphosphoramiditewasfairlyverywellacceptedbutrequiresfairlyharshdeprotectionconditions.Therefore,asecondgenerationbuildingblock (5-Hydroxymethyl-dC II)developedbyCarellandco-workers that iscompatiblewithUltraMilddeprotectionwasintroduced.65-Formyl-dCIIIhasbeendesignedtomeetalloftherequirementstoprepareanoligocontainingallofthemethylatedvariants.7


5-Hydroxymethyl-dC-CEPhosphoramidite 10-1062-95 50µmole 335.00 10-1062-90 100µmole 650.00 10-1062-02 0.25g 1675.00

5-Carboxy-dC-CEPhosphoramidite 10-1066-95 50µmole 230.00 10-1066-90 100µmole 450.00 10-1066-02 0.25g 1200.00

5-Formyl-dC-CEPhosphoramidite 10-1514-95 50µmole 610.00 10-1514-90 100µmole 1200.00 10-1514-02 0.25g 3225.00

5-Hydroxymethyl-dCII-CEPhosphoramidite 10-1510-95 50µmole 345.00 10-1510-90 100µmole 670.00 10-1510-02 0.25g 2100.00

5-Formyl-dCIII-CEPhosphoramidite 10-1564-95 50µmole 360.00 10-1564-90 100µmole 700.00 10-1564-02 0.25g 1800.00

REFERENCES

(1)S.Kriaucionis,andN.Heintz,Science, 2009, 324,929-30.

(2)M.Tahiliani,etal.,Science, 2009, 324, 930-935.

(3)M.Münzel,etal.,Angewandte Chemie-International Edition, 2010, 49,5375-5377.

(4)D.Globisch,etal.,PLoS One, 2010, 5, e15367.

(5)S.C.Wu,andY.Zhang,Nat Rev Mol Cell Biol, 2010, 11,607-20.

(6)M.Münzel,D.Globisch,C.Trindler,andT.Carell,Org Lett, 2010, 12,5671-3.

(7)A.S.Schroder,etal.,Angewandte Chemie-International Edition, 2014, 53, 315-318.

ODMTON

N

NHBz

O

O P N(iPr)2

O CNEt

CH2-O-CNEt

ODMTON

N

NHBz

O

O P N(iPr)2

O CNEt

CO2Et

ODMTON

N

NHAc

O

O P N(iPr)2

O CNEt

OAc OAc

5-Hydroxymethyl-dC 5-Formyl-dC5-Carboxy-dC

ODMTON

N

O

O P N(iPr)2

O CNEt

OHN

O

5-Hydroxymethyl-dC II

ODMTON

N

NH

O

O P N(iPr)2

O CNEt

O

O

O

MeO

5-Formyl-dC III

PCR/SEQUENCING APPLICATIONS

DUPLEX EFFECTS

Thedesignofprimersisfrequentlycomplicatedbythedegeneracyofthegeneticcode.Threestrategiesarenowavailabletoconfrontthisproblem.Inthefirst,amixedbaseaddition(N)isusedtoformthedegeneratesite.Thisapproachisbestifthenumberofdegeneratesitesissmall.Asecondoptionistheuseof2’-deoxyInosineor2’-deoxyNebularinewhichexhibitlow,butunequal,hydrogenbondingtotheotherfourbases.Thethirdoptionistheuseofauniversalnucleoside.Inthisstrategy,thebaseanalogdoesnothybridizesignificantlytotheotherfourbasesandmakesupsomeoftheduplexdestabilizationbyactingasan intercalatingagent. 3-Nitropyrrole2’-deoxynucleoside (M) is thefirstexampleofa setofuniversalbases.Subsequently,5-nitroindolewasdeterminedtobeaneffectiveuniversalbaseandtobesuperiorto3-nitropyrrole,basedonduplexmeltingexperiments.

ThemodifiedbasesdesignatedPandKshowconsiderablepromiseasdegeneratebases.ThepyrimidinederivativeP,whenintroducedintooligonucleotides,basepairswitheitherAorG,whilethepurinederivativeKbasepairswitheitherCorT.AdP+dKmixalsocanserveasamixedbasewithmuchlessdegeneracythandA+dC+dG+dT(N).


dA+dG-CEPhosphoramidites 10-1002-02 0.25g 40.00dC+dT-CEPhosphoramidites 10-1013-02 0.25g 40.00dA+dC+dG+dT-CEPhosphoramidites 10-1023-02 0.25g 40.00

Other packsizes,mixedbasecombinationsandcustomdopingofindividualmonomersareavailableonrequest.Also,mixedbasecolumnsareavailablein0.2and1.0µmolesizesonrequest.

dI-CEPhosphoramidite 10-1040-90 100µmole 50.00 10-1040-02 0.25g 120.00

dI-CPG500 20-2040-01 0.1g 30.00 1µmolecolumns 20-2190-41 Packof4 120.00 0.2µmolecolumns 20-2190-42 Packof4 72.00

dI-CPG1000 20-2041-01 0.1g 30.00 1µmolecolumns 20-2191-41 Packof4 120.00 0.2µmolecolumns 20-2191-42 Packof4 72.00

dU-CEPhosphoramidite 10-1050-90 100µmole 35.00 10-1050-02 0.25g 100.00

dU-CPG500 20-2050-01 0.1g 30.00 1µmolecolumns 20-2150-41 Packof4 120.00 0.2µmolecolumns 20-2150-42 Packof4 72.00

dU-CPG1000 20-2051-01 0.1g 50.00 1µmolecolumns 20-2151-41 Packof4 200.00 0.2µmolecolumns 20-2151-42 Packof4 120.00

2’-deoxyInosine

O

O P N(iPr)2O CNEt

DMTO

O

N

N

N

HN




Expedite EMerMade M




2’-deoxyUridine

O

O P N(iPr)2O CNEt

DMTOO

O

N

HN

SEE ALSO

5-Me-dC on page 465-hmdU on page 61

50 51

MIN

OR

BASE

S

DUPLEX EFFECTS (CONT.)


2’-DeoxyNebularine-CEPhosphoramidite 10-1041-90 100µmole 105.00 (Purine) 10-1041-02 0.25g 255.00

5-Nitroindole-CEPhosphoramidite 10-1044-90 100µmole 125.00 10-1044-02 0.25g 325.00

dP-CEPhosphoramidite 10-1047-90 100µmole 195.00 10-1047-02 0.25g 595.00

dK-CEPhosphoramidite 10-1048-90 100µmole 195.00 10-1048-02 0.25g 595.00

dP+dK-CEPhosphoramidite 10-1049-90 100µmole 195.00 10-1049-02 0.25g 595.00

5-Nitroindole3-Nitropyrrole2’-deoxyNebularine


O

O P N(iPr)2O CNEt

DMTON

N

N

N

O

O P N(iPr)2O CNEt

DMTON

NO2

O

O P N(iPr)2O CNEt

DMTON

NO2

dP dK

O

O P N(iPr)2O CNEt

DMTO

O

O

N

N

HN

O

O P N(iPr)2O CNEt

DMTO

MeO

Me2NN

N

N

N

N

HN


DUPLEX EFFECTS (CONT.)

Unnaturalbasepairsdisplayuniqueabilities induplexDNAand innucleicacidandproteinbiosyntheses. AstandardWatsonandCrickbasepairisformedbetweeniso-Candiso-G,butthehydrogenbondingpatternisquitedifferentfromthenaturalbasepairsA-TandC-G.(The5-methylanaloguewaschosenasthesynthetictargetduetothereportedinstabilityof2’-deoxyisocytidinecausedbydeaminationduringoligonucleotidesynthesisordeprotection.)


dmf-5-Me-isodC-CEPhosphoramidite 10-1065-90 100μmole 100.00 10-1065-02 0.25g 255.00

dmf-isodG-CEPhosphoramidite 10-1078-90 100μmole 165.00 10-1078-02 0.25g 355.00

Tm MODULATION

Anytechniquethatinvolveshybridizationofmultiplesequencessimultaneously,asinDNAchipandreversehybridizationtechnologies,issubjecttoinaccuraciesduetodifferencesinGCcontent.SequenceswithhighGCcontentmaycontainmismatchesandstillhybridize,whereasalowGCcontentprobemaymatchperfectlyandyetdisassociatefromthetarget,leadingtofalsepositivesandnegatives,respectively.

AnelegantwayofcircumventingthisproblemwouldbetouseamodifiedbasethatnormalizedthestabilityoftheGCandATbasepairs.TheN4-ethylanalogue(N4-Et-dC)hybridizesspecificallytonaturaldGbutthestabilityofthebasepairisreducedtoaboutthelevelofanATbasepair.InaseriesofprobeswhoseGCcontentrangedfrom0to100%,therangeinTmvalueswhenN4-Et-dCwasusedwasonly7°C;whendCwasused,thatrangewas39°C.

dmf-isodGdmf-5-Me-isodC

N

N

OCH 3

N(Me)2N

DMTO

CNEtON(iPr)2PO

O

N

N

N

N

N

DMTO

CNEtON(iPr)2PO

O

DPCO

N(Me) 2




Expedite EMerMade M




SEE ALSO

N4-Et-dC on page 47N4-Ac-N4-Et-dC on page 47

52 53

MIN

OR

BASE

S

CLEANAMP™ MONOMERS

CleanAmp™PrimersofferanalternativetootherHotStarttechnologiesandallowgreatercontrolofprimerhybridizationandextensionduringPCR.IthasbeendemonstratedthatCleanAmpPrimersoutperformothertechnologiesinmultipleapplications.Indeed,overabroadrangeofapplications,CleanAmpPrimersreduceoreliminateoff-targetamplification.Greaterampliconyieldisalsoachieved,duetoimprovementinspecificityandsensitivity.Byusingeithertheslow-releasingPrecisionprimerswithtwoCleanAmpphosphotriesterlinkagesorthefaster-releasingTurboPrimerswithasingleCleanAmpphosphotriesterlinkage,therateofformationofunmodifiedprimercanbecontrolledtosuitreactionneeds.AtabletoaidintheselectionofTurboandPrecisionPrimersforspecificapplicationsisshownbelow. TurboPrimers PrecisionPrimers

Fastcycling StandardcyclingMultiplexPCR One-stepreverse-transcriptionPCRImprovesampliconyield ImprovedspecificityandlimitofdetectionReducesmis-priming/primerdimerformation Greatestreductioninmis-priming/primerdimerformation

SynthesisofCleanAmpPrimersrequirestheuseofUltraMildChemistry.

CleanAmp™PrimersandmonomersareavailablefromTriLinkBioTechnologies.



CleanAmp™ is a trademark of TriLink BioTechnologies,Inc.CleanAmp™productsorportionsthereofarecoveredbyTriLinkpendingPatentApplications,US2007281308andWO2007139723, US Provisional Patent ApplicationSerial#61/056,324andUS Patent 6762298 licensed from the Department of Health and Human Services.CleanAmp™productsaresoldexclusivelyforR&Dusebythepurchaser.Theymaynotberesold,distributedorre-packaged.Nolicenseisgrantedorimpliedwiththepurchaseofthisproduct.AmplificationmethodsusedinconnectionwithPolymeraseChainReaction(“PCR”)Processarecoveredbymanypatents.Itmaybenecessarytoobtainaseparatelicenseforcertainpatentedapplicationsinwhichtheproductisused.CleanAmp™LicensesareavailabledirectlyfromTriLinkBioTechnologies.www.trilinkbiotech.com

N

N N

N

ODMTO

OP

O(CH2)9CH3

N(iPr)2

O

HNO

O

ODMTON

N

NHAc

O

OP

O(CH2)9CH3

N(iPr)2

O

Chemical Formula: C52H73N4O9PExact Mass: 928.51

Molecular Weight: 929.13m/z: 928.51 (100.0%), 929.51 (57.7%), 930.52 (18.0%), 931.52

(4.3%), 929.52 (1.2%)Elemental Analysis: C, 67.22; H, 7.92; N, 6.03; O, 15.50; P, 3.33

HN

N N

N

O

ODMTO

OP

O(CH2)9CH3

N(iPr)2

O

NH

O

O

Chemical Formula: C59H77N6O10PExact Mass: 1060.54

Molecular Weight: 1061.25m/z: 1060.54 (100.0%), 1061.55 (65.1%), 1062.55 (22.9%), 1063.55 (6.0%), 1061.54 (2.2%), 1062.54

(1.4%)Elemental Analysis: C, 66.77; H, 7.31; N, 7.92; O, 15.08; P, 2.92

ODMTON

HN

O

O

OP

O(CH2)9CH3

N(iPr)2

O

CleanAmp™-Pac-dA CleanAmp™-dTCleanAmp™-Pac-dGCleanAmp™-Ac-dC

CHAIN TERMINATORS

Insituationswhereligationmustbeblockedatthe5’terminus,5’-OMe-dTmaybeused.5’-OMemodificationofastrandofsiRNAusing5’-OMe-Tcancontrolguidestrandselectionandtargetingspecificity.15’-Amino-dTterminatesanoligonucleotidewitha5’-aminogroupwhichmaybeusedforattachingapeptideoraPNAsequence.Toavoidpolymeraseextensionatthe3’terminus,2’,3’-dideoxynucleosideand3’-deoxynucleosideCPGshaveprovedtobeeffective.2’,3’-Phosphoramiditesaredesignedtobeusedwiththe5’-phosphoramiditesandsupports.SincethesephosphoramiditeshavenoDMTgroup,theyarenotcompatiblewithpurificationbytheDMT-ontechnique.IonexchangeHPLCorPAGEshouldbeusedtopurifythesedideoxyterminatedoligostoensurethatshortersequences(containing3’-OH)groupsareremoved.(3’-Terminationcanalsobeeffectedusinga3’-3’linkageformedusing5’-supports,or3’-spacerC3CPG.)


5’-OMe-dT-CEPhosphoramidite 10-1031-90 100µmole 135.00 10-1031-02 0.25g 355.00

5’-Amino-dT-CEPhosphoramidite 10-1932-90 100µmole 150.00 10-1932-02 0.25g 400.00 3’-dA-CPG 20-2004-01 0.1g 400.00 1µmolecolumns 20-2104-41 Packof4 675.00 0.2µmolecolumns 20-2104-42 Packof4 225.00

3’-dC-CPG 20-2064-01 0.1g 300.00 1µmolecolumns 20-2164-41 Packof4 600.00 0.2µmolecolumns 20-2164-42 Packof4 200.00 3’-dG-CPG 20-2074-01 0.1g 300.00 1µmolecolumns 20-2174-41 Packof4 600.00 0.2µmolecolumns 20-2174-42 Packof4 200.00 3’-dT-CPG 20-2084-01 0.1g 300.00 1µmolecolumns 20-2184-41 Packof4 600.00 0.2µmolecolumns 20-2184-42 Packof4 200.00


3’-dA-CPG 3’-dC-CPG 3’-dG-CPG 3’-dT-CPG 5’-OMe-Thymidine 5’-Amino-dT

O

O P N(iPr)2O CNEt

MeO

CH 3

O

O

N

HN

O

O P N(iPr)2O CNEt

O

O

N

HNCH 3

MMTNH

ODMTO

O succinylCPG

N

N

N

N

NHBz

ODMTO

O succinylCPG

N

NO

NHBz

ODMTO

O succinylCPG

N

O

N

N

N

HNMe2N

ODMTO

O succinylCPG

CH 3

O

O

N

HN

REFERENCE

(1)P.Y.Chen,etal.,RNA, 2008, 14,263-274..




Expedite EMerMade M




SEE ALSO

5’-Phosphoramidites on page 345’-Supports on page 353’-Spacer C3 CPG on page 84

SEE ALSO

UltraMild DNA Synthesis on page 23

54 55

MIN

OR

BASE

S

www.trilinkbiotech.com

www.trilinkbiotech.com

CHAIN TERMINATORS (CONT.)


2’,3’-ddC-CPG 20-2017-01 0.1g 300.00 1µmolecolumns 20-2117-41 Packof4 600.00 0.2µmolecolumns 20-2117-42 Packof4 200.00

2’,3’-ddA-CEPhosphoramidite 10-7001-90 100µmole 130.00 10-7001-02 0.25g 545.00

2’,3’-ddC-CEPhosphoramidite 10-7101-90 100µmole 130.00 10-7101-02 0.25g 545.00

2’,3’-ddG-CEPhosphoramidite 10-7201-90 100µmole 145.00 10-7201-02 0.25g 675.00

2’,3’-ddT-CEPhosphoramidite 10-7301-90 100µmole 130.00 10-7301-02 0.25g 545.00


2’,3’-ddC-CPG

2’,3’-ddA 2’,3’-ddC 2’,3’-ddG 2’,3’-ddT

succinylCPG

ODMTO

NH

O N

N

OP(iPr)2NOCNEt

N

N

N

N

N

O

N(iBu)2

OP(iPr)2NOCNEt

O

N

O N

N

N(iBu)2

OP(iPr)2NOCNEt

O

Me2NN

O

N

N

N

HN

O

CH 3

O

O

N

HN

CNEt O(iPr)2N P O




Expedite EMerMade M




STRUCTURAL STUDIES

7-Deaza-2’-deoxyAdenosine 7-Deaza-2’-deoxyGuanosine

STRUCTURE/ACTIVITY RELATIONSHIP

Thefollowingproductsareusedtoinvestigatetheeffectontheactivityofanoligonucleotidewhenkeystructuralelementsarechanged.The7-deazapurinemonomerslackgroupscriticalforhydrogenbonding.7-Deaza-8-aza-Aand7-deaza-8-aza-G(PPG)monomersareisomersofAandGandhavesimilarelectrondensity.TheirpresenceinoligosisslightlystabilizingrelativetoAandG.UnlikeG,PPGdoesnotleadtoaggregationandG-richoligoscanbeeasilypreparedandisolated.5’-FluoresceinoligoswithPPGatthe5’-terminusaremuchlessquenchedthantheequivalentGoligos.AsapurineanalogueofThymidine,7-deaza-2’-deoxyXanthosine(7-deaza-dX)promisestohaveinterestingeffectsonDNAstructureoftriplexes.7-Deaza-dXalsoformsanon-standardbasepairwitha2,4-diaminopyrimidinenucleosideanalogue.StandardnucleobaseshaveanunsharedpairofelectronsthatprojectintotheminorgrooveofduplexDNA.EnzymesthatinteractwithDNA,polymerases,reversetranscriptases,restrictionenzymes,etc.,mayuseahydrogenbonddonatinggrouptocontactthehydrogenbondacceptorintheminorgroove.3-Deaza-2’-deoxyadenosineisveryinterestinginthatitmaintainstheabilityforregularWatson-CrickhydrogenbondingtoTbutislackingtheelectronpairatthe3-positionnormallyprovidedbyN3.


7-Deaza-dA-CEPhosphoramidite 10-1001-95 50µmole 177.50 10-1001-90 100µmole 355.00 10-1001-02 0.25g 975.00

7-Deaza-8-aza-dA-CEPhosphoramidite 10-1083-95 50µmole 177.50 10-1083-90 100µmole 355.00 10-1083-02 0.25g 975.00

7-Deaza-dG-CEPhosphoramidite 10-1021-95 50µmole 177.50 10-1021-90 100µmole 355.00 10-1021-02 0.25g 975.00

7-Deaza-8-aza-dG-CEPhosphoramidite 10-1073-95 50µmole 207.50 (PPG) 10-1073-90 100µmole 395.00 10-1073-02 0.25g 1150.00

7-deaza-dX-CEPhosphoramidite 10-1076-95 50µmole 177.50 10-1076-90 100µmole 355.00 10-1076-02 0.25g 975.00

3-Deaza-dA-CEPhosphoramidite 10-1088-95 50µmole 177.50 10-1088-90 100µmole 355.00 10-1088-02 0.25g 975.00

O

O P N(iPr)2O CNEt

DMTO

NHBz

NN

N

O

O P N(iPr)2O CNEt

DMTO

Me2NN

O

NN

HN HN

NN

N

O

N

DMTO

CNEtON(iPr)2PO

O

Me2N

7-Deaza-8-Aza-2’-deoxyAdenosine 7-Deaza-8-Aza-2’-deoxyGuanosine


TheuseofPPGissubjecttoproprietaryrights of ELITechGroup and it is sold underlicensefromELITechGroup.

(1)I.V.Kutyavin,etal.,Nucleic Acids Res., 2002, 30, 4952-4959.

STABILITY NOTES

7-Deaza-dGisunstabletoiodineoxidation.Addamaximumof2timeswhenusingiodineoxidationoruse0.5M(10-camphorsulfonyl)-oxaziridine(CSO)inanhydrousacetonitrileand3min.oxidationtime.(SeeGlenReport-Vol.9,No.1,1996,page8.)

O

O P N(iPr)2O CNEt

DMTO

Me2NN

N

NN

N

7-deaza-dX

O

O P N(iPr)2O CNEt

DMTO

O

O

NN

HN

H

N N

N

NHBz

O

O P N(iPr)2O CNEt

DMTO

3-Deaza-dA

56 57

MIN

OR

BASE

S

STRUCTURE/ACTIVITY RELATIONSHIP (CONT.)

TheC-nucleoside2’-deoxypseudouridine,incontrasttodU,formsstableC:pseudoU-Atriplets.2-Aminopurinelacksgroupscriticalforhydrogenbondingandisamildlyfluorescentbase.

Demandforsulfurmodifiedbasescontinuestoexpandforinvestigationsofoligonucleotidestructure,butprimarilyforcross-linkingpurposes. 6-Thio-dG,4-Thio-dTand4-thio-dUare veryusefulmodifications forphoto cross-linkingandphotoaffinitylabelingexperiments.Oligoscontaining2-thio-dTareusefulinexaminingprotein-DNAinteractionbyactingasphotosensitizingprobes.Thethiocarbonylgroupin2-thio-dTisespeciallyinterestinginthatitisavailabletoreactwithcompoundsassociatingwiththeminorgrooveofDNA.2-Amino-AformsaverystablebasepairwithTcontainingthreehydrogenbondsbutthestabilityofthebasepairwith2-thio-Tisgreatlydiminished.Duetostericinteractionsbetweenthe2-thiogroupofthymidineandthe2-aminogroupof2-amino-A,thebasepaircontainsonlyasinglehydrogenbond.Oligos containing 2-amino-dAand2-thio-dTexhibithighaffinityfornaturaloligonucleotidesbutshowlittleaffinityforothersimilaroligosevenofacomplementarysequence.


2’-deoxypseudoU-CEPhosphoramidite 10-1055-95 50µmole 177.50 10-1055-90 100µmole 355.00 10-1055-02 0.25g 975.00

2-Aminopurine-CEPhosphoramidite 10-1046-90 100µmole 135.00 10-1046-02 0.25g 355.00

6-Thio-dG-CEPhosphoramidite 10-1072-95 50µmole 177.50 10-1072-90 100µmole 355.00 10-1072-02 0.25g 975.00

4-Thio-dT-CEPhosphoramidite 10-1034-95 50µmole 165.00 10-1034-90 100µmole 295.00 10-1034-02 0.25g 675.00

4-Thio-dU-CEPhosphoramidite 10-1052-95 50µmole 165.00 10-1052-90 100µmole 295.00 10-1052-02 0.25g 675.00

2-Thio-dT-CEPhosphoramidite 10-1036-95 50µmole 165.00 10-1036-90 100µmole 295.00 10-1036-02 0.25g 675.00

STRUCTURAL STUDIES

4-Thio-dT 2-Thio-dT2-Aminopurine 4-Thio-dU6-Thio-dG2’-dpseudoU

O

O P N(iPr)2O CNEt

DMTOO

O

NHHN

O

O P N(iPr)2O CNEt

DMTO

Me2NN

N NN

N

TFAHN

N

N

N

N

S

DMTO

CNEtON(iPr)2PO

O

CN

O

O P N(iPr)2O CNEt

DMTON

N

O

S

CN

CH 3

O

O P N(iPr)2O CNEt

DMTON

N

O

S

CN

CH 3

O

O P N(iPr)2O CNEt

DMTON

N

O

S

H3CO

STABILITY NOTES

6-Thio-dG,4-Thio-dTand4-thio-dUareprotectedastheS-cyanoethyletherwhichisstableduringsynthesisandreadilyremovedbyammoniumhydroxide.Itiscriticaltoadd50mMsodiumhydrosulfide(NaSH)totheammoniumhydroxideusedfordeprotection.Especiallyifroomtemperaturedeprotectioniscarriedout,thistechniqueradicallyreducesthelevelofammonolysiswhichwouldleadtoundesiredaminatedbases.Moreover,itisalsodesirabletoremovethecyanoethylprotectinggroup(1MDBUinacetonitrile,2-5h/RT)priortotheammoniumhydroxidecleavageanddeprotection.




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STRUCTURE/ACTIVITY RELATIONSHIP (CONT.)

8-Amino-dAand8-amino-dGareusefulintriplexformationduetothepresenceoftheadditionalaminogroups.

2’-DeoxyXanthosine (dX) is a naturally occurring nucleoside thatmay be derived fromoxidative deamination of2’-deoxyGuanosine(dG).dXhasasimilarbondingpatterntothymidineanditmaybasepairwithdA,withsuchpurine-purineinteractionscausingduplexdistortion.dXalsofeaturedinattemptstoextendthegeneticalphabetwithanewbasepairofdXandpyrimidine-2,4-diaminenucleoside.dXhasalsointerestedresearchersinthefieldofDNAdamageandrepairsinceitisaproductofnitricoxide-inducedmutagenesis.


8-Amino-dA-CEPhosphoramidite 10-1086-95 50µmole 177.50 10-1086-90 100µmole 355.00 10-1086-02 0.25g 975.00

8-Amino-dG-CEPhosphoramidite 10-1079-95 50µmole 177.50 10-1079-90 100µmole 355.00 10-1079-02 0.25g 975.00

2’-dX-CEPhosphoramidite 10-1537-95 50µmole 105.00 10-1537-90 100µmole 200.00 10-1537-02 0.25g 420.00

O

N

N

N

N

NN

NMe 2

NMe 2

DMTO

O P N(iPr)2O CNEt

O P N(iPr)2O CNEt

N(Me 2)(Me2)N N

HN

N

N

N

O

N

DMTO O

8-Amino-dA 8-Amino-dG

STABILITY NOTE

Syntheticoligonucleotidescontaining8-amino-dGmustbecleavedanddeprotectedwithammoniumhydroxidecontaining0.25M2-mercaptoethanoltoavoidoxidativedegradationof8-amino-dGsites.

STRUCTURAL STUDIES

N

N N

N

O

ODMTO

O P N(iPr)2

O CNEt

O

NO2

O2N

dX

58 59

MIN

OR

BASE

S

HALOGENATED NUCLEOSIDES

Brominated and iodinated nucleosides are used in X-raycrystallographystudiesofoligonucleotidestructure.Theyarealsophotolabileandareusedforcross-linkingstudiestoprobethestructureofprotein-DNAcomplexes.AntibodiesexisttoBr-dUandoligonucleotidescontainingBr-dUcanbeusedasprobes.5-Fluoro-dUcanbeusedasanon-photoreactivealternativeto5-Br-dUwithsimilarelectrondensity.5-F-dUbasepairsmorestronglythatTtobothdAandthedGmismatch.ItisalsousefulforprobingDNAstructureusing19FNMRspectroscopy.


8-Br-dA-CEPhosphoramidite 10-1007-90 100µmole 115.00 10-1007-02 0.25g 295.00

8-Br-dG-CEPhosphoramidite 10-1027-90 100µmole 105.00 10-1027-02 0.25g 255.00

5-Br-dC-CEPhosphoramidite 10-1080-90 100µmole 60.00 10-1080-02 0.25g 160.00

5-I-dC-CEPhosphoramidite 10-1081-90 100µmole 135.00 10-1081-02 0.25g 355.00

5-Br-dU-CEPhosphoramidite 10-1090-90 100µmole 60.00 10-1090-02 0.25g 160.00

5-I-dU-CEPhosphoramidite 10-1091-90 100µmole 60.00 10-1091-02 0.25g 160.00

5-F-dU-CEPhosphoramidite 10-1092-90 100µmole 135.00 10-1092-02 0.25g 355.00

5-Br-dU-CPG 20-2090-01 0.1g 50.001µmolecolumns 20-2090-41 Packof4 200.000.2µmolecolumns 20-2090-42 Packof4 120.00

STRUCTURAL STUDIES

5-Iodo-2’-deoxyCytidine 5-Bromo-2’-deoxyUridine 5-Iodo-2’-deoxyUridine 5-Fluoro-2’-deoxyUridine

O

O P N(iPr)2O CNEt

DMTO

NHBz

O N

NI

O

O P N(iPr)2O CNEt

DMTOO

O

N

HNBr

O

O P N(iPr)2O CNEt

DMTOO

O

N

HNI

O

O P N(iPr)2O CNEt

DMTOO

O

N

HNF




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8-Bromo-2’-deoxyGuanosine8-Bromo-2’-deoxyAdenosine

O P N(iPr)2O CNEt

DMTO

N

N

N

N

N

Br

NCH 3

CH 3

O O

O P N(iPr)2O CNEt

DMTO

HN

N

N

N

O

NBrMe2N

O

O P N(iPr)2O CNEt

DMTO

NHBz

O N

NBr

5-Bromo-2’-deoxyCytidine

STABILITY NOTE

Oligonucleotidescontainingabromooriodogrouparepreparedconventionallywiththeexceptionthatdeprotectioniscarriedoutinammoniumhydroxideatroomtemperaturefor24hours.Undertheseconditions,degradationofthehalogengroupwaslessthan2%.

DNA DAMAGE/REPAIR

CellularDNAisconstantlybeingdamagedbyoxidationandalkylation,byfreeradicals,andbyultravioletandionizing radiation.Thebodyhasthereforeevolvedanumberofrepairenzymesystemstoexciseandrepairtheselesions.The8-oxopurinemonomersallowinvestigationofthestructureandactivityofoligonucleotidescontainingan8-oxomutationwhichisformednaturallywhenDNAissubjectedtooxidativeconditionsorionizingradiation.5,6-DihydropyrimidinesarenaturallyoccurringcompoundsthatarestructuralcomponentsofalaninetransferRNA.DihydrouracilandthehydroxypyrimidinesaremajorbasedamageproductsformedbyexposureofDNAtoionizingradiation.


8-Oxo-dA-CEPhosphoramidite 10-1008-90 100µmole 135.00 10-1008-02 0.25g 355.00

8-Oxo-dG-CEPhosphoramidite 10-1028-95 50µmole 177.50 10-1028-90 100µmole 355.00 10-1028-02 0.25g 975.00

5,6-Dihydro-dT-CEPhosphoramidite 10-1530-90 100µmole 195.00 10-1530-02 0.25g 595.00

5,6-Dihydro-dU-CEPhosphoramidite 10-1550-90 100µmole 195.00 10-1550-02 0.25g 595.00

5-OH-dC-CEPhosphoramidite 10-1063-90 100µmole 275.00 10-1063-02 0.25g 775.00

5-OH-dU-CEPhosphoramidite 10-1053-90 100µmole 225.00 10-1053-02 0.25g 675.00

5-Hydroxymethyl-dU-CEPhosphoramidite 10-1093-90 100µmole 225.00 10-1093-02 0.25g 675.00

STRUCTURAL STUDIES

8-oxo-2’-deoxyAdenosine 8-oxo-2’-deoxyGuanosine

5,6-Dihydro-dU

5,6-Dihydro-dT

5-OH-dU 5-Hydroxymethyl-dU

STABILITY NOTES

Syntheticoligonucleotidescontaining8-oxo-dGmustbecleavedanddeprotectedwithammoniumhydroxidecontaining0.25M2-mercaptoethanoltoavoidoxidativedegradationof8-oxo-dGsites.

Oligonucleotidessynthesizedusing5,6-dihydro-dUor5,6-dihydro-dTandUltraMILDmonomerscanbecleaved using either concentrated ammoniumhydroxideor50mMpotassiumcarbonateinanhydrousmethanol.Completecleavageanddeprotectioncanbeaccomplishedatroomtemperaturein2-4hourswithoutdamagingeitherthedihydro-dUordihydro-dTbases.

5-OH-dC

N

N N

NHO

NHBz

O P N(iPr)2O CNEt

DMTOO

HN

N

NH

N

O

iBuHNO

O P N(iPr)2O CNEt

DMTOO O

O P N(iPr)2O CNEt

DMTOH

CH 3

O

O

N

HN

O

O P N(iPr)2O CNEt

DMTOO

O

N

HN

Bz

N

NO

NH

OBz

O

O P N(iPr)2O CNEt

DMTOO

O P N(iPr)2O CNEt

DMTO

OAc

O

O

N

HN

O

O P N(iPr)2O CNEt

DMTO O

O

N

HN OAc

SEE ALSO

5-Hydroxymethyl-dC on page 50dX on page 59

60 61

MIN

OR

BASE

S

DNA DAMAGE/REPAIR (CONT.)

8-Amino-Gisformedalongwith8-oxo-GasthemajormutageniclesionsformedinDNAdamagecausedby2-nitropropane.2-Nitropropaneisanindustrialsolventandacomponentofpaints,dyesandvarnishes,andisalsopresentincigarettesmoke. Thymineglycol (5,6-dihydroxy-5,6-dihydrothymine) is formedwhen thymine is subjected tooxidative stress,includingionizingradiation.Oxidationofthe5,6doublebondofThymidinegeneratestwochiralcentersatC5andC6.Thecis-5R,6Sformisgeneratedasthepredominantproductalongwiththeotherdiastereomer,thecis-5S,6Rform.ThepresenceofthymidineglycolinDNAhassignificantbiologicalconsequencesandmanyorganismspossessspecificrepairenzymesfortheexcisionofthislesion.

HydrolysisofnucleosideresiduesinDNAoccurstogenerateabasicsites.Mostcommonly,dAsitesarehydrolyzedcausingdepurinationandleadingtoabasicresidues.ForresearcherstryingtodetermineiftheirsourceofdepurinationinchemicalsynthesisofDNAisreagent,fluidicsorprotocol-based,weofferadepurination-resistantdAmonomer.Anewchemicalmethodallows thegenerationof abasic sites indoubleand single strandedoligonucleotidesusing verymild specificconditionsandwithverylowprobabilityofsidereactions.AbasicIIPhosphoramidite1hastheadvantageofsimplicityinthatthesilylgroupisremovedpost-synthesisusingaqueousaceticacid.dSpacerhasalsobeenusedsuccessfullyasamimicofthehighlybase-labileabasicsite.


8-Amino-dG-CEPhosphoramidite 10-1079-95 50µmole 177.50 10-1079-90 100µmole 355.00 10-1079-02 0.25g 975.00

ThymidineGlycolCEPhosphoramidite 10-1096-95 50µmole 180.00 10-1096-90 100µmole 360.00 10-1096-02 0.25g 975.00

AbasicIIPhosphoramidite 10-1927-95 50µmole 80.00 (dRPrecursor) 10-1927-90 100µmole 150.00 10-1927-02 0.25g 475.00

Abasic II Phosphoramidite

O P N(iPr)2O CNEt

N(Me 2)(Me2)N N

HN

N

N

N

O

N

DMTO ODMTO

O

OTBDMSOTBDMS

H

CH 3

O

O

N

HN

CNEtON(iPr)2PO

8-Amino-dG Thymidine Glycol

STRUCTURAL STUDIES

ODMTO

O P N(iPr)2

O CNEt

OTBDMS

REFERENCE

(1)K.Groebke,andC.J.Leumann,Helv Chim Acta, 1990, 73,608-617.

STABILITY NOTES

Syntheticoligonucleotidescontaining8-amino-dGmustbecleavedanddeprotectedwithammoniumhydroxidecontaining0.25M2-mercaptoethanoltoavoidoxidativedegradationof8-amino-dGsites.

OligonucleotidessynthesizedusingThymidineGlycolandUltraMILDmonomerscanbecleavedusingeitherconcentratedammoniumhydroxideor50mMpotassiumcarbonateinanhydrousmethanol.Completecleavageanddeprotectioncanbeaccomplished at room temperature in2-4hourswithoutdamagingThymidineGlycolbase.Thebestmethod to remove the TBDMS groups wasachievedusingTEA.3HFat40°Covernight.




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DNA DAMAGE/REPAIR (CONT.)

One of the major sources of DNAdamageinallorganismsistheUVcomponentofsunlight.ThepredominantreactioninducedbyUV lightonDNA isdimerizationofadjacentpyrimidinebases leading to cyclobutanedimers (CPDs). Thedimersformedinthemostsignificantquantityarethecis-syncyclobutanedimeroftwothyminebases.Althoughformedroutinely,thesedimerproductsareefficientlyexcisedandrepairedenzymaticallybynucleotideexcisionrepair(NER)orthedimerizationisreversedbyphotolaseenzymes.Afurthermodeofoxidativedamageisradiation-induceddamageofDNA,whichhasbeenshowntoleadtobridgedcyclonucleosides.Thepurines,cyclo-dAandcyclo-dG,arepredominantlyformed,althoughthecyclopyrimidineshavealsobeendetected.Cyclo-dAisdoublyintriguingsinceitcontainsbothdamagedbaseanddamagedsugarresiduesand,assuch,shouldhaveaconsiderablebiologicalimpact.Inamanneranalogoustothyminedimer,cyclopurinescausesignificantdistortionoftheregularDNAhelixandtheselesionsarerepairednotbybaseexcisionrepair(BER)butbyNER.


Cis-synThymineDimerPhosphoramidite 11-1330-95 50µmole 2100.00 11-1330-90 100µmole 4200.00 11-1330-02 0.25g 10200.00 5’,8-Cyclo-dACEPhosphoramidite 10-1098-95 50µmole 950.00 10-1098-90 100µmole 1850.00 10-1098-02 0.25g 5350.00

5’,8-Cyclo-dGCEPhosphoramidite 10-1598-95 50µmole 1250.00 10-1598-90 100µmole 2450.00

Baseexcisionrepair (BER) isoneof themoststudiedrepairmechanisms. In thispathway,DNAglycosylases recognizethedamagedbasesandcatalyzetheirexcisionthroughhydrolysisoftheN-glycosidicbond.AttemptstounderstandthestructuralbasisforDNAdamagerecognitionbyDNAglycosylaseshavebeenhamperedbytheshort-livedassociationoftheseenzymeswiththeirDNAsubstrates.Toovercomethisproblem,theVerdinegroupatHarvardsynthesizedapyrrolidineanalogthatmimicsthechargedtransitionstateoftheenzyme-substratecomplex.Whenincorporatedintodouble-strandedDNA, they found thepyrrolidineanalog (PYR), introducedas thePyrrolidine-CEPhosphoramidite, formsanextremelystablecomplexwiththeDNAglycosylaseAlkA,exhibitingadissociationconstantinthepMrangeandpotentlyinhibitedthereactioncatalyzedbytheenzyme.


Pyrrolidine-CEPhosphoramidite 10-1915-95 50µmole 190.00 (PYR) 10-1915-90 100µmole 380.00 10-1915-02 0.25g 1085.00

STRUCTURAL STUDIES

ODMTO

O P O

NH

N

O

O

OCH 3

N(iPr)2PO

O

O

O

N

HNCH 3

CH 3H

HO

OCH 3

Cis-syn Thymine Dimer

INSTRUMENT TYPES

Fortheseveryexpensivephosphoramidites, an ABI septum vial is thestandardvial.AddEtothecatalogno.foranExpeditevialorVtothecatalogno.foranExpediteVvial.

5’,8-Cyclo-dA

N

NN

N

NHBz

ODMTO

O P N(iPr)2

O CNEt

5’,8-Cyclo-dG

O

THPO

O P N(iPr)2

O CNEt

NH

N

N

O

N NH

O

NDMTO

O P N(iPr)2

O CNEt

OO

Pyrrolidine

SEE ALSO

dSpacer on page 84Pyrrolidine on page 63

62 63

MIN

OR

BASE

S

CLICK DNA AND RNA LIGATION

Ligationofanoligocontaininga5’-azidewithanoligocontaininga3’-propargylgroupusingClickChemistryleadstoatriazolelinkagethathasbeenshowntohavein vivobiocompatibility.ThistechniquehasbeenusedtosynthesizeDNAconstructsupto300basesinlength.WhentheresultanttriazolelinkagewasplacedinaPCRtemplate,variouspolymeraseswereabletocopythesequencecorrectly.Thelinkagehasalsobeenshowntobecompatiblewithtranscriptionandrollingcircleamplification,aswellasgeneexpressioninE. coli.IntheRNAworld,ahammerheadribozymecontainingthetriazolelinkageatthesubstratecleavagesitehasbeenshowntoretainitsactivity.Alargevarietyofapplicationsisenvisagedforthis biocompatiblechemicalligation.SupportforthistechnologyisofferedwiththehelpofTomBrown’sgroupattheUniversityofSouthampton.


3’-Propargyl-5-Me-dCCPG 20-2982-01 0.1g 180.00 20-2982-10 1.0g 1500.00 1µmolecolumns 20-2982-41 Packof4 300.00 0.2µmolecolumns 20-2982-42 Packof4 150.00 10µmolecolumn(ABI) 20-2982-13 Packof1 750.00 15µmolecolumn(Expedite) 20-2982-14 Packof1 1125.00

5’-LABELING OF MicroRNAs

SeveralmethodshavebeendevelopedforthedetectionofmiRNAs,however,fewallowthesimultaneousdetectionofmultiplemiRNAs. Toovercome thisanalyticaldeficiency, theRichertgroupat theUniversityofStuttgarthas recentlydevelopedaningeniousmethodtoselectivelydetectmiRNAsonmicroarrayswithoutinterferencefromendogenouspre-mRNAs,mRNAsandotherRNAspecies.Inthismethod,ashortoligonucleotidecontaining3’-amino-dTanda5’reportermolecule ischemically ligatedtothemicroRNA inaone-stepprocedureby in situactivationofthemicroRNA. This isspecificallyachievedbytakingadvantageofthefactthatmiRNAs,unlikeotherRNAs,are5’-phosphorylated.Thereactionistemplate-directed(andthussequencespecific)andcanbeperformedtogetherwithenzymatic3’-extension/labeling,eitherinsolutionoronasupport.TheshortDNAlabelingstrandmayfeatureoneofavarietyofdifferentlabels,suchasabiotingrouporafluorophore.


3’-Amino-dTCPG 20-2981-01 0.1g 120.00 20-2981-10 1.0g 995.00 1µmolecolumns 20-2981-41 Packof4 200.00 0.2µmolecolumns 20-2981-42 Packof4 120.00 10µmolecolumn(ABI) 20-2981-13 Packof1 500.00 15µmolecolumn(Expedite) 20-2981-14 Packof1 750.00

STRUCTURAL STUDIES

ODMTON

HN

O

O

HN

CH3

CF2

F2C CF2 HN

O

O

ODMTON

N

NH

O

O

CH3

HN

O

O

3’-Propargyl-5-Me-dC CPG 3’-Amino-dT CPG

OO

O

base

DNA

ON3

O

base

DNA

+

OO

O

base

DNA

O

O

base

DNA

NN

N

OO

O

base

DNA

O

O

base

DNA

P O

O

-O

BIOCOMPATIBLE TRIAZOLE LINKAGE

REFERENCES - CLICK LIGATION

(1)A.H.El-Sagheer,A.P.Sanzone,R.Gao,A.Tavassoli,andT.Brown,Proc Natl Acad Sci U S A, 2011, 108,11338-43.

(2)A.H.el-Sagheer,andT.Brown,Chem Commun (Camb), 2011, 47,12057-8.

(3)A.P.Sanzone,A.H.El-Sagheer,T.Brown,andA.Tavassoli,Nucleic Acids Res, 2012.

(4)A.Dallmann,etal.,Chemistry, 2011, 17, 14714-7.

(5)A.H.El-Sagheer,andT.Brown,Proc Natl Acad Sci U S A, 2010, 107,15329-34.

REFERENCES - MicroRNA Labeling

(1)H.Vogel,andC.Richert,ChemBioChem, 2012, 13,1474-82.

(2)R.Eisenhuth,andC.Richert,Journal of Organic Chemistry, 2008, 74,26-37.

(3)E.Kervio,A.Hochgesand,U.E.Steiner,andC.Richert,Proc Natl Acad Sci U S A, 2010, 107,12074-9.

2’-5’ LINKED OLIGONUCLEOTIDES

CellularDNAandRNAaremadeupof ribo-and2’-deoxyribonucleicacids linked together via3’-5’phosphodiesterlinkages andby far comprise thebulkof polynucleic acids found in cells. Much less commonareoligonucleotideswhichhave2’-5’linkages.However,auniquefeatureof2’-5’linkedoligonucleotidesistheirabilitytobindselectivelytocomplementaryRNA.Thesefeaturessuggestanumberofinterestingusesfor2’-5’linkedoligossuchastheiruseasRNAspecificprobesor inantisenseoligos. Recently,oligoshavebeensynthesizedusing3’-deoxy-2’-phosphoramiditesand2’-deoxy-3’-phosphoramiditestoproducechimeraswith2’-5’linkedendsand3’-5’linkedcentralregions.Itwasfoundthat2’-5’phosphorothioateoligos:1)bindselectivelytocomplementaryRNAwiththesameaffinityasphosphodiesteroligos;2)exhibitmuchlessnonspecificbindingtocellularproteins;3)donotactivateRNaseH.A3’-deoxynucleosideatthe3’-terminusofanotherwisenormaloligonucleotideeffectivelyblockspolymeraseextension.


3’-dA-CEPhosphoramidite 10-1004-95 50µmole 177.50 10-1004-90 100µmole 355.00 10-1004-02 0.25g 975.00

3’-dC-CEPhosphoramidite 10-1064-95 50µmole 177.50 10-1064-90 100µmole 355.00 10-1064-02 0.25g 975.00

3’-dG-CEPhosphoramidite 10-1074-95 50µmole 177.50 10-1074-90 100µmole 355.00 10-1074-02 0.25g 975.00

3’-dT-CEPhosphoramidite 10-1084-95 50µmole 177.50 10-1084-90 100µmole 355.00 10-1084-02 0.25g 975.00

3’-dA-CPG 20-2004-01 0.1g 300.00 1µmolecolumns 20-2104-41 Packof4 600.00 0.2µmolecolumns 20-2104-42 Packof4 200.00

3’-dC-CPG 20-2064-01 0.1g 300.00 1µmolecolumns 20-2164-41 Packof4 600.00 0.2µmolecolumns 20-2164-42 Packof4 200.00

3’-dC 3’-dG 3’-dT

STRUCTURAL STUDIES

3’-dA

ODMTO

CNEtON(iPr)2PO

NHBz

N

N

N

NBz

ODMTO

CNEtON(iPr)2PO

NH

O N

NiBu

ODMTO

CNEtON(iPr)2PO

HN

O

N

N

N

HN

ODMTO O

O

N

HN

CNEtON(iPr)2PO

CH 3

3’-dA-CPG 3’-dC-CPG

ODMTO

O succinylCPG

N

N

N

N

NHBz

ODMTO

O succinylCPG

N

NO

NHBz




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SEE ALSO

5’-I-dT in Click Chemistry on page 90Click Chemistry on page 88

SEE ALSO

3’-deoxynucleoside CPG on page 51

64 65

MIN

OR

BASE

S

2’-5’ LINKED OLIGONUCLEOTIDES (CONT.)


3’-dG-CPG 20-2074-01 0.1g 300.00 1µmolecolumns 20-2174-41 Packof4 600.00 0.2µmolecolumns 20-2174-42 Packof4 200.00 3’-dT-CPG 20-2084-01 0.1g 300.00 1µmolecolumns 20-2184-41 Packof4 600.00 0.2µmolecolumns 20-2184-42 Packof4 200.00

MUTAGENESIS

Cellularpolynucleotidesarealkylatedbyendogenouscomponents,suchasS-adenosylmethionine,orafterreactingwithtwogeneralclassesofenvironmentalandlaboratorychemicals.SN1chemicalagentsincludealkylnitrosoureaandN-alkyl-N-nitro-N-nitrosoguanidinethatreactwiththeN7positionofguanine,N3ofadenine,O6ofguanine,O2orO4ofpyrimidines,andthenon-phosphodiesteroxygenatomsofthephosphatebackbone.Incontrast,SN2chemicalagentssuchasmethylmethanesulfonateanddimethylsulfatereactprimarilywiththeN1positionofadenine(1-Methyl-2’-deoxyadenosine)andN3ofcytosine.ToavoidchainbranchingduringsynthesiswhenusingDCIasactivator,N6-Me-dAisofferedwithacetylprotection.


O6-Me-dG-CEPhosphoramidite 10-1070-90 100µmole 105.00 10-1070-02 0.25g 255.00

N6-Me-dA-CEPhosphoramidite 10-1003-90 100µmole 162.50 10-1003-02 0.25g 495.00

N6-Ac-N6-Me-dA-CEPhosphoramidite 10-1503-90 100µmole 162.50 10-1503-02 0.25g 495.00

O4-Me-dT-CEPhosphoramidite 10-1032-90 100µmole 135.00 10-1032-02 0.25g 355.00

1-Me-dA-CEPhosphoramidite 10-1501-95 50µmole 125.00 10-1501-90 100µmole 250.00 10-1501-02 0.25g 750.00

O6-Me-2’-deoxyGuanosine N6-Methyl-2’-deoxyAdenosine O4-Me-Thymidine

STRUCTURAL STUDIES

3’-dG-CPG 3’-dT-CPG

ODMTO

O succinylCPG

N

O

N

N

N

HNMe2N

ODMTO

O succinylCPG

CH 3

O

O

N

HN

O

O P N(iPr)2O CNEt

DMTO

OMe

iBuHN N

N

N

N

O

O P N(iPr)2O CNEt

DMTO

NHMe

N

N

N

N

O

O P N(iPr)2O CNEt

DMTOO N

N

OMeCH 3

1-Methyl-2’-deoxyAdenosine

N

N N

N

NAc

ODMTO

O P N(iPr)2

O CNEt

Me

N6-Ac-N6-Me-dA

IN SITU SYNTHESIS OF DNA ANALOGS

The convertiblenucleosidestrategyisoneofthemostversatilemethodsforproducingmodificationsinbasestoexaminetheireffectsonDNAstructureandactivity.Insomecases,withversatilitycomesdifficultyinthattheconvertiblebaseismodifiedafteroligonucleotidesynthesis.Thechemistryissometimescomplexandbasecompositionanalysisofthefinaloligonucleotideisrequiredtoverifystructure.TheconvertibledUmonomercanbeusedtointroduceavarietyofmodificationsattheconvertibleposition,includingN,OandSmodifications.ConvertibleF-dCisbyfarthesimplestapproachtothepreparationofoligonucleotidescontainingF-dC-normalammoniumhydroxidetreatmenteffectstheconversiontoF-dC.ConvertibledAhasbeenusedtoprepareoligonucleotidescontainingmultiplepointsforattachmenttosolidsupports.Inthisway,highcapacityaffinitysupportsforthepurificationofDNAbindingproteinshavebeenprepared.2-F-dIisaconvertiblenucleosideforthepreparationof2’-dGderivativesfollowingthedisplacementofthe2-fluorinebyprimaryamines.


TMP-F-dU-CEPhosphoramidite 10-1016-90 100µmole 195.00 (ConvertibleF-dC) 10-1016-02 0.25g 495.00

O6-Phenyl-dI-CEPhosphoramidite 10-1042-90 100µmole 135.00 (ConvertibledA) 10-1042-02 0.25g 355.00

O4-Triazolyl-dU-CEPhosphoramidite 10-1051-90 100µmole 135.00 (ConvertibledU) 10-1051-02 0.25g 355.00

2-F-dI-CEPhosphoramidite 10-1082-95 50µmole 180.00 (ConvertibledG) 10-1082-90 100µmole 360.00 10-1082-02 0.25g 975.00

O6-Phenyl-dI O4-Triaz.-dU

STRUCTURAL STUDIES

TMP-F-dU

ABBREVIATION

TMP=2,4,6-trimethylphenyl

O

O P N(iPr)2O CNEt

DMTOO N

N

OF

O

O P N(iPr)2O CNEt

DMTO

OPh

N

N

N

N

O

O P N(iPr)2O CNEt

DMTOO N

N

NN

N

O

O P N(iPr)2O CNEt

DMTO

N

N

N

N

F

O

NO2

2-F-dI




Expedite EMerMade M




SEE ALSO

N6-Me-dA on page 47

66 67

MIN

OR

BASE

S

STRUCTURAL STUDIES

Etheno-2’-deoxyAdenosine

O

O P N(iPr)2O CNEt

DMTON

N

N

N

N

PROBING DNA STRUCTURE WITH FLUORESCENT NUCLEOSIDES

Etheno-dAisafluorescentnucleosidewhichisespeciallyusefulinobservingthetransitionbetweenDNAstructuraltypes.Itisquitebaselabileandshouldbedeprotectedwithammoniumhydroxideatroomtemperaturefor24hours.Alternatively,UltraMildchemistrycanbeused.2-AminopurineandAP-dC(G-Clamp)arealsousefulfluorescentnucleosides.

Pyrrolo-dCisafluorescentdeoxycytidineanalogthatisanidealprobeofDNAstructureanddynamics.1,2Itbase-pairsasanormaldCnucleotide.Anoligofullysubstitutedwithpyrrolo-dChasthesameTmasthecontroldColigowiththesamespecificityfordG.ItssmallsizedoesnotperturbthestructureoftheDNAhelixanditiswelltoleratedbyanumberofDNAandRNApolymerases.Itishighlyfluorescentanditsexcitationandemissionarewelltotheredofmostfluorescentnucleotideanalogs,whicheliminatesorreducesbackgroundfluorescencefromproteins.Pyrrolo-dCTPhaspotentialusesinbiologicalassaydevelopment.


Etheno-dA-CEPhosphoramidite 10-1006-90 100µmole 105.00 10-1006-02 0.25g 255.00

Pyrrolo-dC-CEPhosphoramidite 10-1017-95 50µmole 110.00 10-1017-90 100µmole 220.00 10-1017-02 0.25g 675.00

Pyrrolo-dCTP 81-1017-01 100µL 150.00 (10mM)

O

O P N(iPr)2O CNEt

DMTON

N

O

HN

Pyrrolo-dC

SPECTRAL PROPERTIES

Thespectralpropertiesofpyrrolo-dC,coupledwithitsuniquebase-pairingability,makethisfluorescentanalogextremelyvaluableinprobingDNAstructure.Whenthepyrrolo-dCisbase-paired,itsfluorescenceissignificantlyquenchedthroughwhatismostlikelybasestackingordGinteractions.Thequantumyieldoffluorescenceforpyrrolo-dCisquitesensitivetoitshybridizationstate,makingitideallysuitedforprobingthedynamicstructureofDNA.

QY l e (L/mol.cm)

single-stranded 0.07 260nm 4000 347nm 3700

double-stranded 0.02 (QYdeterminedrelativetoquinine

sulfatein0.5MH2SO4)

O

OH

ON

N

O

HN

POPOPNaOO O O

ONa ONa ONa

Pyrrolo-dCTP

REFERENCES

1. D.A.Berry,etal.,Tetrahedron Lett, 2004, 45,2457-2461.

2. TheGlenReport,2007,19,8-9.3. P.Sandin,etal.,Nucleic Acids Res.,

2008, 36,157-167.4. P.Sandin,etal.,Nucleic Acids Res.,

2005, 33,5019-5025.5. K.C.Engman,etal.,Nucleic Acids Res.,

2004, 32,5087-5095.


Pyrrolo-dCisajointdevelopmentprojectofBerry&Associates,Inc.andGlenResearchCorporation.Pyrrolo-dCiscoveredbyUSPatentNo.:7,144,995.

PROBING DNA STRUCTURE WITH FLUORESCENT NUCLEOSIDES (CONT.)

Byattachingpyreneorperylenetothe5positionofdeoxyuridinethroughatriplebond,thefluorophoreiselectronicallycoupled to thedeoxyuridinebase. Thiselectronic couplingof thebaseand thefluorophoremakes thefluorescencesensitivetothebasepairingofthedUportionofthemolecule,allowingthediscriminationbetweenperfectandonebasemismatchedtargets.


Pyrene-dU-CEPhosphoramidite 10-1590-95 50µmole 105.00 10-1590-90 100µmole 210.00 10-1590-02 0.25g 550.00

Perylene-dU-CEPhosphoramidite 10-1591-95 50µmole 150.00 10-1591-90 100µmole 300.00 10-1591-02 0.25g 720.00

ODMTON

HN

O

O

O P N(iPr)2

O CNEt

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

Perylene-dUPyrene-dU

SPECTRAL PROPERTIES

Absorbance Emission Maximum Maximum

Pyrene-dU 402nm 472nmPerylene-dU 473nm 490nm




Expedite EMerMade M




STRUCTURAL STUDIES

SEE ALSO

2-Aminopurine on page 58AP-dC (G-Clamp) on page 46UltraMild Chemistry on page 23Pyrrolo-C on page 132Pyrrolo-CTP on page 136

68 69

MIN

OR

BASE

S

mol.cm

PROBING DNA STRUCTURE WITH FLUORESCENT NUCLEOSIDES (CONT.)

Thetricyclicfluorescentnucleosideanalogues,1,3-diaza-2-oxophenothiazine,tC,and1,3-diaza-2-oxophenoxazine,tCo, are deoxycytidineanalogsthathavebeenshowntobasepairfaithfullywithdGwithvirtuallynodisruptionofthenormalduplexstructure.3-5ThismeansthatthestabilityoftheDNAduplexisnotcompromisedascomparedtothecontrolregardlessofDNAsequence.ThefluorescencequantumyieldoftCisessentiallyunchangedbetweensinglestrandedanddoublestrandedDNA-0.21forsinglestrandedDNAand0.19forduplexDNA.Also,thefluorescencecharacteristicsoftCarenotsensitivetoneighboringbasecombinations.tCohasbeenshowntobethebrightestfluorescentnucleosideanalogueinduplexcontextreportedsofarandevenretainsthemajorityofitsfluorescencewhensurroundedbyguanineresidues.Indeed, tCohasbeenreportedtobe25-50timesbrighterthan2-aminopurine.

ThebaseanaloguetCnitroisaFRET-acceptortogetherwithtCO(ortC)asthedonormolecule.Thisconstitutesthefirstever

descriptionofanucleobaseFRET-pair.ThisnovelFRET-pairprovidesauniquetoolforinvestigationsofnucleicacidcontainingsystems.tCnitroisvirtuallynon-fluorescentundernormalconditions.


tC-CEPhosphoramidite 10-1516-95 50µmole 250.00 10-1516-90 100µmole 490.00 10-1516-02 0.25g 1460.00

tC°-CEPhosphoramidite 10-1517-95 50µmole 250.00 10-1517-90 100µmole 490.00 10-1517-02 0.25g 1460.00

tCnitro-CEPhosphoramidite 10-1518-95 50µmole 265.00 10-1518-90 100µmole 520.00 10-1518-02 0.25g 1460.00

PHOTO-REGULATION OF DNA FUNCTION

GlenResearch’sinterestliesinthepreparationofcagedoligonucleotideswhosefunctionisrestoredafteruncagingbyUVlightatawavelengththatcausesnoDNAdamage.TheDeitersgroupatNorthCarolinaStateUniversityhasdescribedNPOM-Caged-dT,wherethenucleobaseiscagedwiththephotolabilegroup,6-nitropiperonyloxymethyl(NPOM),whichcanberemovedusingUVlightat365nm.OligonucleotidescontainingNPOM-Caged-dTeveryfiveorsixbasesdonothybridizetotheircomplementarystrand.Photo-uncagingofthecagedoligonucleotideistheneasilycarriedoutwithUVlightat365nmforsecondstominutestorestoretheactivityoftheoligonucleotide.


NPOM-Caged-dT-CEPhosphoramidite 10-1534-95 50µmole 185.00 10-1534-90 100µmole 355.00 10-1534-02 0.25g 895.00

SPECTRAL PROPERTIES

AbsorptionandemisssiondatafortCand tCoarecollectedbelow:

tC QY l e (L/mol.cm)

single-stranded 0.21 385nm 4000

double-stranded 0.19

tCo QY l e (L/mol.cm)

single-stranded 0.30 360nm 9000

double-stranded 0.21 (QYdeterminedrelativetoquinine

sulfatein0.5MH2SO4)

ODMTON

N

O

O P N(iPr)2

O CNEt

S

HN

ODMTON

N

O

O P N(iPr)2

O CNEt

O

HN

tCotC

O

N

N

O

O P N(iPr)2

O CNEt

S

HN

DMTO

NO2

tCnitro


TheseproductsareofferedincollaborationwithModyBaseHB.

ODMTO

N

N

O

O

H3C

O P N(iPr)2

O CNEt

O

NO2

OO

CH3

NPOM-Caged-dT

STRUCTURAL STUDIES STRUCTURAL STUDIES

Ara-C

O

O P N(iPr)2O CNEt

DMTOOAc

NHAc

O N

N

INHIBITION OF DNA METHYLTRANSFERASES

Zebularine(pyrimidin-2-oneribonucleoside)isacytidineanaloguethatactsasaDNAdemethylaseinhibitor,aswellasacytidinedeaminaseinhibitor.ThisstructureisveryactivebiologicallyandZebularineisnowusedasapotentanti-cancerdrug. A2’-deoxynucleosideanalogueofZebularine,5-methyl-pyrimidin-2-one,2’-deoxynucleoside,hasbeenused toprobetheinitiationofthecellularDNArepairprocessbymakinguseofitsmildlyfluorescentproperties.Thiscombinationofbiologicalactivityandfluorescencepropertieswouldmake5-Me-2'-deoxyZebularineastrongadditiontoourarrayofnucleosideanalogues.

Cytosine-5-methyltransferases are found ineverything fromarchaebacteria tomammals andwhen the regulationofcytosine-5-methyltransferasesgoesawry,cancercanresult.ThemechanismofactionforthisfamilyofenzymesinvolvesattackofacysteinethiolgroupontheC6positionofcytosine,leadingtoatransientdihydrocytosineintermediate,whichthenfacilitatesthenucleophilicattackbyC5ontheactivatedmethylgroupoftheS-adenosyl-L-methioninecofactor.Aswithmanyenzymes,theintermediatecanbetrappedusingasuicidesubstrateand5-fluoro-cytosinehasbeenusedextensivelyinthisrole.Analternatestrategyistouseatransition-statemimicthatbindstotheactivesitewithhighaffinity.Anexcellentcandidatewasfoundin5-aza-5,6-dihydrocytosine.Despitenotbeingcovalentlyboundtotheenzyme,itwasfound1,2tobeamorepotentinhibitorofcytosine-5-methyltransferasesthan5-fluoro-cytosine.5-Aza-5,6-dihydro-dCiscompatiblewithstandardoligonucleotidesynthesisanddeprotectionconditionsandisanexcellenttoolforuseinmethyltransferaseresearch.


5-Me-2'-deoxyZebularine-CEPhosphoramidite 10-1061-95 50µmole 200.00 10-1061-90 100µmole 400.00 10-1061-02 0.25g 975.00

5-Aza-5,6-dihydro-dC-CEPhosphoramidite 10-1511-95 50µmole 180.00 10-1511-90 100µmole 360.00 10-1511-02 0.25g 1120.00

LARGE SCALE SYNTHESIS

ThemostcommonsidereactionduringdeprotectionofoligonucleotidesonalargescaleisthealkylationofdTresiduesbyacrylonitrile,formedbyß-eliminationofthecyanoethylphosphateprotectinggroups,togenerateN3-cyanoethyl-dT.


N3-Cyanoethyl-dT 10-1531-90 100µmole 200.00 10-1531-02 0.25g 600.00

5-Me-2'-deoxyZebularine

N

NODMTO

CNEtON(iPr)2PO

O O

O P N(iPr)2O CNEt

DMTO

N

NO

N

NH

N

5-Aza-5,6-Dihydro-dC

REFERENCES

(1)G.Sheikhnejad,etal.,J Mol Biol, 1999, 285,2021-2034.

(2)V.E.Marquez,etal.,Antisense Nucleic Acid Drug D, 1999, 9,415-421.

i

N3-Cyanoethyl-dT




Expedite EMerMade M




SEE ALSO

Ribo-tCo on page 136

SEE ALSO

Convertible F-dC on page 655-Fluoro-2’-deoxyUridine on page 60Pyrrolidine on page 63

70 71

MIN

OR

BASE

S

mol.cm

mol.cm

STRUCTURAL STUDIES STRUCTURAL STUDIES

NON-CANONICAL STRUCTURES

DNAandRNAstructuresaredefinedbyWatson-Crickrulesofhybridization.However,avarietyofDNAandRNAstructureshavebeendefinedwhichdonotrelyonsimpleA-T/UandG-Cbinding.SincethesestructuresdisobeytheWatson-Crickcanon,theyaredescribedasnon-canonical.Non-canonicalDNAandRNAsegmentsareformedasaresultofsecondarystructures.TheseincludeG-quadruplexes,triplexformingoligos,hairpins,cruciforms,andi-Motifstructures.

G-QUADRUPLEX

Oligonucleotide structural analysishasdemonstrated thatDNAandRNAnucleic acid sequences containingG-tractsseparatedbyotherbasesspontaneouslyfoldintoG-quadruplexstructures.G-quadruplexesareformedwhenfouradjacentguanineresiduesstackinacyclicHoogsteenhydrogen-bondingarrangementleadingtofour-strandedhelicalstructures.ThestudyofG-quadruplexesinbasicgeneticprocessesisanactiveareaofresearchintelomeraseactivity,generegulation,andfunctionalgenomics.Guanineanaloguesthathavedifferenthydrogenbondingcharacteristics-7-deaza-8-aza-dGand7-deaza-dG-haveproveduseful inanalyzingG-quadruplexstructures. Similarly,commonDNAlesions-8-oxo-dGandabasicsites-havebeenusedtoinvestigatetheireffectonG-quadruplexstructureandactivity.

TRIPLEX-FORMING OLIGONUCLEOTIDES

Triplex-formingoligonucleotides(TFO)bindinthemajorgrooveofduplexDNAinasequence-specificmannerthroughtheformationofnonWatson-Crick(Hoogsteen)hydrogenbonds.Theformationofatriplexalongthemajorgroovecompeteswiththebindingoftranscriptionfactorsandotherproteinsthatarenecessaryfortranscription,thereby inhibitingtheexpressionofparticulargenes. A varietyofnucleosideanalogueshavebeenused inTFO -8-amino-dG,8-amino-dA,6-thio-dGanddeoxypseudouridine.

i-MOTIF DNA STRUCTURES

IntercalatedMotif(i-Motif)DNAstructuresmaybeformedinregionsrichin2’-deoxyCytidine.EspeciallyatacidicpH,thesestructurescouldbedescribedasC-Quadruplexeswithtwoparallelstrandedsequencesalsoheldtogetherinanantiparallelorientationbycytosine-cytosinebasepairs.SincethesestructuresarestableatacidicpH,theycanactasnanoswitchesbychangeinpH.AstheywerenotconsideredtobestableatphysiologicalpH,theywerenotinitiallyconsideredtoberelevanttobiologicalsystems.However,thestabilityofthecytosine-cytosinebasepairisenhancedbyintercallatingligandsandsoavarietyofi-Motifstructuresarenowconsideredtobebiologicallysignificant.Sincei-Motifstructureshavenowbeenobservedforminganddissolvinginlivingcells,thesestructuresarenowthesubjectofactiveinvestigationofthemeaningoftheiractivityinhumancells.ResearchisalsobeingdirectedtotheeffectofcommonDNAlesions,likedepurinatedsites,8-oxo-dGand5-hydroxymethyl-dC,onthesetransientstructures.

APTAMER DEVELOPMENT

Aptamers,generatedthroughrepetitiveselectionusingSELEXoranequivalent in vivo procedure, are chosen for their abilitytobinddesiredtargetmolecules,whicharefrequentlysmallmoleculesusefulintherapeutics.Insomeways,theymaybedescribedaschemicallyengineeredversionsofantibodies.Ofcourse,nucleicacidaptamershaveadvantagesoverantibodiesinthattheycanbedevelopedrapidlybyin vitromethods,withthereproducibilityofchemicalsynthesisandinherentstabilityofmodifiedoligonucleotides.Afullbatteryofbase,sugarandinternucleotidemodificationsisavailableforaptamerdevelopment.

2’-F-RNAhasbeenusedextensivelyinaptamerdevelopment,aswellas2’-F-ANAmorerecently.AnarticleinTheGlenReportbyJeffCarter,Director,ProcessChemistry,SomaLogic,Inc.described1theuseofaDNAbackbonewith5-substituteddUanaloguesaslowoff-ratemodifiedaptamer(SOMAmer®)reagentstoenablemultiplexedscreeningofthousandsofserumorplasmaproteins.TheseaptamersalsoincludePCBiotinalongwithafluorophore,inthiscaseCyanine3,forsubsequentdetection.

SEE ALSO

7-Deaza-8-Aza-2’-deoxyGuanosine on page 578-oxo-2’-deoxyGuanosine on page 617-Deaza-2’-deoxyGuanosine on page 57Abasic II Phosphoramidite on page 62dSpacer on page 848-Amino-dG on page 628-Amino-dA on page 596-Thio-dG on page 582’-deoxypseudoU-CE on page 585-Hydroxymethyl-dC on page 50

SEE ALSO

2’-F-RNA Phosphoramidites on page 1432’-F-Arabinonucleic Acid (2’-F-ANA) on page 144PC Biotin Phosphoramidite on page 100Cyanine 3 Phosphoramidite on page 106

REFERENCE

(1)J.Carter,The Glen Report, 2015, 27.1, 6-8.

72 73

MIN

OR

BASE

S

MODIFIERS

TERMINUS MODIFIERS

GlenResearch5’-Modifiersaredesigned foruse inDNA synthesizers to functionalize the5’-terminusof the targetoligonucleotide.The5’-Amino-Modifiersareavailablewithavarietyofchainlengthstofitexactlythedesiredapplication.

TheDMS(O)MT-protectedaminogroupiseasiertodeprotectcomparedtotheMMT-protectedone.Thesulfoxyderivativesurvivesconditionsofoligonucleotidesynthesisandcaneitherbecleavedwithstandarddeblocksolution,orleftintactforHPLCpurification.Atthesametime,theDMS(O)MTgroupisfullycompatiblewithcartridgepurification.Whendetritylationonacartridgeiscarriedout,theDMS(O)MT+,whichismorestablethanMMT+,doesnotreattachitselftoanamine.Wenowoffer5’-DMS(O)MT-Amino-ModifierC6utilizingthisnewtritylbasedprotectinggroup.

5’-Amino-ModifierTEG,ahydrophilictriethyleneglycolethylaminederivative,is12atomsinlengthandfullysolubleinaqueousmedia.


5’-Amino-ModifierC3-TFA 10-1923-90 100µmole 50.00 10-1923-02 0.25g 175.00

5’-Amino-ModifierC6 10-1906-90 100µmole 60.00 10-1906-02 0.25g 200.00

5’-Amino-ModifierC6-TFA 10-1916-90 100µmole 30.00 10-1916-02 0.25g 100.00

5’-Amino-ModifierC12 10-1912-90 100µmole 90.00 10-1912-02 0.25g 300.00

5’-Amino-Modifier5 10-1905-90 100µmole 60.00 10-1905-02 0.25g 200.00

5’-DMS(O)MT-Amino-ModifierC6 10-1907-90 100µmole 60.00 10-1907-02 0.25g 200.00

5’-Amino-ModifierTEG 10-1917-90 100µmole 115.00 10-1917-02 0.25g 500.00

ABBREVIATIONS

CNEt=Cyanoethyl CPG = Controlled Pore Glass DMT=4,4’-Dimethoxytrityl Fmoc=Fluorenylmethoxycarbonyl iPr=Isopropyl MMT=4-Monomethoxytrityl T=Trityl TFA=Trifluroacetyl

5’-Amino-Modifier C3-TFA 5’-Amino-Modifier C6

5’-Amino-Modifier C12

5’-Amino-Modifier C6-TFA

5’-Amino-Modifier 5

TFANH

CNEtON(iPr)2PO

MMTNH

CNEtON(iPr)2PO

TFANHO P N(iPr)2

O CNEt

CNEtON(iPr)2POMMTNH

O


5’-Carboxy-ModifierC10isofferedfor sale under license from TriLink BioTechnologies,Inc.Itisintendedfor research and development purposesonly,andmaynotbeusedforcommercial,clinical,diagnosticoranyotheruse.ItiscoveredunderUSPatentNo.6,320,041.

MMTNH

CNEtON(iPr)2PO

i

5’-DMS(O)MT-Amino-Modifier C6

F3C

O

HN

OO

OO P N(iPr)2

O CNEt

5’-Amino-Modifier TEG

TERMINUS MODIFIERS (CONT.)

Ourmorerecent5’-aminomodifiers,protectedbyanovelphthalicaciddiamide(PDA)protectinggroup,arestablesolids.IncontrasttotheTFAprotectedaminomodifiers,whichareviscousoils,theanalogousPDAprotectedcompoundsaregranularpowders.Thisimportantpropertyofthesecompoundsallowsstraightforwardhandling,storageandaliquotingandleadstoasignificantincreaseinstability.

DeprotectionwithmethylamineingasphaseoraqueoussolutionorAMAleadstofastandcompleteremovalofthePDAprotectinggroup.However,ammoniumhydroxidewillnotdrivetheequilibriumreactiontocompletionandonlypartialdeprotectionoccurs-overnightdeprotectionwithammoniumhydroxidewillyieldaround80%activeamine.

WeareofferingthreePDAAmino-Modifiers:

•5’-Amino-ModifierC6-PDA •Hydrophobic5’-Amino-ModifierC12-PDA •Hydrophilic5’-Amino-Modifier-TEG-PDA


5’-Amino-ModifierC6-PDA 10-1947-90 100µmole 30.00 10-1947-02 0.25g 100.00

5’-Amino-ModifierC12-PDA 10-1948-90 100µmole 65.00 10-1948-02 0.25g 240.00

5’-Amino-Modifier-TEG-PDA 10-1949-90 100µmole 105.00 10-1949-02 0.25g 420.00

MODIFIERS


PDAamino-modifierswereevelopedbyStefanPitschandReseaChemGmbH(S.Berger),Patentpending.




Expedite EMerMade M




O

O

HN

HN

O P N(iPr)2

O CNEt

O

O

HN

HN

O P N(iPr)2

O CNEt

O

O

HN

HN

OO

OO P N(iPr)2

O CNEt

5’-Amino-Modifier C6-PDA

5’-Amino-Modifier-TEG-PDA5’-Amino-Modifier C12-PDA

SEE ALSO

PC modifiers on page 86

74 75

MO

DIF

ICAT

ION

/LAB

ELIN

G

MODIFIERS

TERMINUS MODIFIERS (CONT.)

Thedisulfidethiolmodifiermaybeusedforintroducing3’-or5’-thiollinkages.Dithiol Serinol, produced from lipoic acid andourpatentedserinolbackbone,allowseasyconnectionofmultiplydithiol-labeledoligostogoldsurfaces.5’-Carboxy-ModifierC10isauniquelinkerdesignedtobeaddedattheterminusofanoligonucleotidesynthesis. ItgeneratesanactivatedcarboxylicacidN-hydroxysuccinimide(NHS)estersuitableforimmediateconjugationonthesynthesiscolumnwithmoleculescontainingaprimaryamine,resultinginastableamidelinkage.Analternativecarboxylateprotectinggroupisthe2-chlorotritylgroup,whichissimplyremovedusingthestandarddeblockcycletogenerateafreecarboxylgrouponanotherwisefullyprotectedoligonucleotide.The2-chlorotritylgroupisalsoremovedduringoligodeprotectionwithammoniumhydroxideorAMAandisincompatiblewithRPpurificationtechniques.PCAmino-ModifierisaphotocleavableC6amino-modifier,partofourlineofphotocleavable(PC)modifiers.5’-AminoOxy-Modifier11isbasedonatetraethyleneglycollinkageforimprovedsolubilityandforreducingthepotentialnegativeimpactonhybridizationoftheoligo.Theoximeformedfromthereactionofalkyloxyamineswithaldehydescreatesastablecovalentbond.Incomparison,theimineformedbytheconjugationofprimaryamineswithaldehydesisnotstabletoacidicorbasicconditionsandrequiressubsequentreductionwithborohydridetoformstableamineconjugates.5’-MaleimideModifierPhosphoramidite,developedattheUniversityofBarcelona,incorporatesamaleimidecycloadductthatisstabletoammoniumhydroxideatroomtemperature.Thisphosphoramiditecanbe incorporated intoDNAandRNAwithbothphosphateandphosphorothioate linkages. Aretro–Diels-Alderreactiondeprotectsthemaleimideimmediatelypriortoconjugation.


5’-Thiol-ModifierC6 10-1926-90 100µmole 60.00 10-1926-02 0.25g 200.00

Thiol-ModifierC6S-S 10-1936-90 100µmole 150.00 10-1936-02 0.25g 360.00

DithiolSerinolPhosphoramidite 10-1991-95 50µmole 120.00 10-1991-90 100µmole 215.00 10-1991-02 0.25g 585.00

PCAmino-ModifierPhosphoramidite 10-4906-90 100µmole 135.00 10-4906-02 0.25g 395.00

5’-Carboxy-ModifierC10 10-1935-90 100µmole 65.00 10-1935-02 0.25g 265.00

5’-Carboxy-ModifierC5 10-1945-90 100µmole 95.00 10-1945-02 0.25g 330.00

5’-AminoOxy-Modifier11 10-1919-95 50µmole 140.00 10-1919-90 100µmole 265.00 10-1919-02 0.25g 895.00

5’-Maleimide-ModifierPhosphoramidite 10-1938-90 100µmole 70.00 10-1938-02 0.25g 335.00

5’-Thiol-Modifier C6 Thiol-Modifier C6 S-S

TS

CNEtON(iPr)2PO

5’-Carboxy-Modifier C10

DMTOS

SO P N(iPr)2

OCNEt

N

O

O

O

OO P N(iPr)2

O CNEt

TFAHNNH

ONO2

H3C

CNEtON(iPr)2PO

PC Amino-Modifier




Expedite EMerMade M




OO

O P N(iPr)2

O CNEt

OO

HNDMT

5’-AminoOxy-Modifier 11


5’-MaleimideModifierPhosphoramiditeisprotectedbyapatentapplicationandisofferedbyGlenResearchunderanon-exclusivelicenseagreementfromtheUniversityofBarcelona.

O

HH

N

O

O

CH2CH2O P N(iPr)2

O CNEt

5’-Maleimide-Modifier

O

O

Cl

O P N(iPr)2

O CNEt

5’-Carboxy-Modifier C5

SS

HN

HN

O O

ODMT

O P N(iPr)2

O-CNEtDithiol Serinol

SEQUENCE MODIFIERS

SequenceModifiersaredesignedforuseinautomatedsynthesis.Thecarboxy-dTishydrolyzedduringdeprotectionandcanbecoupleddirectlytoamoleculecontainingaprimaryaminogroupbyastandardpeptidecouplingorviatheintermediateN-hydroxysuccinimide (NHS)ester. Amino-ModifierdA,Amino-ModifierdC,N2-Amino-ModifierdGandbothAmino-ModifierdTproductscanbeaddedinplaceofadA,dC,dGanddTresidue,respectively,duringoligonucleotidesynthesis.CorrespondingAmino-Modifiersupportscanreplacetheirrespectivedeoxynucleosidesupports.Afterdeprotection,theprimaryamineontheC6analoguesisseparatedfromtheoligonucleotidebyaspacerarmwithatotalof7-10atomsandcanbelabeledorattachedtoanenzyme.TheC2analogueismoresuitablefortheattachmentofmoleculesdesignedtoreactwiththeoligonucleotide.


Amino-ModifierC6dA 10-1089-90 100µmole 205.00 10-1089-02 0.25g 455.00

Amino-ModifierC6dC 10-1019-90 100µmole 225.00 10-1019-02 0.25g 450.00

N2-Amino-ModifierC6dG 10-1529-95 50µmole 240.00 10-1529-90 100µmole 480.00 10-1529-02 0.25g 1100.00

Carboxy-dT 10-1035-90 100µmole 180.00 10-1035-02 0.25g 360.00

Amino-ModifierC2dT 10-1037-90 100µmole 180.00 10-1037-02 0.25g 360.00 10-1037-05 0.5g 720.00

Amino-ModifierC6dT 10-1039-90 100µmole 180.00 10-1039-02 0.25g 360.00 10-1039-05 0.5g 720.00

MODIFIERS

Carboxy-dT Amino-Modifier C2 dT Amino-Modifier C6 dT

Amino-Modifier C6 dC

HN

N

O

O

O

OMe

O

O P N(iPr)2O CNEt

DMTO

Amino-Modifier C6 dA

O

CNEtON(iPr)2PO

DMTON

N

N

NNH

NHCCF 3

ONHBz

NHNHCCF 3

O O

O

CNEtON(iPr)2PO

N(CH 3)2

N

O N

N

DMTO

N2-Amino-Modifier C6 dG

NHCCF 3

O

HN

N

O

O

NH

O

O

O P N(iPr)2O CNEt

DMTO

HN

N

O

O

NHNHCCF 3

O O

O

O P N(iPr)2O CNEt

DMTO

HN

N

N

O

N

ODMTO

O P N(iPr)2

O CNEt

NH

CF3CNH

O

SEE ALSO

Amino-Modifier supports on page 79

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SEQUENCE MODIFIERS (CONT.)

OurrepertoireofNHSesterderivativeshasbeenexpandedtoincludetheNHS-Carboxy-dT-CEPhosphoramidite.BymakingadTanalogoftheCarboxy-ModifierC10,itispossibletolabeloneormultiplesiteswithinanoligonucleotide.Thisopensupthepossibilitytolabelanynumberofdifferentdyesormoleculeswithinanoligonucleotidewhenthephosphoramiditeisunavailable.Doingsoisstraightforwardandmaybedonemanuallyoffthesynthesizeroreveninafully-automatedmannerontheDNAsynthesizer.

WehaveneverfoundconditionswhichallowtheTFAgrouptoberemovedfromanamino-modifierwhiletheoligonucleotideremainsattachedtothesupport.Weareabletosolvethisproblembyusinga9-fluorenylmethoxycarbonyl(Fmoc)protectinggroup.TheFmocgroupisremovedusingatwostepprocedure,thefirsttoremovethecyanoethylprotectiongroupsandflushtheformedacrylonitrilefromthesynthesiscolumnusing1%diisopropylamineinacetonitrile,andthesecondtoremovetheFmocgroupusing10%piperidineinDMF.Theaminogroupsoformedonthecolumncanbereactedwithavarietyofactivatedesters.WeofferFmoc-Amino-ModifierC6dTPhosphoramiditeasanucleosidicoptionandAmino-ModifierSerinolPhosphoramiditeasanon-nucleosidicalternative.WealsoofferS-Bz-Thiol-ModifierC6-dTtojointheranksofthiol-modifiersforoligonucleotidesynthesis.Thiol-ModifierC6-dTcanbeaddedasusualatthedesiredlocationswithinasequence.


NHS-Carboxy-dT 10-1535-90 100µmole 210.00 10-1535-02 0.25g 550.00

Fmoc-Amino-ModifierC6dT 10-1536-90 100µmole 180.00 10-1536-02 0.25g 360.00

S-Bz-Thiol-ModifierC6-dT 10-1538-95 50µmole 130.00 10-1538-90 100µmole 245.00 10-1538-02 0.25g 550.00

Amino-ModifierSerinolPhosphoramidite 10-1997-95 50µmole 125.00 10-1997-90 100µmole 225.00 10-1997-02 0.25g 595.00

i

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

NH

OHN O

O

NHS-Carboxy-dT Fmoc-Amino-Modifier C6 dT

MODIFIERS




Expedite EMerMade M




ODMT

O P N(iPr)2

O CNEt

HN

HN

Fmoc

OODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

NH

OHN

O

SBz

S-Bz-Thiol-Modifier C6-dT Amino-Modifier Serinol Phosphoramidite

3’-MODIFIERS

3’-Amino-ModifierCPGs,containingaminogroupsprotectedwiththebase-labileFmocgroup,aredesignedtofunctionalizethe3’-terminusofthetargetoligonucleotidebytheintroductionofaprimaryamine.Inanalternativeapproach,thenitrogendestinedtobecomethe3’-aminogroupisincludedinaphthalimide(PT)groupwhichisattachedtothesupportthroughanamidegroupattachedtothearomaticring.Thissimplelinkageisverystabletoallconditionsofoligonucleotidesynthesisandcontainsnochiralcenter.Usinganextendedammoniumhydroxidetreatment(55°Cfor17hours),thecleavageoftheaminefromthephthalimideisaccomplishedalongwiththedeprotectionoftheoligonucleotide.ABI-stylecolumnsaresuppliedunlessotherwiserequested.

Item Cat. No. Pack Price ($)

3’-Amino-ModifierC7CPG1000 20-2958-01 0.1g 95.00 20-2958-10 1.0g 675.00 1µmolecolumns 20-2958-41 Packof4 140.00 0.2µmolecolumns 20-2958-42 Packof4 85.00 10µmolecolumn(ABI) 20-2958-13 Packof1 250.00 15µmolecolumn(Expedite) 20-2958-14 Packof1 375.00

3’-Amino-ModifierSerinolCPG 20-2997-01 0.1g 95.00 20-2997-10 1.0g 675.00 0.2µmolecolumns 20-2997-42 Packof4 85.00 1µmolecolumns 20-2997-41 Packof4 140.00 10µmolecolumn(ABI) 20-2997-13 Packof1 250.00 15µmolecolumn(Expedite) 20-2997-14 Packof1 375.00

3’-PT-Amino-ModifierC3CPG 20-2954-01 0.1g 95.00 20-2954-10 1.0g 675.00 1µmolecolumns 20-2954-41 Packof4 140.00 0.2µmolecolumns 20-2954-42 Packof4 85.00 10µmolecolumn(ABI) 20-2954-13 Packof1 250.00 15µmolecolumn(Expedite) 20-2954-14 Packof1 375.00

3’-PT-Amino-ModifierC6CPG 20-2956-01 0.1g 95.00 20-2956-10 1.0g 675.00 1µmolecolumns 20-2956-41 Packof4 140.00 0.2µmolecolumns 20-2956-42 Packof4 85.00 10µmolecolumn(ABI) 20-2956-13 Packof1 250.00 15µmolecolumn(Expedite) 20-2956-14 Packof1 375.00

3'-PT-Amino-ModifierC6PS 26-2956-01 0.1g 125.00 26-2956-10 1.0g 1025.00 200nmolecolumns(AB3900) 26-2956-52 Packof10 220.00 40nmolecolumns(AB3900) 26-2956-55 Packof10 220.00

MODIFIERS

3’-Amino-Modifier C7 CPG 3’-PT Amino-Modifier C3 CPG 3’-PT Amino-Modifier C6 CPG

-succinyl-lcaa-CPG

FmocNHODMT

O

N ODMTNH

O

O

CPG

O

NNH

O

O

ODMT

CPG

O

ODMT

O-succinyl-CPG

HN

HN

Fmoc

O

3’-Amino-Modifier Serinol CPG

SEE ALSO

Carboxy-Modifiers on page 76

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3’-MODIFIERS (CONT.)

The3’-Thiol-Modifier S-SCPG supports areused to introduce3’-thiol linkageswith threeand six atomspacers intooligonucleotides.3’-DithiolSerinolCPGisusedtointroduceadithiolgroupatthe3’-terminus.InconjunctionwithDithiolSerinolPhosphoramidite,itissimpletoproduceoligonucleotideswithmultiplethiolgroupsatthe3’terminus,whichisidealforconjugationtogoldsurfaces.WithGlycerylCPGthe3’-terminusofanoligonucleotideisreadilyoxidizedbysodiumperiodatetoforma3’-phosphoglycaldehyde.Thealdehydemaybefurtheroxidizedtothecorrespondingcarboxylicacid.Eitherthealdehydeorthecarboxylatemaybeusedforsubsequentconjugationtoamine-containingproducts.


3’-Thiol-ModifierC3S-SCPG 20-2933-01 0.1g 85.00 20-2933-10 1.0g 600.00 1µmolecolumns 20-2933-41 Packof4 125.00 0.2µmolecolumns 20-2933-42 Packof4 75.00 10µmolecolumn(ABI) 20-2933-13 Packof1 225.00 15µmolecolumn(Expedite) 20-2933-14 Packof1 350.00

3’-Thiol-Modifier6S-SCPG 20-2938-01 0.1g 85.00 20-2938-10 1.0g 600.00 0.2µmolecolumns 20-2938-42 Packof4 75.00 1µmolecolumns 20-2938-41 Packof4 125.00 10µmolecolumn(ABI) 20-2938-13 Packof1 225.00 15µmolecolumn(Expedite) 20-2938-14 Packof1 350.00

3’-DithiolSerinolCPG 20-2991-01 0.1g 120.00 20-2991-10 1.0g 995.00 0.2µmolecolumns 20-2991-42 Packof4 120.00 1µmolecolumns 20-2991-41 Packof4 200.00 10µmolecolumn(ABI) 20-2991-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2991-14 Packof1 450.00

3’-GlycerylCPG 20-2902-01 0.1g 85.00 20-2902-10 1.0g 600.00 1µmolecolumns 20-2902-41 Packof4 125.00 0.2µmolecolumns 20-2902-42 Packof4 75.00 10µmolecolumn(ABI) 20-2902-13 Packof1 225.00 15µmolecolumn(Expedite) 20-2902-14 Packof1 350.00

MODIFIERS

3’-Glyceryl CPG

3’-Thiol-Modifier C3 S-S CPG

CPGNH

O ODMTO

O

OAc

-succinyl-lcaa-CPGDMTO S

S O




Expedite EMerMade M




3’-Dithiol Serinol CPG

DMTOO S

S OO-succinyl-CPG

3’-Thiol-Modifier 6 S-S CPG

SS

HN

HN

O O

ODMT

O succinoyl-CPG

3’-MODIFIERS (CONT.)

3’-Amino-ModifierC6dCCPGand3’-Amino-ModifierC6dTCPGreplaceadCandT,respectively,atthe3’-terminus.Theseproductsallowconvenientlabelingatthe3’withoutblockingtheterminusfromdesiredenzymaticactivity.


3’-Amino-ModifierC6dCCPG 20-2019-01 0.1g 120.00 20-2019-10 1.0g 995.00 1µmolecolumns 20-2019-41 Packof4 200.00 0.2µmolecolumns 20-2019-42 Packof4 120.00 10µmolecolumn(ABI) 20-2019-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2019-14 Packof1 450.00

3’-Amino-ModifierC6dTCPG 20-2039-01 0.1g 96.00 20-2039-10 1.0g 800.00 1µmolecolumns 20-2039-41 Packof4 160.00 0.2µmolecolumns 20-2039-42 Packof4 96.00 10µmolecolumn(ABI) 20-2039-13 Packof1 240.00 15µmolecolumn(Expedite) 20-2039-14 Packof1 360.00

Amino-Modifier C6 dC CPG Amino-Modifier C6 dT CPG

NHNHCCF 3

O O

O

O

DMTO

succinyl-lcaa-CPG

N

NO

N

N(CH 3)2

ODMTO

O succinyl-lcaa-CPG

HN

N

O

O

NHNHCCF 3

O O

MODIFIERS

SEE ALSO

Dithiol Serinol on page 76

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CHEMICAL PHOSPHORYLATION

ChemicalPhosphorylationReagentismostcommonlyusedtophosphorylatethe5’-terminusofanoligonucleotide.Althoughthisproductisalsosuccessfulin3’-phosphorylation,3’-PhosphateCPGallowsdirectpreparationofoligonucleotideswitha3’-phosphategroup.ChemicalPhosphorylationReagentIIcontainsaDMTgrouponasidechainwhichisstabletobasecleavageandcanbeleftontheoligonucleotideforuseinRPpurification.TheDMTgroupislaterremovedwithaqueousacidandthesidechainiseliminatedafterbrieftreatmentwithaqueousammoniumhydroxidetoyieldthe5’-phosphate.1 Solid CPR II is similar in performance to CPRIIbutitiseasiertopreparealiquotssinceitisapowder.Manyresearcherstreatsynthesissupportswithahinderedbase(e.g.,diethylamine,diisopropylethylamine,orDBU)post-synthesistoeliminateandremovethecyanoethylphosphategroups.Inthisway,theacrylonitrileformedinsituisremovedfromthesupportandisnotavailabletoalkylatedTresiduesattheN3positionintheoligos.Sincethesulfonylethylgroupin3’-PhosphateCPGisalsosusceptibletoß-eliminationleadingtooligocleavage,thistechniqueisnotcompatiblewith3’-phosphateCPG.UsingCPRIICPG,whichisbaselabilebutdoesnotsupportß-elimination,thecyanoethylgroupscanberemovedfromtheoligopriortocleavageandbasedeprotection.ABI-stylevialsandcolumnsaresuppliedunlessotherwiserequested.


ChemicalPhosphorylationReagent 10-1900-90 100µmole 50.00 10-1900-02 0.25g 160.00

3’-PhosphateCPG 20-2900-01 0.1g 70.00 20-2900-10 1.0g 480.00 1µmolecolumns 20-2900-41 Packof4 100.00 0.2µmolecolumns 20-2900-42 Packof4 60.00 10µmolecolumn(ABI) 20-2900-13 Packof1 180.00 15µmolecolumn(Expedite) 20-2900-14 Packof1 280.00

3'-PhosphatePS 26-2900-01 0.1g 75.00 26-2900-10 1.0g 510.00 200 nmole columns(AB3900) 26-2900-52 Packof10 150.00 40 nmole columns(AB3900) 26-2900-55 Packof10 150.00

3’-PhosphateCPG 25-2900-01 0.1g 85.00 (HighLoad) 25-2900-10 1.0g 600.00 2.5µmolecolumns 25-2900-46 Packof4 120.00

ChemicalPhosphorylationReagentII 10-1901-90 100µmole 60.00 (CPRII) 10-1901-02 0.25g 200.00

SolidChemicalPhosphorylationReagentII 10-1902-90 100µmole 60.00 (SolidCPRII) 10-1902-02 0.25g 200.00

3’-CPRIICPG 20-2903-01 0.1g 70.00 20-2903-10 1.0g 480.00 0.2µmolecolumns 20-2903-42 Packof4 60.00 1µmolecolumns 20-2903-41 Packof4 100.00 10µmolecolumn(ABI) 20-2903-13 Packof1 180.00 15µmolecolumn(Expedite) 20-2903-14 Packof1 280.00

MODIFIERS

Chemical Phosphorylation Reagent IIChemical Phosphorylation Reagent 3’-Phosphate CPG

DMTOS

O O CNEtON(iPr)2PO DMTO

SO

O O

-succinyl-lcaa-CPG DMTOEtO2C CO 2Et

P N(iPr)2O CNEt

O


SolidChemicalPhosphorylationReagent II and related supports arecoveredbyEuropeanPatent:EP0816368.

(1)A.Guzaev,H.Salo,A.Azhayev,andH.Lonnberg,Tetrahedron, 1995, 51, 9375-9384.

Solid Chemical Phosphorylation Reagent II

DMTO O P N(iPr)2

O CNEt

CONHMeMeHNOC

DMTO OCONHMeMeHNOC

succinyl-CPG

3’-CPR II CPG

ALDEHYDE MODIFICATION

AldehydemodifierswouldbeattractiveelectrophilicsubstitutionsinoligonucleotidessincetheyareabletoreactwithaminogroupstoformaSchiff’sbase,withhydrazinogroupstoformhydrazones,andwithsemicarbazidestoformsemi-carbazones. TheSchiff’sbase isunstableandmustbereducedwithsodiumborohydrideto formastable linkagebuthydrazonesandsemicarbazidesareverystablelinkages.

Our collaborationwith ELITechGroup, formerly EpochBiosciences, has allowedus tooffer5'-Aldehyde-ModifierC2Phosphoramidite.TheacetalprotectinggroupissufficientlyhydrophobicforuseinRPHPLCandcartridgepurificationandisreadilyremovedafteroligonucleotidesynthesisunderstandardoligonucleotidedetritylationconditionswith80%aceticacid/20%wateror2%aqueoustrifluoroaceticacidduringcartridgepurification.

A formylindolenucleosideanaloguehasbeenused to introducealdehydegroupswithinanoligonucleotideorat the5’ terminus. Thisproducthasnoprotectinggroupon thealdehyde,whichmeans thatdeprotectionof themodifiedoligonucleotidecanbedonewithoutchangingpreferredconditions.


5'-Aldehyde-ModifierC2Phosphoramidite 10-1933-90 100µmole 85.00 10-1933-02 0.25g 325.00

FormylindoleCEPhosphoramidite 10-1934-90 100µmole 85.00 10-1934-02 0.25g 325.00

5'-Aldehyde-Modifier C2

CH 2CH 2CN

ONPO

OO

O


These Products are for research purposesonly,andmaynotbeusedforcommercial,clinical,diagnosticoranyotheruse.TheseProductsaresubjecttoproprietaryrightsofELITechGroupand are made and sold under license fromELITechGroup.Thereisnoimpliedlicenseforcommercialusewithrespectto these Products and a license must beobtaineddirectlyfromELITechGroupwithrespecttoanyproposedcommercialuseoftheseProducts.“Commercialuse”includesbutisnotlimited to the sale, lease, license or othertransferoftheProductoranymaterial derived or produced from it, the sale, lease, license or other grant of rightstousetheProductoranymaterialderived or produced from it, or the use of the Product to perform services for a feeforthirdparties(includingcontractresearch).

Asimpleagreementmustbesignedbeforeend-usersandcustomoligoservicesmaypurchasetheseproductsforuseasdefinedabove. http://www.glenresearch.com/Reference/ELITechGroupProducts.pdf

MODIFIERS

Formylindole

N

ODMTO

O P N(iPr)2

O CNEt

CHO




Expedite EMerMade M




SEE ALSO

High load supports on page 29

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H.Salo

http://www.glenresearch.com/Reference/EpochProducts.pdf


SPACER MODIFIERS

ThespacerphosphoramiditesC3,9,C12and18areusedtoinsertaspacerarminanoligonucleotide.Thecompoundsmaybeaddedinmultipleadditionswhenalongerspacerisrequired.3’-SpacerC3CPGmayalsoactasablockerofexonucleaseandpolymeraseactivityatthe3’-terminus.dSpacerisusedtointroduceastableabasicsitewithinanoligonucleotide.PCSpacerisaphotocleavableC3spacermodifier,partofourlineofphotocleavable(PC)modifiers.


SpacerPhosphoramidite9 10-1909-90 100µmole 75.00 10-1909-02 0.25g 240.00

SpacerPhosphoramiditeC3 10-1913-90 100µmole 75.00 10-1913-02 0.25g 240.00

dSpacerCEPhosphoramidite 10-1914-90 100µmole 85.00 10-1914-02 0.25g 295.00

SpacerPhosphoramidite18 10-1918-90 100µmole 95.00 10-1918-02 0.25g 240.00

SpacerC12CEPhosphoramidite 10-1928-90 100µmole 95.00 10-1928-02 0.25g 240.00

3’-SpacerC3CPG 20-2913-01 0.1g 70.00 20-2913-10 1.0g 480.00 1µmolecolumns 20-2913-41 Packof4 100.00 0.2µmolecolumns 20-2913-42 Packof4 60.00 10µmolecolumn(ABI) 20-2913-13 Packof1 180.00 15µmolecolumn(Expedite) 20-2913-14 Packof1 280.00

PCSpacerPhosphoramidite 10-4913-90 100µmole 135.00 10-4913-02 0.25g 395.00

MODIFIERS

Spacer 18

dSpacerSpacer 9 Spacer C3

Spacer C12 PC Spacer

DMTO

CNEtON(iPr)2PO O P N(iPr)2

O CNEt

DMTOO

DMTOO

O

CNEtON(iPr)2PO

DMTOO

OO

OO

O P N(iPr)2O CNEt

DMTOO P N(iPr)2

O CNEt NH

ONO2

H3C

CNEtON(iPr)2PO

DMTO

Symmetric Doubler

Trebler

DENDRIMERS

Dendrimersarediscrete,highlybranched,monodispersedpolymersthatpossesspatternsreminiscentofthebranchingoftrees.Plainandmixedoligonucleotidedendrimerscanbesynthesizedusingnoveldoublingandtreblingphosphoramiditesynthons.1,2Dendrimersofferthefollowingadvantages.Incorporationoflabelusingγ-32P-ATPandpolynucleotidekinaseincreasesinproportiontothenumberof5’-ends.Fluorescentsignalalsoincreasesinproportiontothenumberof5’-ends,ifspacersareincorporatedbetweenthelabelsandtheendsofthebranches.WhenusingadendrimericoligonucleotideasaPCRprimer,thestrandbearingthedendrimerisresistanttodegradationbyT7Gene6exonucleasemakingiteasytoconvertthedouble-strandedproductofthePCRtoamultiplylabeled,single-strandedprobe.EnhancedstabilityofDNAdendrimersmakesthemusefulasbuildingblocksforthe‘bottomup’approachtonano-assembly.ThesefeaturesalsosuggestapplicationsinDNAchiptechnologywhenhighertemperaturesarerequired,forexample,tomeltsecondarystructureinthetarget.


SymmetricDoublerPhosphoramidite 10-1920-90 100µmole 150.00 10-1920-02 0.25g 240.00

AsymmetricDoubler(LEV)Phosphoramidite 10-1981-90 100µmole 105.00 10-1981-02 0.25g 250.00

TreblerPhosphoramidite 10-1922-90 100µmole 180.00 10-1922-02 0.25g 300.00

LongTreblerPhosphoramidite 10-1925-90 100µmole 200.00 10-1925-02 0.25g 300.00

BRANCHING PHOSPHORAMIDITE

Abranchingmonomerisrequiredtoconstructcomb-likeoligonucleotideprobes.ThedevelopersofthecombsystemfromChironCorporationevaluated3severalprotectinggroupsforthebranchpointandchoselevulinyl(LEV),whichisspecificallyremovedusingareagentcontaininghydrazinehydrate,aceticacidandpyridine.


5-Me-dCBrancherPhosphoramidite 10-1018-90 100µmole 205.00 10-1018-02 0.25g 505.00

MODIFIERS

REFERENCES

(1)M.S.Shchepinov,I.A.Udalova,A.J.Bridgman,andE.M.Southern,Nucleic Acids Res, 1997, 25, 4447-4454.

(2)M.S.Shchepinov,K.U.Mir,J.K.Elder,M.D.Frank-Kamenetskii,andE.M.Southern, Nucleic Acids Res, 1999, 27, 3035-41.

(3)T.Horn,C.A.Chang,andM.S.Urdea,Nucleic Acids Res, 1997, 25,4842-4849.

NH

NH

DMTO

DMTOO

O

CNEtON(iPr)2PO

ODMTOCNEtON(iPr)2PO

DMTOO

DMTO O

O

O P N(iPr)2O CNEt

DMTO

O

O

ONH

O N

N CH 3

5-Me-dC Brancher

i

Long Trebler




Expedite EMerMade M




SEE ALSO

PC Modifiers on page 86Pyrrolidine on page 63

ONH

DMTONH

O

O

O

OO

P

O

N(iPr)2

CNEt

Asymmetric Doubler (LEV)

84 85

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MODIFIERS

PHOTOCLEAVABLE MONOMERS

PCBiotinPhosphoramiditecanbeusedtoprepare5’-biotinylatedoligonucleotidessuitableforcapturebystreptavidininamodesimilartoourpopular5’BiotinPhosphoramidite.Amino-andthiol-modifiedoligonucleotideshaveproventobeveryusefulfortheattachmentofavarietyofhaptensandfluorophores,aswellasforthetetheringoftheoligonucleotidesto a diversity of beads and surfaces. PCAmino-Modifier Phosphoramidite is used to prepare 5’-amino-modifiedoligonucleotidessuitableforsubsequentphotocleavage.PCSpacerPhosphoramiditecanbeusedasanintermediarytoattachanymodificationreagent,availableasaphosphoramidite,totheterminusofoligonucleotides.Afterphotocleavage,a5’-phosphateisgeneratedontheDNA,renderingitsuitableforfurtherbiologicaltransformations,suchasgeneconstructionandcloningafterligation.

AversatilephotocleavableDNAbuildingblockhasbeendescribedbyresearchersinWashingtonUniversity,Missouriandusedinphototriggeredhybridization.1 ThisreagenthasalsobeenusedinthedesignofmultifunctionalDNAandRNAconjugates2fortheinvitroselectionofnewmoleculescatalyzingbiomolecularreactions.ResearchersatBrukerDaltonikinGermanyhavealsodevelopedgenoSNIP,amethodforsingle-nucleotidepolymorphism(SNP)genotypingbyMALDI-TOFmassspectrometry.3Thismethodusessizereductionofprimerextensionproductsbyincorporationofthephotocleavablelinkerforphototriggeringstrandbreaksneartothe3’endoftheextensionprimer.PCLinkercanbeincorporatedintooligonucleotidesatanypositionby standardautomatedDNAsynthesismethodology. PCLinkerPhosphoramiditehastheaddedadvantage inthatphotocleavageresults inmonophosphatefragmentsatboththe3’-and5’-terminioftheoligonucleotidefragments.


PCBiotinPhosphoramidite 10-4950-95 50µmole 145.00 10-4950-90 100µmole 280.00 10-4950-02 0.25g 675.00

PCAmino-ModifierPhosphoramidite 10-4906-90 100µmole 135.00 10-4906-02 0.25g 395.00

PCSpacerPhosphoramidite 10-4913-90 100µmole 135.00 10-4913-02 0.25g 395.00

PCLinkerPhosphoramidite 10-4920-90 100µmole 255.00 10-4920-02 0.25g 795.00

PC Biotin

PC Amino-Modifier PC Spacer

NHDMTN

SNH

O

ONH

ONO2

H3C

CNEtON(iPr)2PO

TFAHNNH

ONO2

H3C

CNEtON(iPr)2PO

NH

ONO2

H3C

CNEtON(iPr)2PO

DMTO


GlenResearchoffersPCBiotin,PCAmino-ModifierandPCSpacerproductsinassociationwithAmberGen,Inc.andLinkTechnologies,Ltd.Foracommercialapplicationlicense,pleasecontactAmberGen,Inc.,+617-923-9990, ([email protected]),http://www.ambergen.com/.

PCLinkerphosphoramiditeisavailablefromGlenResearchinassociationwithLinkTechnologiesLtd(Scotland).

REFERENCES

(1) P.OrdoukhanianandJ-S.Taylor,J. Am. Chem. Soc., 117,9570-9571,1995.

(2a)F.HauschandA.Jäschke,NucleicAcidsResearch, 2000, 28,e35.

(2b)F.HauschandA.Jäschke,Tetrahedron, 2001, 57,1261-1268.

(3) T.Wenzel,T.Elssner,K.Fahr,J.Bimmler,S.Richter,I.Thomas,andM.Kostrzewa,Nucleosides, Nucleotides & Nucleic Acids, 2003, 22,1579-1581.

PC Linker

NO2

CNEtON(iPr)2PODMTO




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CONJUGATION USING CLICK CHEMISTRY

Thecopper(I)-catalyzedazide-alkynecycloaddition(CuAAC)reactionbetweenazidesandalkynestoform1,2,3-triazoles,as reported1bySharpless,wasfoundtobesoexquisitelyregioselectiveandefficientateventhemostmildconditionsthatSharplesscoinedtheterm‘ClickChemistry’todescribeit.TheuseofthismethodforDNAmodificationhasbeensomewhatdelayedbythefactthatcopperionsdamageDNA,typicallyyieldingstrandbreaks.2Astheseproblemshavenowbeenovercomebytheuseofcopper(I)-stabilizingligands(e.g.,tris(benzyltriazolylmethyl)amine,TBTA3),Carelletal.andSeelaetal.discoveredthattheCuAACreactioncanbeusedtofunctionalizealkyne-modifiedDNAnucleobaseswithextremelyhighefficiency.4

OligonucleotidesbearingasinglenucleosidicalkynegroupcanbepreparedusingaC8-Alkyne-dCordT-CEPhosphoramidite.Purifiedoligonucleotidesareusuallymodifiedwith2-5equivalentsofthecorrespondingmarker-azide(e.g.,fluorescent-dyeazides).AftertheadditionofprecomplexedCu(I),completeconversiontothelabeledoligoisobservedinatimespanbetween30minand4hours.Afterasimpleprecipitationstep,labeledoligonucleotidescanberecoveredinnearquantitativeyields.UsingacombinationofC8-Alkyne,C8-TIPS-AlkyneandC8-TMS-Alkyne,itispossibletolabeloligonucleotidesinuptothreeseparateclickreactions.Thealkynegroupsonthelasttwomonomersareprotected,respectively,withtriisopropylsilyl(TIPS)andtrimethylsilyl(TMS)protectinggroups.5,6ThefirstclickreactiononsolidphaseonaC8-AlkyneyieldsthesinglymodifiedoligonucleotidewithfullretentionoftheTIPSand/orTMSprotectinggroup.Fordoubleclick,aC8-TIPS-AlkyneisusedasthesecondnucleosideandtheTIPSprotectinggroupiscleavedwithtetrabutylammoniumfluoride(TBAF)withoutcausinganydamagetotheDNA.Thesecondclickreactioninsolutionyieldsthedoublymodifiedoligonucleotideinexcellentyield.Fortheintroductionofthreedifferentlabels,allthreenucleosidesareintroducedintooligonucleotides.Thefirstclickreaction isperformeddirectlyontheresin.Thesinglymodifiedoligonucleotide issubsequentlycleavedfromthesupportwithconcomitantcleavageoftheTMSgroupandretentionoftheTIPSprotectinggroup.Thesecondclickreactionisperformedinsolution.Precipitationofthedoublymodifiedoligonucleotide,cleavageoftheTIPSgroupwithTBAF,andasubsequentthirdclickreactioninsolutionfurnishesthedesiredtriplymodifiedoligonucleotideinexcellentoverallyield.


C8-Alkyne-dT-CEPhosphoramidite 10-1540-95 50µmole 165.00 10-1540-90 100µmole 315.00 10-1540-02 0.25g 900.00

C8-TIPS-Alkyne-dC-CEPhosphoramidite 10-1541-95 50µmole 295.00 10-1541-90 100µmole 575.00 10-1541-02 0.25g 1275.00

C8-TMS-Alkyne-dC-CEPhosphoramidite 10-1542-95 50µmole 270.00 10-1542-90 100µmole 525.00 10-1542-02 0.25g 1275.00

C8-Alkyne-dC-CEPhosphoramidite 10-1543-95 50µmole 225.00 10-1543-90 100µmole 435.00 10-1543-02 0.25g 1125.00

MODIFIERS

REFERENCES

[1] C.W.Tornoe,C.Christensen,M.Meldal,J. Org. Chem. 2002, 67,3057-3064;V.V.Rostovtsev,L.G.Green,V.V.Fokin,K.B.Sharpless,Angew. Chem. 2002, 114, 2708-2711;Angew. Chem. Int. Ed. 2002, 41,2596-2599.

[2] C.J.Burrows,J.G.Muller,Chem. Rev. 1998, 98,1109–1151.

[3] T.R.Chan,R.Hilgraf,K.B.Sharpless,V.V.Fokin,Org. Lett. 2004, 6, 2853 – 2855.

[4]J.Gierlich,G.A.Burley,P.M.E.Gramlich,D.M.Hammond,T.Carell,Org. Lett. 2006, 8,3639-3642.F.Seela,V.R.Sirivolu,Chem. Biodiversity 2006, 3,509-514.

[5]P.M.E.Gramlich,S.Warncke,J.Gierlich,T.Carell,Angew. Chem. 2008, 120, 3491–3493;Angew. Chem. Int. Ed. 2008, 47,3442–3444.

[6]P.M.E.Gramlich,C.T.Wirges,A.Manetto,T.Carell, Angew. Chem. Int. Ed. 2008, 47,8350-8358.


baseclickGmbHhasbeengrantedthefollowingpatents(1-3)besidesitsfurtherpatentapplications(4-5).

1. WO2006/117161(Newlabelingstrategiesforthesensitivedetectionofanalytes)

2. WO2008/952775(Clickchemistryfortheproductionofreportermolecules)

3. WO2010/115957(ClickChemistryonheterogeneouscatalysts)

4. PCT/EP2013/064610(Anandamide-modifiednucleicmolecules)

5. PCT/EP2015/056007(Self-assemblyofDNAOrigami:adiagnostictool)

baseclickGmbHholdsaworldwideexclusivelicenseforgrantedpatentapplicationWO03/101972(Copper-catalysedligationofazidesandacetylenesforthenucleicacidfield)intheareaofdiagnosticsandresearch.

AsGlenResearchandbaseclickarepartners,GlenResearchisnowabletohelpinsublicensingthisoutstandingtechnology.

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

ODMTO

N

N

NHBz

O

O P N(iPr)2

O CNEt

TIPS

ODMTO

N

N

NHBz

O

O P N(iPr)2

O CNEt

TMS

C8-Alkyne-dT C8-TMS-Alkyne-dCC8-TIPS-Alkyne-dC

ODMTO

N

N

NHBz

O

O P N(iPr)2

O CNEt

C8-Alkyne-dC

SEE ALSO

5’-Biotin on page 99

86 87

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[email protected]

http://www.ambergen.com/

http://www.ambergen.com/

CONJUGATION USING CLICK CHEMISTRY (CONT.)

5-Ethynyl-dUoffersconvenientclickconjugationwithanazidetogeneratealabelrigidlyattachedtooneoftheoligonucleotidebases.5-Ethynyl-dUissubjecttobase-catalyzedhydrationduringcleavageanddeprotection,especiallywhenusingastrongbaseorheat.Hydrationofanethynylgroupformsamethylketonewhichsubsequentlyblockspotentialclickreactions.Milddeprotectionconditionsarenecessarywhenusing5-Ethynyl-dU-CEPhosphoramiditetopreventthissidereaction.TIPS-5-Ethynyl-dU-CEPhosphoramidite,containingaprotectedalkyne,offersbroadercompatibilitywitholigonucleotidesynthesisanddeprotection.Protectingthe5-ethynylgroupwithatriisopropylsilyl(TIPS)protectinggrouppreventsacidorbasecatalyzedhydrationduringoligonucleotidesynthesisandworkup.AquicktreatmentwithTBAFremovestheTIPSprotectinggroup.


C8-TIPS-Alkyne-dT-CEPhosphoramidite 10-1544-95 50µmole 220.00 10-1544-90 100µmole 425.00 10-1544-02 0.25g 1020.00

C8-TMS-Alkyne-dT-CEPhosphoramidite 10-1545-95 50µmole 205.00 10-1545-90 100µmole 395.00 10-1545-02 0.25g 1050.00

5-Ethynyl-dU-CEPhosphoramidite 10-1554-95 50µmole 130.00 10-1554-90 100µmole 245.00 10-1554-02 0.25g 775.00

TIPS-5-Ethynyl-dU-CEPhosphoramidite 10-1555-95 50µmole 195.00 10-1555-90 100µmole 370.00 10-1555-02 0.25g 975.00

THPTALigand 50-1004-92 25µmole 50.00 (Watersoluble) 50-1004-90 100µmole 180.00

Click-Solution(DMSO/t-BuOH) 50-1002-11 10x1.0mL 185.00

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

TIPS

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

TMS

C8-TMS-Alkyne-dTC8-TIPS-Alkyne-dT

MODIFIERS




Expedite EMerMade M




ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

5-Ethynyl-dU

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

TIPS

TIPS-5-Ethynyl-dU

REFERENCES

(1)R.Kumar,etal.,Journal of the American Chemical Society, 2007, 129,6859-6864.

(2)J.Lietard,A.Meyer,J.J.Vasseur,andF.Morvan, Tetrahedron Letters, 2007, 48, 8795-8798.


Oligonucleotides prepared using 5’-Hexynyl Phosphoramidite are stable to standard deprotection conditions andexhibitaslightlyincreasedretentiontimeonRPHPLC.Azidesarenotcompatiblewitholigonucleotidesynthesisusingphosphoramiditessoapost-synthesisreactionisrequired.AzidobutyrateNHSEsterisused1forazido-modificationofaminesateitherthe3’-endorthe5’-endofanoligoanditcanevenbeusedforinternalmodificationonanAmino-Modifier-C6dXresiduewithinthesequence.Specifictothe5’-terminus,5’-BromohexylPhosphoramiditeisaddedinthelastcycle.Thismodifiercanthenbeeasilytransformedintoa5’-azidogroupbydisplacementofbromideusingsodiumazide.2AlkyneNHSesterallowsthefunctionalizationofanaminomoietyinavarietyofmolecules,includingDNAandRNAoligonucleotidesaswellaspeptidesorproteins.WealsooffertwoproductsforuseinClickChemistrybaseduponour1,3-diolproductportfoliowiththeserinolbackbone-aphosphoramiditeforaddinganalkynegroupatthe5’terminusorwithinthesequence,andasynthesissupportforlabelingthe3’terminusofoligonucleotideswithanalkynegroup.


5’-HexynylPhosphoramidite 10-1908-90 100µmole 60.00 10-1908-02 0.25g 200.00

AzidobutyrateNHSEster 50-1904-23 2.3mg 60.00 (Dissolve2.3mgin60µLofDMSO) 50-1904-24 23mg 300.00

5’-BromohexylPhosphoramidite 10-1946-90 100µmole 60.00 10-1946-02 0.25g 200.00

Alkyne-NHSEster 50-1905-23 2.3mg 60.00 (Dissolve2.3mgin60µLofDMSO) 50-1905-24 23mg 300.00

Alkyne-ModifierSerinolPhosphoramidite 10-1992-95 50µmole 100.00 10-1992-90 100µmole 185.00 10-1992-02 0.25g 575.00

3’-Alkyne-ModifierSerinolCPG 20-2992-01 0.1g 105.00 20-2992-10 1.0g 800.00 0.2µmolecolumns 20-2992-42 Packof4 100.00 1µmolecolumns 20-2992-41 Packof4 175.00 10µmolecolumn(ABI) 20-2992-13 Packof1 260.00 15µmolecolumn(Expedite) 20-2992-14 Packof1 390.00

O P N(iPr)2

O CNEt

5’-Hexynyl Phosphoramidite

BrO P N(iPr)2

O CNEt

N3O N

O

OO

Azidobutyrate NHS Ester 5’-Bromohexyl Phosphoramidite

O

O

NH

NH

O

OODMT

succinoyl CPGO

O

ON

O

O

Alkyne-NHS Ester 3’-Alkyne-Modifier Serinol CPG

MODIFIERS

O

NH

NH

O

OODMT

P N(iPr)2

O CNEt

Alkyne-Modifier Serinol Phosphoramidite

SEE ALSO

3’-Propargyl-5-Me-dC CPG on page 64

SEE ALSO

Serinol Products on page 94

88 89

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1-Ethynyl-dSpacerCEPhosphoramiditecanbeusedinanypositionwithinanoligonucleotidewhilestillretainingthehighefficiencyofclickchemistry.Themodifierisefficientlyincorporatedintooligonucleotidesusingstandardphosphoramiditechemistry,isstabletocommondeprotectionconditions,andiscompatiblewithGlen-Pak™purification.1-Ethynyl-dSpacergeneratesasubstituted1,2,3-triazolepseudo-nucleobaseafterclickchemistryconjugationwithanazideThe1-ethynyl-dSpacermodificationexhibitssimilarduplexstabilitytothestandarddSpacer(10-1914)anddestabilizestheduplexwheninternallyincorporated.Uponcycloaddition,theduplexstabilityismoderatedbytheresultingstructureofthemodification.Simple1,2,3-triazolesweredestabilizing,asweremodificationsthatincorporatedTEGlinkers(6-FAM-TEGandAmino-TEG).Modificationsthatincorporatedaromaticfunctionalgroupsrestoredduplexstabilitytovaryingdegreeswithcoumarinandpsoralensignificantlyrestoringstability.A5’-iodo-modifiedoligonucleotide(preparedusing5’-Iodo-dT)canbequantitativelyconvertedtothecorresponding5’-azide.


1-Ethynyl-dSpacerCEPhosphoramidite 10-1910-95 50µmole 180.00 10-1910-90 100µmole 340.00 10-1910-02 0.25g 1250.00

5’-I-dT-CEPhosphoramidite 10-1931-90 100µmole 85.00 10-1931-02 0.25g 295.00

OLIGO-CLICK KITS

Oligo-ClickKitscontainanair-stable,insolubleCu(I)sourceinpelletforminapre-loadedandready-to-usevial.Withinthekit,theTBTAligandisreplacedbyanactivatorwhichiscompatiblewithbothaqueousandorganicsolvents.Thisinnovativecombinationofcatalystandligand/activatorresultsinamucheasierlabelingwork-flowofonlythreesimplesteps.ThepreparationoftheoligonucleotidelabelingviaCuAACnowrequiresonlyaminimalhands-ontimeofafewminutesorevenlessandcanbecarriedoutinairwithoutanyadditionalprecautions.GlenResearchisofferingthefollowingkitsincollaborationwithbaseclickGmbH.• Oligo-KitMReload:Thiskithassufficientreagentsforconjugatinguptoninealkyne-containingoligonucleotidesona

100nmolescaleorasingleoligonucleotideona1µmolescale.The user must supply the azide and a solvent such as DMSO for dissolving the azide.

• Oligo-KitMBiotin,Oligo-KitMFluoresceinandOligo-KitMTAMRA:Eachkithassufficientreagentsforconjugatinguptosevenalkyne-containingoligonucleotidesona100nmolescaleorasingleoligonucleotideona1µmolescale.Each kit contains all of the ingredients necessary, including the azide and DMSO solvent.


baseclickOligo-Click-M-Reload 50-2100-01 each 120.00

baseclickOligo-Click-M-Biotin 50-2101-01 each 200.00

baseclickOligo-Click-M-Fluorescein 50-2102-01 each 240.00

baseclickOligo-Click-M-TAMRA 50-2103-01 each 270.00

MODIFIERS

STABILITY NOTES

Oligonucleotidescontaininga5’-iodogrouparepreparedconventionallywiththeexceptionthatdeprotectioniscarriedoutinammoniumhydroxideatroomtemperaturefor24hours.Undertheseconditions,degradationoftheiodogroupwaslessthan2%.

5’-I-dT

O

O P N(iPr)2O CNEt

IO

O

N

HNCH 3

ODMTO

O P N(iPr)2

O CNEt

1-Ethynyl-dSpacer

COPPER-FREE CLICK CHEMISTRY

AtGlenResearch,ourgoalwastoofferacopper-freeclickphosphoramiditereagentwiththefollowingproperties:

• Simple to use •Stableinsolutiononthesynthesizer •StabletoammoniumhydroxideandAMA •Excellentclickperformancein17hoursorlessatroomtemperature

Fromthevarietyofcyclooctyne-basedcopper-freeclickreagentssofardescribed,wehavechosentooffercompoundsbasedonadibenzo-cyclooctyne(DBCO)structure.Weareoffering5’-DBCO-TEGPhosphoramiditeforpreparingoligoswitha5’-DBCOmodificationandDBCO-dT-CEPhosphoramiditeforinsertingaDBCOgroupatanypositionwithintheoligonucleotide.Inaddition,weofferafurtherDBCOphosphoramidite–DBCO-SerinolPhosphoramidite. Usingourproprietaryserinolbackboneasanon-nucleosidicspacerallowstheDBCOgrouptobeplacedatanylocationwithinasequencewithmultipleadditionsclearlypossible.DBCO-sulfo-NHSEsterisalsoofferedforpost-synthesisconjugationreactions.DBCO-modifiedoligosmaybeconjugatedwithazidesinorganicsolvents,suchasDMSO,oraqeousbuffers.Dependingontheazideused,thereactionwillgotocompletionin4-17hoursatroomtemperature.SimpledesaltingonaGlenGel-Pak™leadstoaproductwithvirtuallyquantitativeconjugationefficiency.

Note:Wenow recommend that synthesisofoligos containingDBCO-dTbecompletedusing0.5MCSO inanhydrousacetonitrile(40-4632-xx).AcceptableresultscanbeachievedwithiodineoxidationifDBCO-dTissubjectedtonomorethan8-10cycles.


5’-DBCO-TEGPhosphoramidite 10-1941-95 50µmole 125.00 10-1941-90 100µmole 230.00 10-1941-02 0.25g 775.00

DBCO-dT-CEPhosphoramidite 10-1539-95 50µmole 250.00 10-1539-90 100µmole 485.00 10-1539-02 0.25g 975.00

DBCO-sulfo-NHSEster 50-1941-23 5.2mg 60.00 (Dissolve5.2mgin60µLwaterorDMSO) 50-1941-24 52mg 300.00

DBCO-SerinolPhosphoramidite 10-1998-95 50µmole 180.00 10-1998-90 100µmole 340.00 10-1998-02 0.25g 895.00

N HN

OO

OO

O

O P N(iPr)2

O CNEt

NO

OO

N

O

OSO3Na

DBCO-sulfo-NHS Ester

5’-DBCO-TEGODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

NH

OHN

N

OO

DBCO-dT

MODIFIERS




Expedite EMerMade M




N

OO

HN

OP

NiPr2

ODMT

OCNEt

DBCO-Serinol

SEE ALSO

0.5M CSO on page 32Serinol Products on page 94

SEE ALSO

dSpacer on page 84

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MODIFIERS

HN

OS

NHHN

O

OO

ON3

HN

O

NHHN

O

OO

ON3

O

HN

O

OO

O

O

OO

OO

ON3

O

HN

O

OHHO

O

O

OO

ON3

BiotinTEG Azide DesthiobiotinTEG Azide

Dipivaloyl 6-FAM-TEG Azide 6-FAM-TEG Azide

REFERENCE

(1)J.Gierlich,G.A.Burley,P.M.Gramlich,D.M.Hammond,andT.Carell,Org Lett, 2006, 8,3639-42.

O

N3

OHO

Coumarin Azide

O

HN

O

OHHO

O

O

N3

Cl

Cl

Cl

ClCl

Cl

O

HN

O

OHHO

O

O

N3

Cl

Cl

ClCl

6-TET Azide6-HEX Azide


GlenResearchisofferingfirstourmostpopularlabelsforgeneralinterestand,subsequently,wewilladdazideproductsthatarenotcompatiblewithphosphoramiditechemistry.

BiotinisstillourmostcommonlyusedlabelandbiotinTEG,withitshydrophilictriethyleneglycolspacer,isthemostpopularbiotinproduct.Desthiobiotinisabiotinanaloguethatiswellcapturedbystreptavidinbutthecapturedproductcanbeeasilyreleasedbyapplyingabiotinsolutiontothestreptavidinbeads.6-FAMisourmostpopularfluoresceinderivativeandweofferazidesofboth6-FAMandpivaloyl-protected6-FAMforsituationswheresubsequentreactionsrequirethe6-FAMtobeprotected.Inboth6-FAMproducts,thehydrophilicTEGspacerisagainused.Theazidesareofferedin25and100µmolepacksforconvenientoligonucleotidelabeling.

7-Hydroxycoumarin,alsoknownasumbelliferone,isahighlyfluorescent,pH-sensitivefluorophorethatemitsintheblueregionofthespectrum.However,itsfluorescenceisstronglyquenchedifthehydroxylisalkylatedorphosphorylated,makingitusefulinhigh-throughputscreeningforphosphatasesandlipases.Interestingly,itwasfoundthatthe3-azidoderivativeisalsohighlyquenchedbut,uponreactionwithanalkyneinthepresenceofcoppertoformthetriazole,thefluorescenceisrestored.1Theclickedcoumarinemitsatalambdamaxof480nmandabsorbsat358nm.

HEXandTETaretwoofourmostpopularfluorescein-baseddyesforlabelingoligonucleotides.Wearehappytooffer6-HEXand6-TETAzidesforuseinclickconjugations.


BiotinTEGAzide 50-2000-92 25µmole 150.00 50-2000-90 100µmole 450.00

DesthiobiotinTEGAzide 50-2001-92 25µmole 135.00 50-2001-90 100µmole 400.00

Dipivaloyl6-FAM-TEGAzide 50-2002-92 25µmole 230.00 50-2002-90 100µmole 690.00

6-FAM-TEGAzide 50-2003-92 25µmole 180.00 50-2003-90 100µmole 540.00

CoumarinAzide 50-2004-92 25µmole 115.00 50-2004-90 100µmole 350.00

6-HEXAzide 50-2005-92 25µmole 150.00 50-2005-90 100µmole 450.00

6-TETAzide 50-2006-92 25µmole 150.00 50-2006-90 100µmole 450.00


Twonitroxidespinlabels,TEMPOAzideandTEMPO-TEGAzide,forsitedirectedspinlabeling(SDSL)arenowoffered.

ClickChemistrywithpsoralenazideandoneofourmanynucleosidic andnon-nucleosidic alkynederivativeshas thepotentialtogenerateavarietyofpracticalcross-linkers.Thewellknownreversiblecross-linkingbehaviorofpsoralenwithanadjacentthymidineresiduecouldbeveryuseful.

Tobetteraddressapplicationsinnear-infrared(NIR)imaging,GlenResearchisofferingawatersolubleDisulfo-Cyanine7azidethatcanbeeasilyconjugatedtoDNAandRNAthroughstandardclickchemistry.Thislongwavelengthdyeoffersthebenefitsofimprovedsolubility,reducedaggregation,andimprovedstabilityinthenear-infraredspectrumalongwiththeconvenienceofclickchemistry.


TEMPOAzide 50-2007-92 25µmole 115.00 50-2007-90 100µmole 350.00

TEMPO-TEGAzide 50-2008-92 25µmole 135.00 50-2008-90 100µmole 400.00

PsoralenAzide 50-2009-92 25µmole 115.00 50-2009-90 100µmole 350.00

Disulfo-Cyanine7Azide 50-2010-92 25µmole 325.00 50-2010-90 100µmole 975.00

O O

N3

O

Psoralen Azide

N

SO3-K+

N+

-O3S

HNN3

O

Disulfo-Cyanine 7 Azide

N•O N3 N•O O

O

O

O

N3

TEMPO Azide TEMPO-TEG Azide

MODIFIERS

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LABELING

SERINOL REAGENTS FOR MODIFICATION AND LABELING

Mostpopularnon-nucleosidicphosphoramiditesformodificationandlabelingarebasedontwostructuraltypes:1,2-diolsand1,3-diols.Productsbasedona1,2-diolbackbonewerefirstdescribedtoallowamino-modificationandbiotinlabeling.Technically, the1,2-diolbackbonehas somedrawbacks relative to the1,3-diolbackbone. The1,2-diolbackbonecanparticipateinadephosphorylationreactionsincethe1,2-diolcanformafavored5-memberedcyclicphosphateintermediate.Thisreactioniscompetitivewithsimplehydrolysisoftheprotectinggroupsandleadstosomelossoflabel.However,thedegreeoflossatthe3’terminuscanbelimitedbytheremovalofthecyanoethylprotectinggroupusingDBUordiethylaminepriortothecleavageanddeprotectionsteps.Similarly,lossatthe5’terminuscanbeeliminatedbyretainingtheDMTgroupuntiltheoligoisfullydeprotected.Fortunately,theeliminationreactionisvirtuallynon-existentinthe1,3-diolbackbonesincethecyclicintermediatewouldbea6-memberedringwhichisnotfavoredforacyclicphosphateintermediate.

IVDcustomershaverequestedanewbackbonebasedona1,3-diolthatwouldovercomeanytechnicalorIPissuessurroundingourcurrentproducts.Wenowofferalineofproductsbasedontheserinolbackbone,whichhavebeendevelopedinclosecollaborationbetweenGlenResearchandNelsonBiotechnologies.ProtectedBiotinSerinolPhosphoramiditeandCPGareprotectedwithat-butylbenzoylgrouponthebiotinring.Thisgroupisdesignedtostopanyphosphoramiditereactionsatthisactivepositioninbiotin.ThisprotectionavoidsbranchingwhenusingnucleophilicactivatorslikeDCI.Theprotectinggroupiseasilyremovedduringoligonucleotidecleavageanddeprotection.TheBiotinLCversionsaresimilarlyprotectedandshouldbeusefulforthesynthesisofhighlysensitivebiotinylatedprobes.6-FluoresceinSerinolPhosphoramiditeandCPGaredesignedtoprepareoligonucleotidescontainingoneorseveral6-Fluorescein(6-FAM)residues.Amino-ModifierSerinolPhosphoramiditeandCPGareusedtoaddaminogroupsintooneorseveralpositionsinoligonucleotides.TheaminogroupisprotectedwithFmoc,whichmayberemovedonthesynthesiscolumnpriortosolid-phaseconjugationtotheaminogroups,orwhichmayberemovedduringdeprotectionforsubsequentsolutionphaseconjugationtotheaminogroups.

Combininglipoicacidandourpatentedserinolbackbone,wenowofferDithiolSerinolPhosphoramiditeandtherelated3’-DithiolSerinolCPG.Thisuniquearchitecturemovesthebulkydithiolawayfromthephosphatebackbone,makingitsuitablefor conjugationtogoldsurfaces.ThelongspacerarmofDithiolSerinolalsoallowsmultipleconsecutiveincorporationsofthemodifierwithouttheneedforintermediatespacerphosphoramiditeadditionstoachieveoptimalstepwisecouplingefficiency.

WeofferthreeproductsforuseinClickChemistrybaseduponour1,3-diolproductportfoliowiththeserinolbackbone-aphosphoramiditeforaddinganalkynegroupatthe5’terminusorwithinthesequence,asynthesissupportforlabelingthe3’terminusofoligonucleotideswithanalkynegroup,andDBCO-Serinolphosphoramiditeasacopper-freeclickreagent.


ProtectedBiotinSerinolPhosphoramidite 10-1993-95 50µmole 165.00 10-1993-90 100µmole 295.00 10-1993-02 0.25g 675.00

6-FluoresceinSerinolPhosphoramidite 10-1994-95 50µmole 165.00 10-1994-90 100µmole 295.00 10-1994-02 0.25g 595.00

ODMT

O P N(iPr)2

O CNEt

HN

HN

OOS

NHN

O O

O

HN

O

OO

O

O

OO

ODMT

O P N(iPr)2

O CNEt

HN

O

Protected Biotin Serinol Phosphoramidite 6-Fluorescein Serinol Phosphoramidite




Expedite EMerMade M





SerinolReagentsforModificationandLabelingarecoveredbyUSPatentNo.:8,394,948.

SERINOL REAGENTS FOR MODIFICATION AND LABELING (CONT.)


ProtectedBiotinLCSerinolPhosphoramidite 10-1995-95 50µmole 205.00 10-1995-90 100µmole 365.00 10-1995-02 0.25g 675.00

Amino-ModifierSerinolPhosphoramidite 10-1997-95 50µmole 125.00 10-1997-90 100µmole 225.00 10-1997-02 0.25g 595.00

DithiolSerinolPhosphoramidite 10-1991-95 50µmole 120.00 10-1991-90 100µmole 215.00 10-1991-02 0.25g 585.00

Alkyne-ModifierSerinolPhosphoramidite 10-1992-95 50µmole 100.00 10-1992-90 100µmole 185.00 10-1992-02 0.25g 575.00

DBCO-SerinolPhosphoramidite 10-1998-95 50µmole 180.00 10-1998-90 100µmole 340.00 10-1998-02 0.25g 895.00

LABELING

O

NH

NH

O

OODMT

P N(iPr)2

O CNEt

Alkyne-Modifier Serinol Phosphoramidite

HN

OS

NHN

O O

OO

O

O P N(iPr)2

O CNEt

HN

O

O

HN

O

ODMT

ODMT

O P N(iPr)2

O CNEt

HN

HN

Fmoc

O

Protected BiotinLC Serinol Phosphoramidite

Amino-Modifier Serinol Phosphoramidite

SS

HN

HN

O O

ODMT

O P N(iPr)2

O-CNEt

Dithiol Serinol

N

OO

HN

OP

NiPr2

ODMT

OCNEt

DBCO-Serinol

SEE ALSO

DBCO on page 91

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3’-ProtectedBiotinSerinolCPG 20-2993-01 0.1g 120.00 20-2993-10 1.0g 995.00 0.2µmolecolumns 20-2993-42 Packof4 120.00 1µmolecolumns 20-2993-41 Packof4 200.00 10µmolecolumn(ABI) 20-2993-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2993-14 Packof1 450.00

3’-6-FluoresceinSerinolCPG 20-2994-01 0.1g 120.00 20-2994-10 1.0g 995.00 0.2µmolecolumns 20-2994-42 Packof4 120.00 1µmolecolumns 20-2994-41 Packof4 200.00 10µmolecolumn(ABI) 20-2994-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2994-14 Packof1 450.00

3’-ProtectedBiotinLCSerinolCPG 20-2995-01 0.1g 120.00 20-2995-10 1.0g 995.00 0.2µmolecolumns 20-2995-42 Packof4 120.00 1µmolecolumns 20-2995-41 Packof4 200.00 10µmolecolumn(ABI) 20-2995-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2995-14 Packof1 450.00

3’-Amino-ModifierSerinolCPG 20-2997-01 0.1g 95.00 20-2997-10 1.0g 675.00 0.2µmolecolumns 20-2997-42 Packof4 85.00 1µmolecolumns 20-2997-41 Packof4 140.00 10µmolecolumn(ABI) 20-2997-13 Packof1 250.00 15µmolecolumn(Expedite) 20-2997-14 Packof1 375.00

Protected Biotin Serinol CPG Amino-Modifier Serinol CPG 6-Fluorescein Serinol CPG

HN

OS

NHN

O O

ODMT

O-succinyl-CPG

HN

O

O

HN

O

OO

O

O

OO

ODMT

O-succinyl-CPG

HN

O

HN

OS

NHN

O O

OO

O ODMT

O-succinyl-CPG

HN

O

O

HN

O

ODMT

O-succinyl-CPG

HN

HN

Fmoc

O

Protected BiotinLC Serinol CPG




Expedite EMerMade M




LABELING



3’-DithiolSerinolCPG 20-2991-01 0.1g 120.00 20-2991-10 1.0g 995.00 0.2µmolecolumns 20-2991-42 Packof4 120.00 1µmolecolumns 20-2991-41 Packof4 200.00 10µmolecolumn(ABI) 20-2991-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2991-14 Packof1 450.00

3’-Alkyne-ModifierSerinolCPG 20-2992-01 0.1g 105.00 20-2992-10 1.0g 800.00 0.2µmolecolumns 20-2992-42 Packof4 100.00 1µmolecolumns 20-2992-41 Packof4 175.00 10µmolecolumn(ABI) 20-2992-13 Packof1 260.00 15µmolecolumn(Expedite) 20-2992-14 Packof1 390.00

COT SERINOL PHOSPHORAMIDITE

Bright,long-lastingandnon-phototoxicorganicfluorophoresareessentialforthecontinuedoptimizationofadiverserangeofimagingapplications.However,allcurrentlyavailabletechnologiesremainsusceptibletoundesirabletransitionstodarkstates.Darkstatesarisefromnon-fluorescenttripletelectronicconfigurationsfromwhichtherateofreturntothegroundstateisslow.Wheninthetripletstate,thefluorophoreissusceptibletophotobleachingandfluorescenceapplicationsarecompromisedbyunpredictablyreducingthesignal-to-noiseratio(SNR),aswellaslimitingthetotaldurationoftimeoverwhichinformationcanbegathered.Thedirectconjugationofsmall-moleculeprotectiveagents(PAs)hasenabledsignificantimprovementsthroughintra-moleculartripletquenching.ThroughapartnershipwithLumidyneTechnologies,GlenResearchhascreatedanovelPA-linkedphosphoramiditeusingcyclooctatetraene(COT).COTSerinolPhosphoramiditeprovidesameanstoimprovethephotostabilityofvirtuallyanyfluorophoreinamodularfashion.OurspectrofluorometricstudiesshowthatthepresenceofCOTlimitedtheamountofphotobleachingofanoligocontainingthecyanine5dye.


COTSerinolPhosphoramidite 10-1996-95 50µmole 310.00 10-1996-90 100µmole 600.00 10-1996-02 0.25g 1800.00

O

O

NH

NH

O

OODMT

succinoyl CPG

3’-Alkyne-Modifier Serinol CPG3’-Dithiol Serinol CPG

SS

HN

HN

O O

ODMT

O succinoyl-CPG

HN

HN

O O

ODMT

O P N(iPr)2

O-CNEt

COT Serinol


This product is covered under US Patent 8,945,515B2.

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Dabsyl CPG

Dabcyl-dT 5’-Dabcyl Phosphoramidite

Dabcyl CPG

REFERENCE

(1)S.TyagiandF.R.Kramer,Nature Biotechnology, 1996, 4, 303-308.

DABCYL LABELING

Amolecularbeaconprobe1hasitsnaturalfluorescencequenchedinsolutionunlessitishybridizedtothetargetsequence.Consequently,thedesignofamolecularbeaconrequiresafluorophoretobeinonepartofthesequenceandthequenchermoleculetobeinanother,withbothmoleculesbeingseparatedfromtheoligonucleotidebyahydrocarbonspacer.TheDabcylgrouphasbeenfoundtobeauniversalquencher.3’-DabsylCPGand3’-DabcylCPGareusedtoprepareprobeswiththequencherblockingthe3’-terminus.5’-DabcylPhosphoramiditelocatesthequencheratthe5’-terminusandDabcyl-dTplacesitwithinthesequence,leavingthe3’-terminusavailableforpolymeraseextension.


3’-DabsylCPG 20-5911-01 0.1g 120.00 20-5911-10 1.0g 975.00 1µmolecolumns 20-5911-41 Packof4 200.00 0.2µmolecolumns 20-5911-42 Packof4 120.00 10µmolecolumn(ABI) 20-5911-13 Packof1 350.00 15µmolecolumn(Expedite) 20-5911-14 Packof1 500.00

3’-DabcylCPG 20-5912-01 0.1g 120.00 20-5912-10 1.0g 975.00 1µmolecolumns 20-5912-41 Packof4 200.00 0.2µmolecolumns 20-5912-42 Packof4 120.00 10µmolecolumn(ABI) 20-5912-13 Packof1 350.00 15µmolecolumn(Expedite) 20-5912-14 Packof1 500.00

3'-DabcylPS 26-5912-01 0.1g 125.00 26-5912-10 1.0g 1025.00 200 nmole columns(AB3900) 26-5912-52 Packof10 300.00 40 nmole columns(AB3900) 26-5912-55 Packof10 300.00

Dabcyl-dT 10-1058-95 50µmole 180.00 10-1058-90 100µmole 325.00 10-1058-02 0.25g 675.00

5’-DabcylPhosphoramidite 10-5912-95 50µmole 125.00 10-5912-90 100µmole 225.00 10-5912-02 0.25g 650.00

O

NH

O

NHHN

N

O

ODMTO

CNEtON(iPr)2PO

O

NN N(Me) 2

O

NH CPGO

OHNODMTO

N(Me) 2NNSO 2

O

NH CPGO

OHNODMTO

NN N(Me) 2O

O

HNN

N(Me)2NCNEtON(iPr)2PO

LABELING

300 400 500 600 700 800

wavelength (nm)

____ Dabcyl____ Eclipse____ BHQ-1____ BHQ-2____ BHQ-3

FAM

TET

HEX Cy3

TMR

Cy3

.5

Cy5

Cy5

.5

____ BBQ-650

DYE QUENCHER PLOT

http://www.glenresearch.com/ProductFiles/Dye_Quencher_Plot.pdf

BIOTIN LABELING

GlenResearchbiotinphosphoramiditesfordirectlabelingofsyntheticoligonucleotidesexhibitthefollowingfeatures:1. AllaresolubleinacetonitrileatconcentrationsusefulforDNAsynthesis.2. AllincludeaDMTgroupforcartridgepurificationswhichisessentialforthepreparationofbiotinylatedPCRprimers

becauseofthepotentialforcrosscontaminationinHPLCpurifications.3.Forthedevelopmentofdiagnosticprobes,biotinphosphoramiditeiscapableofbranchingtoallowmultiplebiotins

tobeintroducedatthe3’-or5’-terminus.BiotinTEGPhosphoramiditecontainsa15atommixedpolarityspacerarmbasedonatriethyleneglycol.

4. ProtectedBiotinSerinolPhosphoramiditeandCPGareprotectedwithat-butylbenzoylgrouponthebiotinring.Thisgroupisdesignedtostopanyphosphoramiditereactionsatthisactivepositioninbiotin.ThisprotectionavoidsbranchingwhenusingnucleophilicactivatorslikeDCI.Theprotectinggroupiseasilyremovedduringoligonucleotidecleavageanddeprotection.TheBiotinLCversionsaresimilarlyprotectedandshouldbeusefulforthesynthesisofhighlysensitivebiotinylatedprobes.


BiotinPhosphoramidite 10-1953-95 50µmole 165.00 10-1953-90 100µmole 295.00 10-1953-02 0.25g 675.00

BiotinTEGPhosphoramidite 10-1955-95 50µmole 165.00 10-1955-90 100µmole 295.00 10-1955-02 0.25g 675.00

ProtectedBiotinSerinolPhosphoramidite 10-1993-95 50µmole 165.00 10-1993-90 100µmole 295.00 10-1993-02 0.25g 675.00

ProtectedBiotinLCSerinolPhosphoramidite 10-1995-95 50µmole 205.00 10-1995-90 100µmole 365.00 10-1995-02 0.25g 675.00

Biotin Phosphoramidite BiotinTEG Phosphoramidite

LABELING

O

O

S

NH NH

NHODMT

O P N(iPr)2O CNEt

NH OO

OO ODMT

O

CNEtON(iPr)2PO

O

S

NH NH




Expedite EMerMade M




ODMT

O P N(iPr)2

O CNEt

HN

HN

OOS

NHN

O O

HN

OS

NHN

O O

OO

O

O P N(iPr)2

O CNEt

HN

O

O

HN

O

ODMT

Protected Biotin Serinol Phosphoramidite

Protected BiotinLC Serinol Phosphoramidite

98 99

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BIOTIN LABELING (CONT.)

Biotin-dTcanreplacedTresidueswithintheoligonucleotidesequence.5’-BiotinphosphoramiditecanbeaddedONLYONCEtothe5’-terminusofanoligonucleotide.However,theDMTgrouponthebiotincanbeusedinRPcartridgeandHPLCpurificationtechniques.PCBiotinisaphotocleavable5’-biotinphosphoramidite.BiotinTEGCPGandProtectedBiotinLCSerinolCPGaredesignedforthedirectsynthesisofoligonucleotidescontainingbiotinatthe3’terminus.

Desthiobiotinisabiotinanaloguethatexhibitslowerbindingtobiotin-bindingproteinssuchasstreptavidin.Thisbiotinanalogueislackingthesulfurgroupfromthemoleculeandhasadissociationconstant(Kd)severalordersofmagnitudelessthanbiotin/streptavidin.Asaresult,biomoleculescontainingdesthiobiotinaredissociatedfromstreptavidinsimplyinthepresenceofbufferedsolutionsofbiotin.WeofferdesthiobiotinTEGphosphoramiditeandthecorrespondingCPG.

ABI-stylevialsandcolumnsaresuppliedunlessotherwiserequested(seenotebox).

IItem Catalog No. Pack Price ($)

5’-BiotinPhosphoramidite 10-5950-95 50µmole 125.00 10-5950-90 100µmole 225.00 10-5950-02 0.25g 650.00

Biotin-dT 10-1038-95 50µmole 167.50 10-1038-90 100µmole 325.00 10-1038-02 0.25g 625.00

PCBiotinPhosphoramidite 10-4950-95 50µmole 145.00 10-4950-90 100µmole 280.00 10-4950-02 0.25g 675.00

DesthiobiotinTEGPhosphoramidite 10-1952-95 50µmole 185.00 10-1952-90 100µmole 335.00 10-1952-02 0.25g 775.00

LABELING

PC Biotin Phosphoramidite

NHDMTN

SNH

O

ONH

ONO2

H3C

CNEtON(iPr)2PO

DesthiobiotinTEG Phosphoramidite

NH OO

OO ODMT

O

CNEtON(iPr)2PO

O

NH NH

Biotin-dT

HN

S

O

O

N

O

O

O P N(iPr)2O CNEt

DMTO

HN

N

O

O

NH

ONH

5’-Biotin Phosphoramidite

NHDMTN

SNH

O

O

O P N(iPr)2O CNEt

BIOTIN LABELING (CONT.)

IItem Catalog No. Pack Price ($)

3’-BiotinTEGCPG 20-2955-01 0.1g 120.00 20-2955-10 1.0g 995.00 0.2µmolecolumns 20-2955-42 Packof4 120.00 1µmolecolumns 20-2955-41 Packof4 200.00 10µmolecolumn(ABI) 20-2955-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2955-14 Packof1 450.00

3’-BiotinTEGPS 26-2955-01 0.1g 125.00 26-2955-10 1.0g 1025.00 200 nmole columns(AB3900) 26-2955-52 Packof10 300.00 40 nmole columns(AB3900) 26-2955-55 Packof10 300.00

3’-ProtectedBiotinSerinolCPG 20-2993-01 0.1g 120.00 20-2993-10 1.0g 995.00 0.2µmolecolumns 20-2993-42 Packof4 120.00 1µmolecolumns 20-2993-41 Packof4 200.00 10µmolecolumn(ABI) 20-2993-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2993-14 Packof1 450.00

3’-ProtectedBiotinLCSerinolCPG 20-2995-01 0.1g 120.00 20-2995-10 1.0g 995.00 0.2µmolecolumns 20-2995-42 Packof4 120.00 1µmolecolumns 20-2995-41 Packof4 200.00 10µmolecolumn(ABI) 20-2995-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2995-14 Packof1 450.00

DesthiobiotinTEGCPG 20-2952-01 0.1g 140.00 20-2952-10 1.0g 1150.00 0.2µmolecolumns 20-2952-42 Packof4 140.00 1µmolecolumns 20-2952-41 Packof4 230.00 10µmolecolumn(ABI) 20-2952-13 Packof1 345.00 15µmolecolumn(Expedite) 20-2952-14 Packof1 520.00

LABELING




Expedite EMerMade M




-succinyl-lcaa-CPG

NH OO

OO ODMT

O O

O

S

NH NH

NH OO

OO ODMT

O O-succinyl-lcaa-CPG

O

NH NH

HN

OS

NHN

O O

ODMT

O-succinyl-CPG

HN

O

HN

OS

NHN

O O

OO

O ODMT

O-succinyl-CPG

HN

O

O

HN

O

BiotinTEG CPG

Protected Biotin Serinol CPG

Protected BiotinLC Serinol CPG

DesthiobiotinTEG CPG

SEE ALSO

PC Biotin on page 86

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FLUORESCEIN LABELING

5’-Fluoresceinphosphoramidite contains no4,4’-dimethoxytrityl (DMT) group and canbe addedonly once at the5’-terminus, thereby terminating synthesis. Thisproduct ispreparedusing the6-carboxyfluoresceinderivative. Thetetrachloro-,hexachloro-anddichloro-dimethoxy-fluorescein(TET,HEXandJOE,respectively)phosphoramiditesaredesignedtotakeadvantageofthemulticolordetectioncapabilityofmodernDNAsequencersandgeneticanalyzers.Fluoresceinphosphoramidite isdesigned toproduce the samefluorescein-type structureashadbeenpreviouslypreparedusingfluoresceinisothiocyanate(FITC).OurfluoresceinphosphoramiditealsocontainsaDMTgrouptoallowquantificationofcoupling.Theanalogousstructure,6-FluoresceinPhosphoramidite,preparedusing6-FAM,isalsoavailable,alongwith6-FluoresceinSerinolPhosphoramidite.Fluorescein-dTcanbeinsertedintothedesiredsequenceasareplacementforadTresidue.

Weofferfivefluoresceinsupports.FluoresceinCPGhastraditionallybeenusedtoaddthefluoresceinlabelatthe3’-terminus.Theanalogousstructure,3’-(6-Fluorescein)CPG,preparedusing6-FAM,isnowalsoavailable,alongwith6-FluoresceinSerinolCPG.Wealsooffer3’-(6-FAM)CPGandFluorescein-dTCPG,bothderivativesof6-carboxyfluorescein(6-FAM).Botharesingleisomersanduseanamidelinkagewhichisstableduringcleavageanddeprotectionanddoesnotallowisomerformation.3’-(6-FAM)CPGallowseffectiveblockageofthe3’-terminusfrompolymeraseextensionaswellasexonucleasedigestion.Fluorescein-dTCPGallowsbothoftheseenzymaticactivitiestoproceed.Normalcleavageanddeprotectionwithammoniumhydroxidereadilygeneratesthefluoresceinlabeledoligos.

Thespectralcharacteristicsofthesedyesaredetailedonthefollowingpage.


5’-FluoresceinPhosphoramidite 10-5901-95 50µmole 110.00 (6-FAM) 10-5901-90 100µmole 215.00 10-5901-02 0.25g 575.00

5’-Hexachloro-Fluorescein 10-5902-95 50µmole 190.00 Phosphoramidite 10-5902-90 100µmole 375.00 (HEX) 10-5902-02 0.25g 875.00

5’-Tetrachloro-Fluorescein 10-5903-95 50µmole 180.00 Phosphoramidite 10-5903-90 100µmole 350.00 (TET) 10-5903-02 0.25g 875.00

5’-Dichloro-dimethoxy-FluoresceinPhosphoramiditeII 10-5906-95 50µmole 105.00 (JOE) 10-5906-90 100µmole 198.00 10-5906-02 0.25g 495.00

5’-Fluorescein Phosphoramidite 5’-Tetrachloro-FluoresceinPhosphoramidite

5’-Hexachloro-Fluorescein Phosphoramidite

O

O

O

OO

O O

HN

O PN

O

OCN

O

O

O

OO

O O

HN

O PN

O

OCN

Cl

Cl

Cl

ClCl

Cl

O

O

O

OO

O O

HN

O PN

O

OCN

Cl Cl

Cl

Cl

LABELING

O

HN

O

MeO

OO

O

O

OO

OP

N

O

CN

OMe

Cl Cl

5’-Dichloro-dimethoxy-FluoresceinPhosphoramidite II

300 400 500 600 700 800

wavelength (nm)


FAM

TET

HEX Cy3

TMR

Cy3

.5

Cy5

Cy5

.5

____ BBQ-650

DYE QUENCHER PLOT


FLUORESCEIN LABELING (CONT.)


FluoresceinPhosphoramidite 10-1963-95 50µmole 165.00 10-1963-90 100µmole 295.00 10-1963-02 0.25g 595.00

6-FluoresceinPhosphoramidite 10-1964-95 50µmole 165.00 10-1964-90 100µmole 295.00 10-1964-02 0.25g 595.00

6-FluoresceinSerinolPhosphoramidite 10-1994-95 50µmole 165.00 10-1994-90 100µmole 295.00 10-1994-02 0.25g 595.00

Fluorescein-dTPhosphoramidite 10-1056-95 50µmole 180.00 10-1056-90 100µmole 325.00 10-1056-02 0.25g 675.00

Fluorescein Phosphoramidite Fluorescein dT

FLUORESCENT DYES

Absorbance Emission Color Maximum Maximum

Fluorescein 494nm 525nm GreenTetrachloro- 521nm 536nm OrangeFluoresceinHexachloro- 535nm 556nm PinkFluoresceinSIMA (HEX) 538nm 551nm PinkDichloro- 525nm 548nm Orange/Pinkdimethoxy-FluoresceinTAMRA 565nm 580nm RoseCy3 546nm 563nm RedCy3.5 588nm 604nm PurpleCy5 646nm 662nm VioletCy5.5 683nm 707nm Dark BlueYakima Yellow 530nm 549nm YellowRedmond Red 579nm 595nm Red

LABELING

6-Fluorescein Phosphoramidite

OO

O O

O

O

O

P N(iPr)2O CNEt

O

ODMT

NH

O

O

O

O

OO

O O

HNNH

ODMTS

OCNEtON(iPr)2P

�

O

O P N(iPr)2O CNEt

DMTO O

O

N

HNNH

O

NH

O

OO

O O

O

O

O

O

HN

O

OO

O

O

OO

ODMT

O P N(iPr)2

O CNEt

HN

O

6-Fluorescein Serinol Phosphoramidite




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102 103

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3’-FluoresceinCPG 20-2963-01 0.1g 120.00 20-2963-10 1.0g 995.00 1µmolecolumns 20-2963-41 Packof4 200.00 0.2µmolecolumns 20-2963-42 Packof4 120.00 10µmolecolumn(ABI) 20-2963-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2963-14 Packof1 450.00

3’-(6-Fluorescein)CPG 20-2964-01 0.1g 120.00 20-2964-10 1.0g 995.00 1µmolecolumns 20-2964-41 Packof4 200.00 0.2µmolecolumns 20-2964-42 Packof4 120.00 10µmolecolumn(ABI) 20-2964-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2964-14 Packof1 450.00

3’-(6-FAM)CPG 20-2961-01 0.1g 120.00 20-2961-10 1.0g 995.00 1µmolecolumns 20-2961-41 Packof4 200.00 0.2µmolecolumns 20-2961-42 Packof4 120.00 10µmolecolumn(ABI) 20-2961-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2961-14 Packof1 450.00

3’-(6-FAM)PS 26-2961-01 0.1g 130.00 26-2961-10 1.0g 1045.00 200nmolecolumns(AB3900) 26-2961-52 Packof10 300.00 40nmolecolumns(AB3900) 26-2961-55 Packof10 300.00

3’-6-FluoresceinSerinolCPG 20-2994-01 0.1g 120.00 20-2994-10 1.0g 995.00 0.2µmolecolumns 20-2994-42 Packof4 120.00 1µmolecolumns 20-2994-41 Packof4 200.00 10µmolecolumn(ABI) 20-2994-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2994-14 Packof1 450.00

3’-Fluorescein CPG

O-succinyl-CPG

O

O

O

OO

O O

HN

S

NH

ODMT

LABELING

3’-(6-FAM) CPG 3’-(6-Fluorescein) CPG

OO

O O

O

O

O

O

ODMT

NH

O

-succinyl-CPG

NH

O

ODMT

OO

NHCPG

O

O

O

O

O

OO

O O

O

HN

O

OO

O

O

OO

ODMT

O-succinyl-CPG

HN

O

3’-6-Fluorescein Serinol CPG

300 400 500 600 700 800

wavelength (nm)


FAM

TET

HEX Cy3

TMR

Cy3

.5

Cy5

Cy5

.5

____ BBQ-650

DYE QUENCHER PLOT




3’-Fluorescein-dTCPG 20-2056-01 0.1g 120.00 20-2056-10 1.0g 995.00 1µmolecolumns 20-2056-41 Packof4 200.00 0.2µmolecolumns 20-2056-42 Packof4 120.00 10µmolecolumn(ABI) 20-2056-13 Packof1 300.00 15µmolecolumn(Expedite) 20-2056-14 Packof1 450.00

FLUORESCEIN LABELING (SIMA)

Dichloro-diphenyl-fluorescein,SIMA(HEX)exhibitsvirtuallyidenticalabsorbanceandemissionspectratoHEX.SIMA(HEX)ismuchmorestabletobasicdeprotectionconditionsthanHEXandoligonucleotidescanbedeprotectedusingammoniumhydroxideatelevatedtemperaturesandevenammoniumhydroxide/methylamine(AMA)atroomtemperatureor65°Cfor10minutes.SIMAabsorptionmaximumwas3nmblue-shiftedcomparedtoHEXatpH7.Theabsorbanceisbroader,sotheextinctioncoefficientissmallerthanthatofHEX,butwhenexcitingat500nmwheretheabsorbancewasnormalized,theemissionwasstill90%ofHEXandtheemissionwasred-shiftedby5nm.AsecondSIMA(HEX)product,SIMA(HEX)-dT,canbeusedtointroduceSIMA(HEX)inthesyntheticoligonucleotidesequence,usuallyasareplacementforthenativedT linkage. Again,thisproduct is fullycompatiblewithdeprotectionschemesusingammoniumhydroxideatelevatedtemperaturesorAMAatroomtemperatureand65°C.


SIMA(HEX)Phosphoramidite 10-5905-95 50µmole 90.00 10-5905-90 100µmole 175.00 10-5905-02 0.25g 400.00

SIMA(HEX)-dTPhosphoramidite 10-5945-95 50µmole 345.00 10-5945-90 100µmole 675.00 10-5945-02 0.25g 995.00

LABELING

3’-Fluorescein-dT CPG

O

O

DMTO O

O

N

HNNH

O

NH

O

OO

O O

O

O

O

-Succinyl-lcaa-CPG




Expedite EMerMade M




O

HN

O

OO

O

O

OO

OP

N

O

CN

Cl

Cl

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

NH

HN

O

O OO

O

O

OO

Cl

Cl

O

SIMA (HEX) Phosphoramidite SIMA (HEX)-dT Phosphoramidite

300 400 500 600 700 800

wavelength (nm)


FAM

TET

HEX Cy3

TMR

Cy3

.5

Cy5

Cy5

.5

____ BBQ-650

DYE QUENCHER PLOT


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CYANINE LABELING

Twocyaninederivatives,Cyanine3andCyanine5,whichdiffer in structure simplyby thenumberof carbons in theconjugatedpoly-enelinkage,arejoinedbythecloselyrelatedanalogues,Cyanine3.5andCyanine5.5,andareavailableasphosphoramidites.Cyaninedyesarenormallyaddedonceatthe5’-terminusandtheMMTgroupshouldberemovedonthesynthesizer.TheabsorbanceoftheMMTcation(yellow)isnoticeablydifferentfromtheDMTcation(orange),andso,absorbance-basedtritylmonitorswilldetectitincorrectlyasalowcoupling.Ontheotherhand,conductivitydetectorswillinterpretthereleasemorecorrectly.Cyaninedyephosphoramiditeshavealsobeenusedsuccessfullyadjacenttothe3’-terminus. Cyanine3andCyanine5supportsarealsoofferedtoallowsimplerproductionof3’cyaninedye-labeledoligonucleotides.

Deprotectionofoligos containingCyaninedyesmaybecarriedoutwithammoniumhydroxideat room temperature,regardlessofthebaseprotectinggroupsonthemonomersused.Ifthereisaneedtouseammoniumhydroxideatelevatedtemperature,Cyanine3andCyanine3.5aremorestablethanCyanine5andCyanine5.5.However,itisalwaysprudenttousemonomerswithbaselabileprotectinggroupstolimittheexposuretimeto2hoursorlessat65°Cduringdeprotection.

Tobetteraddressapplicationsinnear-infrared(NIR)imaging,GlenResearchisofferingawatersolubleDisulfo-Cyanine7azidethatcanbeeasilyconjugatedtoDNAandRNAthroughstandardclickchemistry.Thislongwavelengthdyeoffersthebenefitsofimprovedsolubility,reducedaggregation,andimprovedstabilityinthenear-infraredspectrumalongwiththeconvenienceofclickchemistry.


Cyanine3Phosphoramidite 10-5913-95 50µmole 205.00 10-5913-90 100µmole 375.00 10-5913-02 0.25g 925.00

Cyanine3.5Phosphoramidite 10-5914-95 50µmole 220.00 10-5914-90 100µmole 400.00 10-5914-02 0.25g 925.00

Cyanine5Phosphoramidite 10-5915-95 50µmole 205.00 10-5915-90 100µmole 375.00 10-5915-02 0.25g 925.00

Cyanine5.5Phosphoramidite 10-5916-95 50µmole 245.00 10-5916-90 100µmole 450.00 10-5916-02 0.25g 925.00

LABELING

Cyanine 5 Phosphoramidite

Cyanine 3 Phosphoramidite

Cyanine 5.5 Phosphoramidite

Cyanine 3.5 Phosphoramidite

SPECTRAL DATA FOR CYANINE DYES


Cyanine 3 546nm 563nm RedCyanine 3.5 588nm 604nm PurpleCyanine 5 646nm 662nm VioletCyanine 5.5 683nm 707nm Dark BlueCyanine 7 750nm 773nm Dark Green(Measured in an oligo in 0.1M TEAA buffer, pH7.)

N N

OMMT

Cl

O P N(iPr)2

O CNEt

N N

OMMT

Cl

O P N(iPr)2

O CNEt

N N

OMMT

Cl

O P N(iPr)2

O CNEt

N N

OMMT O P N(iPr)2

O CNEt

I-

300 400 500 600 700 800

wavelength (nm)


FAM

TET

HEX Cy3

TMR

Cy3

.5

Cy5

Cy5

.5

____ BBQ-650

DYE QUENCHER PLOT


LABELING

CYANINE LABELING (CONT.)


Cyanine3CPG 20-5913-01 0.1g 160.00 20-5913-10 1.0g 1250.00 1µmolecolumns(TWISTformatonly) 20-5913-41 Packof4 250.00 0.2µmolecolumns 20-5913-42 Packof4 70.00

Cyanine5CPG 20-5915-01 0.1g 160.00 20-5915-10 1.0g 1250.00 1µmolecolumns(TWISTformatonly) 20-5915-41 Packof4 250.00 0.2µmolecolumns 20-5915-42 Packof4 70.00

Disulfo-Cyanine7Azide 50-2010-92 25µmole 325.00 50-2010-90 100µmole 975.00

N N

OMMT OO

ON

H

Cl

N N

OMMT OO

ON

H

Cl

Cyanine 5 CPGCyanine 3 CPG

N

SO3-K+

N+

-O3S

HNN3

O

Disulfo-Cyanine 7 Azide




Expedite EMerMade M




300 400 500 600 700 800

wavelength (nm)


FAM

TET

HEX Cy3

TMR

Cy3

.5

Cy5

Cy5

.5

____ BBQ-650

DYE QUENCHER PLOT


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LABELING

ELITECHGROUP DYES AND QUENCHER

GlenResearch’sagreementwithELITechGroup,formerlyEpochBiosciences,allowsustoofferseveraloftheirproprietaryproductsdesignedforthesynthesisofnovelDNAprobes.WearepleasedtoofferproductsbasedonELITechGroup’sRedmondRed®,YakimaYellow®andAquaPhluor®593fluorophoresandEclipse®non-fluorescentquencher.UnderouragreementwealsosupplyPPG,amodifiednucleoside,and5’-Aldehyde-ModifierC2Phosphoramidite.Thefluorescentdyes,YakimaYellow,RedmondRedandAquaPhluor593,areavailableasphosphoramiditesandsupports.YakimaYellowhasanabsorbancemaximumat530nmandemissionmaximumat549nm,RedmondRed’sabsorbanceandemissionmaximaareat579nmand595nm,respectively,andAquaPhluor593hasanabsorbancemaximumat593nmandemissionmaximumat613nm.

TheEclipsequencherfromELITechGroupsolvesmostoftheproblemsinherentinthesynthesisofmolecularbeaconandFRETprobes.TheEclipsemoleculeishighlystableandcanbeusedsafelyinallcommonoligodeprotectionschemes.TheabsorbancemaximumforEclipseQuencherisat522nm,comparedto479nmfordabcyl.Inaddition,thestructureoftheEclipseQuencherissubstantiallymoreelectrondeficientthanthatofdabcylandthisleadstobetterquenchingoverawiderrangeofdyes,especiallythosewithemissionmaximaatlongerwavelengths(redshifted)suchasRedmondRedandCyanine5.Inaddition,withanabsorptionrangefrom390nmto625nm,theEclipseQuencheriscapableofeffectiveperformanceinawiderangeofcoloredFRETprobes.


RedmondRed®Phosphoramidite 10-5920-95 50µmole 220.00 10-5920-90 100µmole 420.00 10-5920-02 0.25g 1045.00

YakimaYellow®Phosphoramidite 10-5921-95 50µmole 230.00 10-5921-90 100µmole 440.00 10-5921-02 0.25g 1045.00

5’-AquaPhluor®593Phosphoramidite 10-5923-95 50µmole 405.00 10-5923-90 100µmole 795.00 10-5923-02 0.25g 1575.00

Eclipse®QuencherPhosphoramidite 10-5925-95 50µmole 250.00 10-5925-90 100µmole 480.00 10-5925-02 0.25g 1185.00


These Products are for research purposesonly,andmaynotbeusedforcommercial,clinical,diagnosticoranyotheruse.TheseProductsaresubjecttoproprietaryrightsofELITechGroupand are made and sold under license fromELITechGroup.Thereisnoimpliedlicenseforcommercialusewithrespectto these Products and a license must beobtaineddirectlyfromELITechGroupwithrespecttoanyproposedcommercialuseoftheseProducts.“Commercialuse”includesbutisnotlimited to the sale, lease, license or othertransferoftheProductoranymaterial derived or produced from it, the sale, lease, license or other grant of rightstousetheProductoranymaterialderived or produced from it, or the use of the Product to perform services for a feeforthirdparties(includingcontractresearch).

Asimpleagreementmustbesignedbeforeend-usersandcustomoligoservicesmaypurchasetheseproductsforuseasdefinedabove. http://www.glenresearch.com/Reference/ELITechGroupProducts.pdf AquaPhluor®, Yakima Yellow®, Redmond Red® and Eclipse®, are registered Trademarks of ELITechGroup. Redmond Red® Yakima Yellow®

Epoch Eclipse™ Quencher

FLUORESCENT DYES


Yakima Yellow 530nm 549nm YellowRedmond Red 579nm 595nm RedAquaPhluor 593 593nm 613nm Red

O

NO

O DMT

O P NO

CH 2CH 2CNN

O

O O

Yakima Yellow Phosphoramidite

C49H60Cl4N3O10P1023.81

1021.277044C 57.5% H 5.9% Cl 13.9% N 4.1% O 15.6% P 3.0%

Cl

Cl

O

O

Cl

ClCH 3

O

OOO

O

CH 2CH 2CN

ONPO

O

NH

OCH 3

N

NN

ClO2N

N CH 2CH 2CN

ONPO

DMTO

ON+ N

N

PO

O

O

O O

PO N

NH

N

F3C O

PF6-

5’-AquaPhluor® 593

LABELING

Redmond Red® CPG

Yakima Yellow® CPG

Eclipse® Quencher CPG

Redmond Red CPG

NHO

O

CPG

OO

O

N

O

DMTOO

N

O

O

Cl

Cl

Cl

ClCH 3

O

OO

O

O

ONH CPG

O

O

O

O

N

O DMT

OCH 3

N

NN

ClO2N

O

O

O

NH CPG

N

DMTO




Expedite EMerMade M




300 400 500 600 700 800

wavelength (nm)


FAM

TET

HEX Cy3

TMR

Cy3

.5

Cy5

Cy5

.5

____ BBQ-650

DYE QUENCHER PLOT


O N+N

N

PO

N

DMTO

O

NH-CPG

O

O

O

O

O-O

AquaPhluor® 593 CPG

ELITECHGROUP DYES AND QUENCHER (CONT.)


RedmondRed®CPG 20-5920-01 0.1g 180.00 20-5920-10 1.0g 1500.00 1µmolecolumns 20-5920-41 Packof4 300.00 0.2µmolecolumns 20-5920-42 Packof4 150.00 10µmolecolumn(ABI) 20-5920-13 Packof1 750.00 15µmolecolumn(Expedite) 20-5920-14 Packof1 1125.00

YakimaYellow®CPG 20-5921-01 0.1g 180.00 20-5921-10 1.0g 1500.00 1µmolecolumns 20-5921-41 Packof4 300.00 0.2µmolecolumns 20-5921-42 Packof4 150.00 10µmolecolumn(ABI) 20-5921-13 Packof1 750.00 15µmolecolumn(Expedite) 20-5921-14 Packof1 1125.00

AquaPhluor®593CPG 20-5923-01 0.1g 215.00 20-5923-10 1.0g 1800.00 1µmolecolumns 20-5923-41 Packof4 325.00 0.2µmolecolumns 20-5923-42 Packof4 165.00 10µmolecolumn(ABI) 20-5923-13 Packof1 925.00 15µmolecolumn(Expedite) 20-5923-14 Packof1 1395.00

Eclipse®QuencherCPG 20-5925-01 0.1g 230.00 20-5925-10 1.0g 1925.00 1µmolecolumns 20-5925-41 Packof4 350.00 0.2µmolecolumns 20-5925-42 Packof4 175.00 10µmolecolumn(ABI) 20-5925-13 Packof1 995.00 15µmolecolumn(Expedite) 20-5925-14 Packof1 1495.00

SEE ALSO

PPG on page 575’-Aldehyde-Modifier C2 on page 83

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BLACK HOLE QUENCHER DYES

Withthegrowingpopularityofredandnear-infrareddyes,weareofferingtheBlackHoleQuencherTMdyes(BHQs),whosephysicalpropertiesaredetailedinTable1.BHQdyesarerobustdarkquenchersthatverynicelycomplementourexistingproductline.Theyarecompatiblewithammoniumhydroxidedeprotection,exhibitexcellentcouplingefficiencies,havelargeextinctioncoefficientsandarecompletelynon-fluorescent.Theirabsorbancesarewell-tunedtoquenchavarietyofpopularfluorophores–eventhosefarintothered,suchasCy3andCy5.ThedarkquenchermosttypicallyusedinaMolecularBeaconisDabcyl.BecausethequenchingdoesnotinvolveFRET,thereislittle,ifany,dependenceupondonor-acceptorspectraloverlap.InacomprehensivepaperbyMarras,KramerandTyagi,1 theabilityofBHQ-1andBHQ-2toquench22differentfluorophoreswasevaluated.Forshorterwavelengthfluorophoressuchasfluorescein,thequenchingefficiencywasroughlythesameasDabcyl(91%–93%).However,fordyesemittinginthefarred,suchasCy5,theBHQdyeswerefarsuperior–quenchingtheCy5with96%efficiency,comparedto84%withDabcyl.ThismayreflecttheBHQ’sabilitytoformstable,non-fluorescentcomplexeswhichcanbeapluseveninFRETprobes.Indeed,recentworksuggeststhatthesenon-fluorescentcomplexeswillformevenintheabsenceofahairpinstemstructureusedbyMolecularBeacons.2


5’-BHQ-1Phosphoramidite 10-5931-95 50µmole 100.00 10-5931-90 100µmole 200.00 10-5931-02 0.25g 700.00

5’-BHQ-2Phosphoramidite 10-5932-95 50µmole 100.00 10-5932-90 100µmole 200.00 10-5932-02 0.25g 700.00

BHQ-1-dT 10-5941-95 50µmole 265.00 10-5941-90 100µmole 525.00 10-5941-02 0.25g 925.00

BHQ-2-dT 10-5942-95 50µmole 265.00 10-5942-90 100µmole 525.00 10-5942-02 0.25g 925.00


"BlackHoleQuencher","BHQ-0","BHQ-1","BHQ-2"and"BHQ-3"aretrademarks of Biosearch Technologies, Inc.,Novato,CA.TheBHQdyetechnologyisthesubjectofpendingpatents and is licensed and sold under agreementwithBiosearchTechnologies,Inc..ProductsincorporatingtheBHQdyemoietyaresoldexclusivelyforR&Dusebytheend-user.Theymaynotbeusedforclinicalordiagnosticpurposesandtheymaynotbere-sold,distributedorre-packaged.

TABLE 1: BLACK HOLE QUENCHERS

Quencher lmax E260 Emax (nm) (L/mol.cm) (L/mol.cm)

BHQ-1 534 8,000 34,000BHQ-2 579 8,000 38,000BHQ-3 672 13,000 42,700

REFERENCES

(1)S.A.E.Marras,F.R.Kramer,andS.Tyagi,Nucleic Acids Res., 2002, 30,E122.

(2)M.K.Johansson,H.Fidder,D.Dick,andR.M.Cook,J Am Chem Soc, 2002, 124, 6950-6956.

BHQ-1-dT BHQ-2-dT

NN N

N N

CNEtON(iPr)2PO

OCH 3

H3COO2NN

N NN N

CNEtON(iPr)2PONO2

H3C

OCH 3

H3C

O

NH

O

NHHN

N

O

ODMTO

CNEtON(iPr)2PO

O

CH 3

CH 3O

CH 3

O

N NN N

N

O2N

O

NH

O

NHHN

N

O

ODMTO

CNEtON(iPr)2PO

O

O

NO2

CH 3O

N NN N

NOCH 3

5’-BHQ-1 5’-BHQ-2

LABELING

BLACK HOLE QUENCHER DYES (CONT.)


3'-BHQ-1CPG 20-5931-01 0.1g 190.00 20-5931-10 1.0g 1500.00 1µmolecolumns 20-5931-41 Packof4 300.00 0.2µmolecolumns 20-5931-42 Packof4 80.00 10µmolecolumn(ABI) 20-5931-13 Packof1 575.00 15µmolecolumn(Expedite) 20-5931-14 Packof1 825.00



3'-BHQ-2 CPG 3'-BHQ-3 CPG

NN N

N

NO2

H3C

OCH 3

H3CODMT

O-glycolate-CPG

N

NN N

N

OCH 3

H3COO2N N

O-glycolate-CPG

ODMTN

N+N

NN

ODMT

O-glycolate-CPG

N

X-

3'-BHQ-1 CPG

LABELING




Expedite EMerMade M




300 400 500 600 700 800

wavelength (nm)


FAM

TET

HEX Cy3

TMR

Cy3

.5

Cy5

Cy5

.5

____ BBQ-650

Dye Quencher Plot


SEE OTHER QUENCHERS

Dabcyl on page 98Eclipse™ on page 109BBQ-650® on page 112

110 111

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mol.cm



BLACKBERRY® QUENCHER (BBQ-650®)

WearehappytoofferseveralproductscontainingtheBlackBerry®Quencher(BBQ-650®),whichexhibitsabroadabsorptionprofilefrom550nmto750nm,centeredat650nm.ThisrangeoffersmoreeffectivequenchingofsomeofourpopularlongwavelengthdyeslikeTAMRA,RedmondRed,CydyesandDyLightdyes.WeofferBBQ-650productsforthe3’and5’termini,aswellasBBQ-650-dTforinclusionwithintheoligonucleotidesequence,withthefollowingproperties:

• Quenchesthefluorescenceoflongwavelengthdyes• Quenches in FRET and contact mode• Absorbancemaximumat~650nm• Quenchingrange–550-750nm• Compatiblewithstandardoligosynthesischemistry• CompatiblewithregulardeprotectionbutrequiresmilddeprotectionwithAMAatroomtemperature• Availablefor3’,5’,andinternalsubstitution• MorestablethanBHQ-3


5’-BBQ-650®Phosphoramidite 10-5934-95 50µmole 160.00 10-5934-90 100µmole 305.00 10-5934-02 0.25g 925.00

BBQ-650®-dT 10-5944-95 50µmole 280.00 10-5944-90 100µmole 545.00 10-5944-02 0.25g 925.00

3’-BBQ-650®CPG 20-5934-01 0.1g 190.00 20-5934-10 1.0g 1500.00 1µmolecolumns 20-5934-41 Packof4 300.00 0.2µmolecolumns 20-5934-42 Packof4 80.00 10µmolecolumn(ABI) 20-5934-13 Packof1 575.00 15µmolecolumn(Expedite) 20-5934-14 Packof1 825.00


BlackBerry®Quenchertechnology:USPatent7,879,986.ThepurchaseofBlackBerry®Quencherreagentsincludes a limited license to use these reagentsexclusivelyforresearchanddevelopmentpurposes.Theymaynotbeusedforclinicalordiagnosticpurposesandtheymaynotbere-sold,distributed,orre-packagedwithoutprioragreementandconsentofBerry&Associates,Inc.Subsequentsaleof products that are derived from BlackBerry®Quencherreagentsispermittedsolongasthefollowingwrittendisclaimerisincludedinwrittenand electronic catalogs, in commercial advertisement,andinpackageswithcontainersofsuchderivativeproducts:“BlackBerry is a trademark of Berry & Associates, Inc. Products derived from BlackBerry® Quencher reagents are sold exclusively for research and development use by the purchaser. They may not be used for clinical or diagnostic purposes without prior agreement and consent of Berry & Associates, Inc.”

BBQ-650™-dT

N O

NN

NN

NO2

OCH3

H3CO

O P N(iPr)2

O CNEt

5’-BBQ-650™ 3’-BBQ™-650™ CPG

LABELING

NO

NN

NN

O2N

H3CO

OCH3

O

DMTO

glycolate-lcaa-CPG

NO

NN

NN

O2N

H3CO

OCH3ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

NH

HN

O

O

RHODAMINE (TAMRA) LABELING

Rhodaminederivativesarenotsufficientlystabletosurviveconventionaldeprotectionandthesemustbeattachedtoamino-modifiedoligonucleotidesusingpost-synthesislabelingtechniques.BecauseTetramethylRhodamine(TAMRA)isnotbasestable,theproceduretocleaveanddeprotectthelabeledoligonucleotidemustbecarefullyconsidered.UsingtheUltraMILDmonomersanddeprotectionwithpotassiumcarbonateinmethanol,TAMRAoligonucleotidescanbefairlyconvenientlyisolated.TostreamlinethepreparationofTAMRAoligos,weoffer3’-TAMRACPGfor3’labelingandTAMRA-dTforlabelingwithinthesequence.WealsoofferTAMRANHSesterforlabelingamino-modifiedoligonucleotides.


3’-TAMRACPG 20-5910-01 0.1g 120.00 20-5910-10 1.0g 995.00 1µmolecolumns 20-5910-41 Packof4 200.00 0.2µmolecolumns 20-5910-42 Packof4 120.00

3'-TAMRAPS 26-5910-01 0.1g 130.00 26-5910-10 1.0g 1045.00 200 nmole columns(AB3900) 26-5910-52 Packof10 300.00 40 nmole columns(AB3900) 26-5910-55 Packof10 300.00

TAMRA-dT 10-1057-95 50µmole 250.00 10-1057-90 100µmole 495.00 10-1057-02 0.25g 975.00

TAMRANHSEster 50-5910-66 60µL 240.00 (SolutioninanhydrousDMSO)

LABELING

TAMRA NHS Ester

TAMRA CPG TAMRA-dT

O N+N

NHS

O

-O2C

O

NH CPGO

OHNODMTO

O

N+

O

NCO 2-

N+

O

NCO 2-

O

NH

O

NHHN

N

O

ODMTO

CNEtON(iPr)2PO

O




Expedite EMerMade M




SEE ALSO

UltraMILD monomers on page 23

112 113

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ACRIDINE LABELING

Acridinephosphoramiditeisdesignedtoproduceanoligonucleotidecontainingacridineatanypositioninthemolecule.AcridineCPGisusedtolabelthe3’-terminus.Acridineisaneffectiveintercalatingagent.


AcridinePhosphoramidite 10-1973-95 50µmole 165.00 10-1973-90 100µmole 295.00 10-1973-02 0.25g 675.00

3’-AcridineCPG 20-2973-01 0.1g 120.00 20-2973-10 1.0g 995.00 1µmolecolumns 20-2973-41 Packof4 200.00 0.2µmolecolumns 20-2973-42 Packof4 120.00 10µmolecolumn(ABI) 20-2973-13 Packof1 300.00 15µmolecloumn(Expedite) 20-2973-14 Packof1 450.00

DNP LABELING

Ananalyticaltestbasedondetectionof2,4-dinitrophenyl(DNP)labeledoligonucleotideswithanti-DNPantibodieshasbeenproposed.Wehavechosenthebranchedtriethyleneglycol(TEG)spacerinourversionofDNPphosphoramiditesinceitcanbeaddedonceorseveraltimestothe3’or5’terminus.


DNP-TEGPhosphoramidite 10-1985-95 50µmole 165.00 10-1985-90 100µmole 295.00 10-1985-02 0.25g 675.00

LABELING

Acridine Acridine CPG DNP-TEG

O-CNEt

O-P-N( iPr)2

ODMT

MeO

Cl

NH

N

-succinyl-lcaa-CPG

N

NH

Cl

MeO

O

ODMTNO2

O2N

O P N(iPr)2O CNEt

ODMTOO

OONH




Expedite EMerMade M




CHOLESTEROL LABELING

Potentialtherapeuticoligonucleotidesmustpermeatethecellmembraneforoptimalactivity.Theadditionoflipophilicgroupstoanoligonucleotidewouldbeexpectedtoenhancecellularuptake/membranepermeation.Theuseofcholesteryloligosandtheconsequentimprovementinactivityhasbeendescribed.WehavedesignedourCholesterylproductswithtriethyleneglycol(TEG)spacersformaximumsolubility.


Cholesteryl-TEGPhosphoramidite 10-1975-95 50µmole 140.00 10-1975-90 100µmole 265.00 10-1975-02 0.25g 545.00

5’-Cholesteryl-TEGPhosphoramidite 10-1976-95 50µmole 95.00 10-1976-90 100µmole 175.00 10-1976-02 0.25g 525.00

3’-Cholesteryl-TEGCPG 20-2975-01 0.1g 85.00 20-2975-10 1.0g 700.00 1µmolecolumns 20-2975-41 Packof4 140.00 0.2µmolecolumns 20-2975-42 Packof4 84.00 10µmolecolumn(ABI) 20-2975-13 Packof1 210.00 15µmolecolumn(Expedite) 20-2975-14 Packof1 315.00

TOCOPHEROL LABELING

VitaminEisbothlipophilicandnon-toxicevenathighdosessowouldbeanexcellentcandidateasalipophiliccarrierforoligonucleotides.Therefore,asanadditiontoourcholesterylproductline,weoffersimplea-tocopheryl(vitaminE)labeling.Totallysynthetica-tocopherolisracemicatitsthreechiralcentersandisusedtopreparethisproduct.


a-Tocopherol-TEGPhosphoramidite 10-1977-95 50µmole 160.00 10-1977-90 100µmole 300.00 10-1977-02 0.25g 575.00

STEARYL LABELING

We nowofferasimpleC18lipidasaneconomicalandeffectivecarriermolecule.Weenvisagethatthe5’-stearylgroupwillbecomeafavoredlipophiliccarrierforexperimentationwithsyntheticoligonucleotides.


5’-StearylPhosphoramidite 10-1979-90 100µmole 45.00 10-1979-02 0.25g 180.00

LABELING

3’-Cholesteryl-TEG CPG

Cholesteryl-TEGON

HO

OO

O

ODMTO

O P N(iPr)2

O CNEt

ONH

OO

O

O

ODMTO

O

HN CPGO

O

ONH

OO

O

O

O

P N(iPr)2

O CNEt

5’-Cholesteryl-TEG

OO

OODMTO

O P N(iPr)2

O CNEtO

a-Tocopherol-TEG

O P N(iPr)2

O CNEt5’- Stearyl

SEE ALSO

Spermine on page 48

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LABELING

N-ACETYLGALACTOSAMINE (GalNAc) LABELING

A directedapproach to thedeliveryof therapeuticoligonucleotides specifically to the liverhasbeen to target theasialoglycoprotein receptor (ASGPR)usingasuitableglycoconjugate. Indeed,ASGPR is the ideal target fordeliveryoftherapeuticoligonucleotidestotheliversinceitcombinestissuespecificity,highexpressionlevelsandrapidinternalizationandturnover.Theuseofoligonucleotideglycoconjugateshasledtosignificantadvancesintherapeuticdeliveryasevidencedby theworkofAlnylamPharmaceuticalsand IonisPharmaceuticalsusingmultivalentN-acetylgalactosamine (GalNAc)oligonucleotideconjugates.

GlenResearch isdelighted to introduceaGalNAcmodification strategyusingamonomericGalNAc support and theequivalentGalNAcphosphoramidite. Ourexperimentalworkhasshownthattheseproductsarefullycompatiblewithregularoligonucleotidesynthesisanddeprotection.OligonucleotidescontainingGalNAccanbedeprotectedusingstandardproceduresduringwhichtheacetylprotectinggroupsonGalNAcareremoved.Wehavedemonstratedthat5’-GalNAcC3phosphoramiditecanbeusedtoprepareoligonucleotideswithmultipleconsecutiveGalNAcadditionsatthe5’terminus.GlenResearchofferstheseGalNAcC3productsunderanagreementwithAMChemicalsLLC.


5’-GalNAcC3Phosphoramidite 10-1974-95 50µmole 137.50 10-1974-90 100µmole 255.00 10-1974-02 0.25g 500.00

GalNAcC3CPG 20-2974-01 0.1g 40.00 20-2974-10 1.0g 320.00 1µmolecolumns 20-2974-41 Packof4 100.00 0.2µmolecolumns 20-2974-42 Packof4 60.00 10µmolecolumn(ABI) 20-2974-13 Packof1 180.00 15µmolecolumn(Expedite) 20-2974-14 Packof1 280.00

OP

N(iPr)2

O CNEt

NNH

O

OO

OAc OAc

AcHN

AcO O OTMT

ONN

HO

OO

OAc OAc

AcHN

AcO O OTMT

NH

O

O CPG

5’-GalNAc C3 Phosphoramidite

GalNAc C3 CPG




Expedite EMerMade M




LABELING

CDPI3 MGB™ LABELING

The tripeptideofdihydropyrroloindole-carboxylate (CDPI3) is aminorgroovebinding (MGB)moietyderived from thenaturalproductCC-1065withstrongDNAbindingproperties.Syntheticoligonucleotideswithcovalently-attachedCDPI3 haveenhancedDNAaffinityandhaveimprovedthehybridizationpropertiesofsequence-specificDNAprobes.ShortCDPI3-oligonucleotideshybridizewithsingle-strandedDNAtogivemorestableDNAduplexesthanunmodifiedODNsofsimilarlength.CDPI3MGB-oligonucleotideconjugateshavebeenfoundtobeusefulinthefollowingapplications:

• ArrestofprimerextensionandPCRblockers• ShortandfluorogenicPCRprimers• Real-timePCRprobes• miRNAInhibitors

ThesimplestapproachtoMGBprobedesignistouseanMGBsupport,addaquenchermoleculeasthefirstadditionandcompletethesynthesiswitha5’-fluorophore.Alternatively,afluorophoresupportcouldbeusedwiththe5’terminuscontainingaquenchermoleculefollowedbyafinalMGBadditionatthe5’terminus.GlenResearchoffers5’-CDPI3 MGB™ Phosphoramiditeand3’-CDPI3MGB™CPG.

5’-CDPI3MGBphosphoramiditewasfoundtobehydrophobicenoughthatitrequired10%THFinACNtogocompletelyintosolutionata0.1Mconcentrationandrequireda3minutecouplingtime.DeprotectioncanbecarriedoutinEtOH/NH4OH1:3(v/v)17hrat55°CandCDPI3MGBiscompatiblewithGlenPak™purification.

With the CDPI3MGBCPG,optimalresultsareobtainedifUltraMildmonomersandCapAareusedduringsynthesisalongwith0.5MCSOoxidizer.However,theuseofstandardmonomerswithiodineoxidationfollowedbydeprotectionwithEtOH/NH4OH1:3(v/v)for17hrat55°Cwillgiveacceptableresults.


5’-CDPI3MGB™Phosphoramidite 10-5924-95 50µmole 705.00 10-5924-90 100µmole 1390.00 10-5924-02 0.25g 2600.00

CDPI3MGB™CPG 20-5924-01 0.1g 215.00 20-5924-10 1.0g 1800.00 1µmolecolumns 20-5924-41 Packof4 325.00 0.2µmolecolumns 20-5924-42 Packof4 165.00 10µmolecolumn(ABI) 20-5924-13 Packof1 925.00 15µmolecolumn(Expedite) 20-5924-14 Packof1 1395.00

LEGAL NOTICE

NOTICE TO PURCHASER: LIMITED LICENSE

This product is sold under licensing

arrangementsbetweenELITechGroupInc.andGlenResearch.Thepurchaseprice of this product includes limited, nontransferablerightstousetheproductsolelyforactivitiesofthepurchaserwhicharedirectlyrelatedtohumandiagnostics.Otheruses,includingincorporationoftheproductinto another commercial product, are prohibitedwithoutadditionallicenserights.Forinformationonpurchasinga license to this product for purposes otherthanthosestatedabove,contact:

ELITechGroupMolecularDiagnostics,21720 23rd Drive SE, Suite 150,

Bothell,WA98021. Phone(425)482-5555. Fax(425)482-5550. Email:[email protected].

This limited license permits the person orlegalentitytowhichthisproducthasbeenprovidedtousetheproduct,andthedatageneratedbyuseoftheproduct,onlyforhumandiagnostics.NeitherELITechGroupInc.noritslicensorsgrantsanyotherlicenses,expressedorimpliedforanyotherpurposes.

Some components of nucleic acid analysis,suchasspecificmethodsandcompositionsformanipulatingorvisualizingnucleicacidsforanalysis,maybecoveredbyoneormorepatentsownedbyotherparties.Similarly,nucleicacidscontainingspecificnucleotidesequencesmaybepatented.Making,using,offeringforsale,orselling such components or nucleic acidsmayrequireoneormorelicenses.Nothing in this document should beconstruedasanauthorizationorimplicitlicensetomake,useorsellanyso covered component or nucleic acid underanysuchpatents

5’-CDPI3 MGB™ Phosphoramidite CDPI3 MGB™ CPG

116 117

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LABELING

PSORALEN LABELING

PsoralenC2at the5’-terminusof anoligonucleotide serveseffectivelyasa cross-linking reagent indouble-strandedoligonucleotides.The6atomspacerarmofPsoralenC6allowscross-linkingwithatriplexoligonucleotidestrand.ClickChemistrywithpsoralenazideandoneofourmanynucleosidicandnon-nucleosidicalkynederivativeshasthepotentialtogenerateavarietyofpracticalcross-linkers.Thewellknownreversiblecross-linkingbehaviorofpsoralenwithanadjacentthymidineresiduecouldbeveryuseful.


PsoralenC2Phosphoramidite 10-1982-90 100µmole 195.00 10-1982-02 0.25g 495.00

PsoralenC6Phosphoramidite 10-1983-90 100µmole 195.00 10-1983-02 0.25g 495.00

PsoralenAzide 50-2009-92 25µmole 115.00 50-2009-90 100µmole 350.00

EDTA LABELING

EDTA-C2-dTphosphoramiditecontainsthetriethylesterofEDTAwhichallowssequence-specificcleavageofsingle-anddouble-strandedDNAandRNA. Thecleavagereactionisonly initiatedonceFe(II)anddithiothreitolareaddedandsoisreadilycontrolled.CouplingofEDTA-dTisnormalbutcleavageanddeprotectionshouldbecarriedoutwithsodiumhydroxideinaqueousmethanol(0.4MNaOHinmethanol/water4:1)overnightatroomtemperature.


EDTA-C2-dT-CEPhosphoramidite 10-1059-95 50µmole 250.00 10-1059-90 100µmole 495.00 10-1059-02 0.25g 975.00




Expedite EMerMade M




Psoralen C2 Psoralen C6

OO

CH 3

CH 3

CH 3

O

OO P N(iPr)2

O CNEtOO

CH 3

CH 3

CH 3

O

O

CNEtON(iPr)2PO

O O

N3

O

Psoralen Azide EDTA-C2-dT

O

O P N(iPr)2O CNEt

DMTO

NNH

NH

O

O

N

HN O OEt

O

NOEt

O

O

EtOO

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

NH

HN

O

O Fe

Ferrocene-dT

S+

N

N N

OO N

O

OClO4

-

Methylene Blue NHS Ester

LABELING

S

N

ClN N

DMTO O P N(iPr)2

O CNEt

Methylene Blue II


MethyleneBlueIIiscoveredunderpatentapplicationsFR1251739andPCT/FR2013/050356 and is sold under licensefromtheUniversityofLyon.

FERROCENE LABELING

Withanexcellent stabilityprofile, ferrocenehasalwaysattractedconsiderable interest forDNA labeling togenerateprobes forelectrochemicaldetection. BasedonourAmino-ModifierC6-dTstructure,Ferrocene-dT iseasilyaddedtooligonucleotideswithnodisruptionofregularhybridizationbehavior.Multipleincorporationsintoanoligonucleotideprobearealsosimplyachieved.Oligonucleotidesaredeprotectedusingstandardtechniques.FerroceneoligonucleotidesshouldbestoredunderArgonandaqueoussolutionsshouldbedegassedimmediately.


Ferrocene-dT-CEPhosphoramidite 10-1576-95 50µmole 170.00 10-1576-90 100µmole 330.00 10-1576-02 0.25g 670.00

METHYLENE BLUE LABELING

MethyleneBlue,whichbelongstothephenothiazinefamilyofdyes,isauniquedyewithavarietyofusefulproperties.Despiteitshighextinctioncoefficientinthevisibleregion(81,000L/mol.cm),itisweaklyfluorescentduetoitshighrateofintersystemcrossingfromtheS1excitedstatetotheT1tripletstate.Thispropertymakesitanexcellentphotosensitizer,andithasbeenusedextensivelytoproducehighlyreactivesingletoxygen.MethylenebluehastheabilitytobothintercalateinduplexDNA,preferringG:CoverT:Abasepairs,andcanactasanelectrochemicalredoxprobe.Methylenebluehasalsobeenshowntobeunmatchedinperformanceasaredox-activereporterforelectrochemicalbiosensors.

Earlier,we introducedMethyleneBlueC3Phosphoramiditebutthisproductprovedtohavequite limitedstabilityandhasbeendiscontinued.Asanalternativeoption,weintroducedMethyleneBlueNHSEstertoallowresearcherstolabelamino-modifiedoligonucleotideswiththisinterestingdye.WiththeencouragementandtechnicalexpertiseofCaroleChaixandhercolleaguesattheUniversityofLyon,wedecidedtoprepareanalternativestructurethatseemedtohaveamuchsuperiorstabilityprofile-MethyleneBlueIIPhosphoramidite.Fortunately,thisstructuredidindeedprovemorestableandwearenowabletoofferagainaMethyleneBluePhosphoramidite.


MethyleneBlueNHSEster 50-1960-23 5.4mg 540.00 (Dissolve5.4mgin60µLofDMSO)

MethyleneBlueIIPhosphoramidite 10-5961-95 50µmole 310.00 10-5961-90 100µmole 595.00 10-5961-02 0.25g 1500.00

118 119

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SEE ALSO

3’-Phosphate CPG on page 82Sulfurizing Reagent on page 41Fluorescein-dT on page 103

120 121

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LABELING WITH METAL CHELATES

2,2’-DipicolylaminePhosphoramiditehasbeendiscontinuedThisproductwasmanufacturedanddevelopedbySyntrixBiosystemsInc.Forfurtherinformation,pleasecontact:

DeanY.Maeda,Ph.D.,M.B.A.Director,ChemistryandPreclinicalDevelopmentSyntrixBiosystems215ClayStNWSteB5Auburn,WA98001tel:253-833-8009ext.23fax:[email protected]

LABELING WITH POLYAROMATIC HYDROCARBONS

Pyreneandperylenearefluorescentpolycyclicaromatichydrocarbonsthathavetheabilitytoform‘excitedstatedimers’knownasexcimers.Thisunstructured,long-wavelengthemissionarisesfromtheformationofacharge-transfercomplexbetweentheexcitedstateandthegroundstateoftwofluorescentmolecules.InPyrene-dUandperylene-dU,thehydrocarbonisattachedatthe5positionofdeoxyuridinethroughatriplebondandiselectronicallycoupledtothedeoxyuridinebase.ThiselectroniccouplingofthebaseandthehydrocarbonmakesthefluorescencesensitivetothebasepairingofthedUportionofthemolecule,allowingthediscriminationbetweenperfectandonebasemismatchedtargets.


Pyrene-dU-CEPhosphoramidite 10-1590-95 50µmole 105.00 10-1590-90 100µmole 210.00 10-1590-02 0.25g 550.00

Perylene-dU-CEPhosphoramidite 10-1591-95 50µmole 150.00 10-1591-90 100µmole 300.00 10-1591-02 0.25g 720.00FLUORESCENT DYES

Absorbance Emission Excimer Maximum Maximum

Pyrene-dU 402nm 472nm 486nmPerylene-dU 473nm 490nm Not Determined

Perylene-dUPyrene-dU

ODMTON

HN

O

O

O P N(iPr)2

O CNEt

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

N

NN

DMTO

O P N(iPr)2

O CNEt

2,2’-Dipicolylamine




Expedite EMerMade M




LABELING

PUROMYCIN CPG

Oneofthemostchallengingrequirementsassociatedwithcombinatorialchemistryistherecoveryofsequenceinformationoftheoligonucleotideorpeptideselectedbythescreeningassay.Amethod1hasbeendevelopedtogenerateafusionproductbetweenmRNAandthepolypeptideitencodesusing in vitrotranslationofsyntheticRNAs3’-labeledwithpuromycin,anantibioticthatmimicstransferRNA.Puromycinbindsintheribosome’sAsite,formsapeptidebondwiththegrowingpeptidechain,andblocksfurtherpeptideelongation.BylinkingpuromycintomRNA,apeptide-RNAfusionproductresultsfromthetranslationofthemessagelinkingtheencodingmRNAwithitspeptideproduct.


PuromycinCPG 20-4040-01 0.1g 120.00 20-4040-10 1.0g 995.00 1µmolecolumns 20-4140-41 Packof4 200.00 0.2µmolecolumns 20-4140-42 Packof4 120.00 10µmolecolumn(ABI) 20-4140-13 Packof1 360.00 15µmolecolumns(Expedite) 20-4140-14 Packof1 540.00

QUENCHED AUTOLIGATION (QUAL) PROBES

QUALprobes1consistoftwooligonucleotides,thefirstcontaininganucleophilicgroupatthe3’-terminus,whilethesecondhasanelectrophilicgroupatthe5’-terminus.Whentheprobepairfindsthetarget,theoligoslineupwiththe3’-terminusofthefirstdirectlyadjacenttothe5’-terminusofthesecond.Anautoligationreactionthentakesplacetocombinethetwooligosintoasingleprobe.Asusual,the3’nucleophilicgroupisthe3-thiophosphate,easilypreparedusing3’-phosphateCPGwithasulfurizingstepinthefirstcycle.Inthiscase,theelectrophilicgroupisa5’-dabsylgroup,whichisanexcellentleavinggroupaswellasafinequencheroffluorescence.Thesecondoligo,therefore,containsafluorophorewhichisquenchedbythedabsylgroup.Apopularchoiceforfluorophoreisfluorescein-dTbutitiseasytoimaginethatavarietyoffluorophorescouldbeattachedtoanyofthecommerciallyavailableamino-modifiednucleosidephosphoramidites.


5’-Dabsyl-dT-CEPhosphoramidite 10-1532-90 100µmole 250.00 10-1532-02 0.25g 775.00

Puromycin CPG

OCH 3

succinyl-lcaa-CPG

ODMTO

O

N

N

N

N

N(CH 3)2

ONHCOCF 3

H

NH

LABELING

REFERENCE

(1)R.W.RobertsandJ.W.Szostak,Proc. Natl. Acad. Sci. USA, 1997, 94,12297-302.

i

5’-Dabsyl-dT

REFERENCE

(1)S.SandoandE.T.Kool,J Amer Chem Soc, 2002, 124,2096-2097.

[email protected]

N

ODMTO

O P N(iPr)2

O CNEt

CN

3-Cyanovinylcarbazole

REFERENCES

(1)Y.Yoshimura,andK.Fujimoto,Org Lett, 2008, 10,3227-30.

(2)K.Fujimoto,K.Konishi-Hiratsuka,T.Sakamoto,andY.Yoshimura,ChemBioChem, 2010, 11,1661-4.

(3)Y.Yoshimura,T.Ohtake,H.Okada,andK.Fujimoto,ChemBioChem, 2009, 10, 1473-6.

LABELING WITH ULTRAFAST PHOTO CROSS-LINKER

When3-cyanovinylcarbazolenucleoside(CNVK)isincorporatedintoanoligonucleotide,veryrapidphoto cross-linkingtothecomplementarystrandcanbeinducedatonewavelengthandrapidreversalofthecross-linkispossibleatasecondwavelength.NeitherwavelengthhasthepotentialtocausesignificantDNAdamage.IrradiationofaduplexcontainingasingleincorporationofCNVKat366nmledto100%cross-linkingtothyminebasein1second,althoughcompletecross-linkingtocytosinetakes25seconds.1A30secondirradiationtimeshouldcoverallsituations.Inaddition,itwasdemonstratedthatthepurinebaseswereunreactivetocross-linking,allowingdifferentiationbetweenpyrimidinesandpurinesatthetargetsite.TheauthorsalsodeterminedtheeffectofsequencecontextsaroundtheCNVK site and demonstrated that the identityofbasesoneithersideofthecross-linkingsitehaslittleeffectonthereaction.Oncecross-linked,theUVmeltingtemperatureoftheduplexwasraisedbyaround30°Crelativetotheduplexbeforeirradiation.Completereversalofthecross-linktakesplaceat312nmin3minutes.Thisfacilereversalreactionis,therefore,accomplishedwithnodamagetonormalDNA.

Inalaterpublication,afurtherapplicationofthiscross-linkingtechniquewasinvestigated.2 When CNVKwascross-linkedwithadCresidueinduplexDNA,heatingat90°Cfor3.5hoursledtodeaminationofthecytosinebasetoformuracilinthecomplementarystrand.Reversalofthecross-linkat312nmledtoaDNAstrandinwhichdChadbeenconvertedtodU.TheauthorsshowedthatthistransformationisspecificforthedCresidueoppositetheCNVKandanyfurtheradjacentdCresiduesareunaffected.Similarly,theauthorshaveshownthatCNVKcanbecross-linkedtoanadjacentRNAstrand.3


3-CyanovinylcarbazolePhosphoramidite 10-4960-95 50µmole 200.00 (CNVK) 10-4960-90 100µmole 390.00 10-4960-02 0.25g 1125.00

122 123

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LABELING FOR PHOTO-REGULATION OF OLIGONUCLEOTIDES

Photo-control,theuseofultravioletorvisiblelighttocontrolareaction,hasanumberofadvantagesoverotherexternalstimuli:

• Lightdoesnotintroducecontaminantsintothereactionsystem,• Excitationwavelengthcanbecontrolledthroughthedesignofthephoto-responsivemolecule,and• Itisnowstraightforwardtocontrolirradiationtimeand/orlocalexcitation. Whenaphoto-responsivemoleculeisdirectlyattachedtoDNAasareceptor,photo-regulationofthebioprocessregulatedbythatDNAmoleculecould,inprinciple,beachieved.Suchphoto-responsiveDNAcouldalsobeusedasaswitchinaDNA-basednano-machine.ProfessorHiroyukiAsanumaandhisgroupatthedepartmentofMolecularDesignandEngineeringof the Graduate School of Engineering of the NagoyaUniversity(Japan)havedevelopedanefficientmethodtoachievethisgoal.TheyhaveattachedazobenzenetoDNAandmadeitphoto-responsive1,2.Azobenzeneisatypicalphoto-responsivemolecule that isomerizes from its planar trans-formtothenon-planarcis-formafterUV-lightirradiationwithawavelengthbetween300nmand400nm (lmaxisaround330nm).Interestingly,thesystemrevertsfromthecis-formtothetrans-formafterfurtherirradiationwithvisiblelight(wavelengthover400nm).Thisprocessiscompletelyreversible,andtheazobenzenegroupdoesnotdecomposeorinduceundesirablesidereactionsevenonrepeatedtrans-cisisomerization.ByintroducingazobenzenesintoDNAthroughD-threoninolasalinker,Asanumaandco-workerssucceededinachievingphoto-regulationof:

• FormationanddissociationofaDNAduplex3,4 and • TranscriptionbyT7-RNApolymerasereaction5,6,7.


AzobenzenePhosphoramidite 10-5800-95 50µmole 105.00 10-5800-90 100µmole 200.00 10-5800-02 0.25g 550.00

LABELING

REFERENCES

(1)H.Asanuma,etal.,Angew Chem Int Ed, 2001, 40,2671-2673.

(2)T.Takarada,etal.,Chem Lett., 2001, 30, 732.

(3)H.Asanuma,X.G.Liang,T.Yoshida,andM.Komiyama,Chembiochem, 2001, 2, 39-44.

(4)H.Asanuma,D.Matsunaga,andM.Komiyama,NUCLEIC ACIDS SYMP SER (OXF), 2005, 49,35.

(5)H.Asanuma,etal.,Chembiochem, 2002, 3,786.

(6)M.Liu,H.Asanuma,andM.Komiyama,J. Amer. Chem. Soc., 2006 , 128,1009.

(7)H.Asanuma,etal.,Nature Protocols, 2007, 2,203-212.

NN

O

NH

DMTO

H3CO

P

O

N(iPr)2

CNEt

Azobenzene Phosphoramidite




Expedite EMerMade M




LABELING

124 125

RNA

AND

2’-O

Me-

RNA

RNA SUPPORTS

ABBREVIATIONS

Ac=Acetyl Bz=Benzoyl CNEt=Cyanoethyl CPG = Controlled Pore Glass DMT=4,4’-Dimethoxytrityl

RNA SUPPORTS FOR 3’ MODIFICATION

GlenResearchoffersRNAsupportsinwhichprotectedribonucleosidesareattachedtoCPG.With5’-DMTprotection,andallotherprotectinggroupsbase-labile,theuseofthesesupportsisidenticaltoDNAsupports.Thesesupportsaresuitableforuseinproducingoligodeoxynucleotidesmodifiedatthe3’-terminusoroligoribonucleotides.ABI-stylecolumnsaresuppliedunlessotherwiserequested(seenotebox).


Bz-A-RNA-CPG 20-3303-01 0.1g 40.00 20-3303-02 0.25g 95.00 20-3303-10 1.0g 355.00 1µmolecolumns 20-3403-41 Packof4 100.00 0.2µmolecolumns 20-3403-42 Packof4 75.00 10µmolecolumns(ABI) 20-3403-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3403-14 Packof1 300.00

Ac-C-RNA-CPG 20-3315-01 0.1g 40.00 20-3315-02 0.25g 95.00 20-3315-10 1.0g 355.00 1µmolecolumns 20-3415-41 Packof4 100.00 0.2µmolecolumns 20-3415-42 Packof4 75.00 10µmolecolumn(ABI) 20-3415-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3415-14 Packof1 300.00 Ac-G-RNA-CPG 20-3324-01 0.1g 40.00 20-3324-02 0.25g 95.00 20-3324-10 1.0g 355.00 1µmolecolumns 20-3424-41 Packof4 100.00 0.2µmolecolumns 20-3424-42 Packof4 75.00 10µmolecolumn(ABI) 20-3424-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3424-14 Packof1 300.00

U-RNA-CPG 20-3330-01 0.1g 40.00 20-3330-02 0.25g 95.00 20-3330-10 1.0g 355.00 1µmolecolumns 20-3430-41 Packof4 100.00 0.2µmolecolumns 20-3430-42 Packof4 75.00 10µmolecolumn(ABI) 20-3430-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3430-14 Packof1 300.00

Bz-A-CPG Ac-C-CPG U-CPG

ODMTO

O OAc

NHBz

N

N

N

N

succinyl-CPG succinyl-CPG

ODMTO

O OAc

NHAc

O N

N

ODMTO

O OAc

O

O

N

HN

succinyl-CPG

ODMTO

O

succinyl-CPG

OAc

HN

N

N

O

NAcHN

Ac-G-CPG

LABELING

126 127

RNA

AND

2’-O

Me-

RNA

RNA SYNTHESIS

TOM-Protecting-Group™

O OSi

2'-

TOM-RNA Phosphoramidites are supplied under agreement with QIAGEN. RNA synthesis using the TOM-Protecting-Group is covered by US Patent No. 5,986,084.

TOM-Protecting-Group is a trademark

of QIAGEN.

TOM-PROTECTED RNA PHOSPHORAMIDITES

RNAsynthesisusingmonomerscontainingthe2’-O-TriisopropylsilylOxyMethyl(TOM)group(TOM-Protecting-Group™)ischaracterizedbyveryhighcouplingefficiencyalongwithfast,simpledeprotection.HighcouplingefficiencyisachievedbecausetheTOM-Protecting-Groupexhibitslowersterichindrancethanthe2’-O-t-butyldimethylsilyl(TBDMS)groupusedinouralternativeRNAmonomers.Fastandreliabledeprotectionisachievedusingmethylamineinethanol/wateratroomtemperature.AfurtherfeatureoftheTOM-Protecting-Groupisthatduringbasicstepsitcannotundergo2’to3’migration.Thismigrationunderbasicconditionsleadstonon-biologicallyactive2’-5’linkageswhenusingtheTBDMSgroup.ThesefeaturesallowtheTOM-Protectedmonomerstoproducelongeroligonucleotides.TOM-ProtectedRNAmonomersarealsofullycompatiblewithminorbaseswith2’-O-TBDMSprotection.


A-TOM-CEPhosphoramidite 10-3004-02 0.25g 75.00 10-3004-05 0.5g 150.00 10-3004-10 1.0g 275.00 C-TOM-CEPhosphoramidite 10-3014-02 0.25g 75.00 10-3014-05 0.5g 150.00 10-3014-10 1.0g 275.00

G-TOM-CEPhosphoramidite 10-3024-02 0.25g 75.00 10-3024-05 0.5g 150.00 10-3024-10 1.0g 275.00

U-TOM-CEPhosphoramidite 10-3034-02 0.25g 75.00 10-3034-05 0.5g 150.00 10-3034-10 1.0g 275.00

RNA SUPPORTS FOR TOM RNA SYNTHESIS


Ac-A-RNA-CPG 20-3304-01 0.1g 40.00 20-3304-02 0.25g 95.00 20-3304-10 1.0g 355.00 1µmolecolumns 20-3404-41 Packof4 100.00 0.2µmolecolumns 20-3404-42 Packof4 75.00 10µmolecolumn(ABI) 20-3404-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3404-14 Packof1 300.00

A-TOM C-TOM G-TOM U-TOM

O

O P N(iPr)2O CNEt

DMTO

OTOM

NHAc

N

N

N

N

O

O P N(iPr)2O CNEt

DMTO

OTOM

NHAc

O N

N

O

O P N(iPr)2O CNEt

DMTO

OTOM

AcHN

O

N

N

N

HN

O

O P N(iPr)2O CNEt

DMTO

OTOM

O

O

N

HN





Expedite EMerMade M




RNA SUPPORTS FOR TOM RNA SYNTHESIS (CONT.)


Ac-C-RNA-CPG 20-3315-01 0.1g 40.00 20-3315-02 0.25g 95.00 20-3315-10 1.0g 355.00 1µmolecolumns 20-3415-41 Packof4 100.00 0.2µmolecolumns 20-3415-42 Packof4 75.00 10µmolecolumn(ABI) 20-3415-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3415-14 Packof1 300.00

Ac-G-RNA-CPG 20-3324-01 0.1g 40.00 20-3324-02 0.25g 95.00 20-3324-10 1.0g 355.00 1µmolecolumns 20-3424-41 Packof4 100.00 0.2µmolecolumns 20-3424-42 Packof4 75.00 10µmolecolumn(ABI) 20-3424-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3424-14 Packof1 300.00


RNA SYNTHESIS

128 129

RNA

AND

2’-O

Me-

RNA

Ac-C-CE PhosphoramiditeBz-A-CE Phosphoramidite

RNA SYNTHESIS

ABBREVIATIONS

Bz=Benzoyl CNEt=Cyanoethyl CPG = Controlled Pore Glass dmf=Dimethylformamidine DMT=4,4’-Dimethoxytrityl iPr=Isopropyl lcaa=longchainalkylamino Pac=Phenoxyacetyl PhOAc=Phenoxyacetyl TBDMS=t-Butyl-dimethylsilyl

TBDMS-PROTECTED RNA PHOSPHORAMIDITES

Glen Research CE (ß-cyanoethyl) Phosphoramidites for RNA synthesis are produced and packaged to ensure the highest performance on commercial synthesizers. Every batch is accompanied by a Certificate of Analysis and an HPLC trace, showing the results of our QC testing. RNA Phosphoramidites are synthesis-tested with a minimum coupling efficiency of 97%. Glen Research RNA monomers are packaged in industry standard vials which are specially cleaned to eliminate particulate contamination. These monomers are available in a variety of packs, including high throughput (HT) and low cost (LC). An UltraMild set is also available for situations where sensitive bases are in use. Dmf-G (10-3029) has been discontinued and may be substituted with Ac-G (10-3025).


Bz-A-CE Phosphoramidite 10-3003-02 0.25g 40.00 10-3003-05 0.5g 80.00 10-3003-10 1.0g 160.00 Ac-C-CE Phosphoramidite 10-3015-02 0.25g 40.00 10-3015-05 0.5g 80.00 10-3015-10 1.0g 160.00

Ac-G-CE Phosphoramidite 10-3025-02 0.25g 40.00 10-3025-05 0.5g 80.00 10-3025-10 1.0g 160.00

U-CE Phosphoramidite 10-3030-02 0.25g 40.00 10-3030-05 0.5g 80.00 10-3030-10 1.0g 160.00

RNA PHOSPHORAMIDITES - SPECIAL PACKAGING

We offer our high quality DNA phosphoramidites specifically packaged for high throughput and large-scale synthesis customers. These customers normally require high quality materials produced under the guidelines of a validated quality management system while still being priced aggressively. These products include the usual Glen Research certification and guarantees and they are available in larger packs or in bulk. The core catalog numbers for regular DNA phosphoramidites are shown below. For these products, please request a quote.


Bz-A-CE Phosphoramidite 10-3003-SPAc-C-CE Phosphoramidite 10-3015-SPAc-G-CE Phosphoramidite 10-3025-SPU-CE Phosphoramidite 10-3030-SP

N

N

N

N

NHBz

ODMTO

O

CNEtON(iPr)2P

OTBDMS

ODMTO

OTBDMSO

NHAc

O N

N

P N(iPr)2O CNEt

INSTRUMENT TYPES

Glen Research packages these monomersinavarietyofindustry-standardvialsandbottles.Pleaseprovidetheexactspecificationofthebottlerequiredpriortoreceivingaquotation.

U-CE Phosphoramidite

DMTO O

O

O

N

HN

O

P N(iPr)2O CNEt

OTBDMS

Ac-G-CE Phosphoramidite

ODMTO

O P N(iPr)2

OH

OTBDMS

HN

N

N

O

NAcHN

ULTRAMILD TBDMS RNA PHOSPHORAMIDITES


Pac-A-CEPhosphoramidite 10-3000-02 0.25g 75.00 10-3000-05 0.5g 150.00 10-3000-10 1.0g 275.00 Ac-C-CEPhosphoramidite 10-3015-02 0.25g 40.00 10-3015-05 0.5g 80.00 10-3015-10 1.0g 160.00

iPr-Pac-G-CEPhosphoramidite 10-3021-02 0.25g 75.00 10-3021-05 0.5g 150.00 10-3021-10 1.0g 275.00

U-CEPhosphoramidite 10-3030-02 0.25g 40.00 10-3030-05 0.5g 80.00 10-3030-10 1.0g 160.00

TBDMS RNA SUPPORTS

ABI-stylecolumnsaresuppliedfor1µmoleand0.2µmolescalesunlessotherwiserequested(seenotebox).


Pac-A-RNA-CPG 20-3300-01 0.1g 40.00 20-3300-02 0.25g 95.00 20-3300-10 1.0g 355.00 1µmolecolumns 20-3400-41 Packof4 100.00 0.2µmolecolumns 20-3400-42 Packof4 75.00 10µmolecolumn(ABI) 20-3400-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3400-14 Packof1 300.00

Bz-A-RNA-CPG 20-3303-01 0.1g 40.00 20-3303-02 0.25g 95.00 20-3303-10 1.0g 355.00 1µmolecolumns 20-3403-41 Packof4 100.00 0.2µmolecolumns 20-3403-42 Packof4 75.00 10µmolecolumn(ABI) 20-3403-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3403-14 Packof1 300.00

RNA SYNTHESIS

U-CE Phosphoramidite

DMTO O

O

O

N

HN

O

P N(iPr)2O CNEt

OTBDMS

Pac-A-CE Phosphoramidite

DMTO O

NHAcOPh

N

N

N

N

O

P N(iPr)2O CNEt

OTBDMS

Ac-C-CE Phosphoramidite iPr-Pac-G-CE Phosphoramidite

ODMTO

OTBDMSO

NHAc

O N

N

P N(iPr)2O CNEt

HN

N

N

N

O

HNDMTO O

O

P N(iPr)2O CNEt

iPr-PhOAc

OTBDMS




Expedite EMerMade M




SEE ALSO

Minor TBDMS monomers on page 133Pyrrolo-CTP on page 136rSpacer TBDMS on page 134

130 131

RNA

AND

2’-O

Me-

RNA

TBDMS RNA SUPPORTS (CONT.)


Ac-C-RNA-CPG 20-3315-01 0.1g 40.00 20-3315-02 0.25g 95.00 20-3315-10 1.0g 355.00 1µmolecolumns 20-3415-41 Packof4 100.00 0.2µmolecolumns 20-3415-42 Packof4 75.00 10µmolecolumn(ABI) 20-3415-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3415-14 Packof1 300.00

iPr-Pac-G-RNA-CPG 20-3321-01 0.1g 40.00 20-3321-02 0.25g 95.00 20-3321-10 1.0g 355.00 1µmolecolumns 20-3421-41 Packof4 100.00 0.2µmolecolumns 20-3421-42 Packof4 75.00 10µmolecolumn(ABI) 20-3421-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3421-14 Packof1 300.00

Ac-G-RNA-CPG 20-3324-01 0.1g 40.00 20-3324-02 0.25g 95.00 20-3324-10 1.0g 355.00 1µmolecolumns 20-3424-41 Packof4 100.00 0.2µmolecolumns 20-3424-42 Packof4 75.00 10µmolecolumn(ABI) 20-3424-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3424-14 Packof1 300.00






RNA SYNTHESIS




Expedite EMerMade M




MINOR RNA PHOSPHORAMIDITES (TOM PROTECTED)

GlenResearchoffersminorRNAphosphoramiditeswitheitherTOMorTBDMSprotectinggroups.4-Thio-U,5-Methyl-Cytidine,and2-Amino-AdenosineareusefulforanalyzingRNAstructureandactivityrelationships,forexample,inribozymestudies.

Pyrrolo-C is afluorescentnucleosidewhosefluorescence is sensitive to itsenvironmentand is ideal forprobingRNAstructure.Itbase-pairsasanormalCnucleotide.Itishighlyfluorescentanditsexcitationandemissionarewelltotheredofmostfluorescentnucleotideanalogs,whicheliminatesorreducesbackgroundfluorescencefromproteins.Pyrrolo-CTPhaspotentialusesinbiologicalassaydevelopment.

rSpacerisusedtointroduceanabasicsitetoanRNAsequence.TheTOMprotectedversionhasbeendiscontinuedandisreplacedwiththeTBDMSversion.

Theprotectingschemefor2,6-Diaminopurinehasbeenchangedandtheoriginalproduct(10-3084)hasbeenreplacedwiththeoptimizedproduct(10-3085)below.


4-Thio-U-TOM-CEPhosphoramidite 10-3052-95 50µmole 212.50 10-3052-90 100µmole 425.00 10-3052-02 0.25g 975.00

5-Me-C-TOM-CEPhosphoramidite 10-3064-95 50µmole 95.00 10-3064-90 100µmole 190.00 10-3064-02 0.25g 475.00 2,6-Diaminopurine-TOM-CEPhosphoramidite 10-3085-95 50µmole 212.50 (2-amino-A) 10-3085-90 100µmole 425.00 10-3085-02 0.25g 975.00

MINOR RNA BASES

2,6-diaminopurine-TOM5-Me-C-TOM4-Thio-U-TOM

ODMTO

N

N

S

O

O P N(iPr)2

O CNEt

OTOM

CN

O

O P N(iPr)2O CNEt

DMTO

OTOM

NHAc

O N

NMe

ODMTO

O P N(iPr)2

O CNEt

OTOM

N

N

N

NMeOAcHN

NHiBu

SEE ALSO

Pyrrolo-dC on page 68Pyrrolo-CTP on page 136

SEE ALSO

Minor TOM monomers on page 131

132 133

RNA

AND

2’-O

Me-

RNA

MINOR RNA PHOSPHORAMIDITES (TOM PROTECTED) (CONT.)


Pyrrolo-C-TOM-CEPhosphoramidite 10-3017-95 50µmole 212.50 10-3017-90 100µmole 425.00 10-3017-02 0.25g 975.00

rSpacerCEPhosphoramidite 10-3914-95 50µmole DISCONTINUED (SeerSpacerTBDMSCEPhosphoramidite) 10-3914-90 100µmole 10-3914-02 0.25g

RNA SEQUENCE MODIFIER (TOM PROTECTED)

Amino-ModifierC6-UhasbeenaddedtothegrowingfamilyofsequencemodifiersandweenvisageapplicationsinRNAstructuralstudiesaswellasforlabelingsiRNAtoprobeuptakeandcellulardistribution.


Amino-ModifierC6-UPhosphoramidite 10-3039-95 50µmole 360.00 10-3039-90 100µmole 720.00 10-3039-02 0.25g 1475.00

O

O P N(iPr)2O CNEt

DMTO O N

N

OTOM

HN

O

O P N(iPr)2O CNEt

DMTO

OTOM

rSpacerPyrrolo-C-TOM

MINOR RNA BASES

HN

N

O

O

NHNHCCF 3

O O

DMTO

CNEtON(iPr)2PO

O

OTOM

Amino-Modifier C6-U




Expedite EMerMade M




MINOR RNA BASES

Br-U I-U

O

OP N(iPr)2O CNEt

DMTO

Br

O

O

N

HN

OTBDMS

I

O

O

DMTON

HN

O

O

OTBDMS

P N(iPr)2O CNEt

REFERENCES

(1)C.J.Adams,J.B.Murray,M.A.Farrow,J.R.P.Arnold,andP.G.Stockley,Tetrahedron Lett., 1995, 36,5421-5424.

(2)D.A.Berry,etal.,Tetrahedron Lett, 2004, 45,2457-2461.

iBuHN

N

N

N

N

S

DMTO

CNEtON(iPr)2PO

O

CN

OTBDMS

6-Thio-G

MINOR RNA PHOSPHORAMIDITES (TBDMS PROTECTED)

Inosineand5-Methyl-Uridineareuseful foranalyzingRNAstructureandactivity relationships. 5-Bromo-Uridineand5-Iodo-Uridinehavebeenusedforcrystallographystudiesandcross-linkingexperiments.6-Thioguanosine(6-thio-G)hasapplicationsinribozymeandsiRNAresearch,aswellasinRNA-proteininteractions.Theremovalofthesilylprotectinggroupwithoutinterferingwiththesulfuriscritical.Thisisremoved1cleanlybytriethylaminetrihydrofluorideinDMSObut t-butylammoniumfluoride (TBAF) leads todegradationof the thio-nucleotideanalogueand shouldnotbeused.2-AminopurineribosideisusefulforanalyzingRNAstructureandactivityrelationships,forexample,inribozymestudies.


I-CEPhosphoramidite 10-3040-95 50µmole 95.00 10-3040-90 100µmole 190.00 10-3040-02 0.25g 475.00 5-Me-U-CEPhosphoramidite 10-3050-95 50µmole 95.00(T) 10-3050-90 100µmole 190.00 10-3050-02 0.25g 475.00

Br-U-CEPhosphoramidite 10-3090-95 50µmole 98.00 10-3090-90 100µmole 195.00 10-3090-02 0.25g 475.00

I-U-CEPhosphoramidite 10-3091-95 50µmole 98.00 10-3091-90 100µmole 195.00 10-3091-02 0.25g 475.00

6-Thio-G-CEPhosphoramidite 10-3072-95 50µmole 250.00 10-3072-90 100µmole 500.00 10-3072-02 0.25g 1200.00

2-Aminopurine-CEPhosphoramidite 10-3070-95 50µmole 212.50 10-3070-90 100µmole 425.00 10-3070-02 0.25g 975.00

5-Me-U

HN

N

O

O

CH 3

DMTO

CNEtON(iPr)2PO

O

OTBDMS

Inosine

O

O P N(iPr)2O CNEt

DMTO

O

N

N

N

HN

OTBDMS

N

N N

N

ODMTO

O P N(iPr)2

O CNEt

NH

O

OTBDMS

2-Aminopurine

SEE ALSO

5-Me-C on page 131Pseudouridine on page 134

134 135

RNA

AND

2’-O

Me-

RNA

MINOR RNA (TBDMS PROTECTED) (CONT.)

8-Aza-7-deaza-Adenosine is an isomerofAdenosinewithvirtually identicalelectrondensity. TheN7nitrogen isnotavailableforhydrogenbonding.

Ribozymeactivityissubstantiallyaffectedbythesubstitutionofmodifiedpyrimidinebases.Zebularine(pyrimidin-2-oneribonucleoside)mayberegardedasaCytidinederivativelackingtheexocyclicaminogroup.ZebularineandPyridin-2-oneRibonucleoside, the3-deazaanalogueofZebularine,areprimecandidates foruse inevaluating ribozymeactivityandfunction.ItshouldbenotedthatZebularineismildlyfluorescent,absorbingat298nmandemittingat367nm.

PseudoUridineisoneofthemostcommonmodifiednucleosidesfoundinRNA.TheavailabilityofaphosphoramiditewillallowdetailedresearchintotheeffectsofthismodifiedbaseonRNAstructureandactivity.

rSpacerisusedtointroduceanabasicsitetoanRNAsequence.


Zebularine-CEPhosphoramidite 10-3011-95 50µmole 125.00 10-3011-90 100µmole 250.00 10-3011-02 0.25g 650.00

Pyridin-2-one-CEPhosphoramidite 10-3012-95 50µmole 210.00 10-3012-90 100µmole 420.00 10-3012-02 0.25g 1200.00

PseudoUridine-CEPhosphoramidite 10-3055-95 50µmole 175.00 10-3055-90 100µmole 350.00 10-3055-02 0.25g 995.00 8-Aza-7-deaza-A-CEPhosphoramidite 10-3083-95 50µmole 300.00 10-3083-90 100µmole 600.00 10-3083-02 0.25g 1500.00

rSpacerTBDMSCEPhosphoramidite 10-3915-95 50µmole 80.00 10-3915-90 100µmole 135.00 10-3915-02 0.25g 395.00

Pyridin-2-one PseudoUridineZebularine 8-Aza-7-deaza-A

ODMTO

O P N(iPr)2

O CNEt

OTBDMS

N

NOODMTO

O P N(iPr)2

O CNEt

OTBDMS

NOODMTO

O P N(iPr)2

O CNEt

OTBDMS

HN NH

O

O

ODMTO

O P N(iPr)2

O CNEt

OTBDMS

N

N NN

N N




Expedite EMerMade M




MINOR RNA BASES

ODMTO

O P N(iPr)2

O CNEt

OTBDMS

rSpacer TBDMS


Methylationofadenosineatposition1producesadrasticfunctional changeinthenucleobase.1-Methyladenosine(pKa 8.25)isa muchstrongerbasethanadenosine(pKa3.5). N-1methylation excludesparticipationoftheadeninebaseincanonical Watson–Crick basepairingandprovidesapositivechargetothenucleobase.Thismodificationalsoaltersthehydrophobicityofthebase,thestackingproperties,theorderingofwatermoleculesandthechelationproperties. Thebasemaybecomeinvolvedinnon-canonicalhydrogenbonding, inelectrostaticinteractionsand,ingeneral,itmaycontribute to theconformationaldynamicsofthetRNA.

Inthecentraldogmaofmolecularbiology,geneticinformationflowsfromDNAtoRNAandthentoprotein.ReversibleepigeneticmodificationsongenomicDNAandhistonehavebeenknowntosubstantiallyregulategeneexpression.Ontheotherhand,thereexistsmorethan100naturallyoccurringchemicalmodificationsinRNA;however,thefunctionsoftheseRNAmodificationsarelargelyunknown.WhethersomeofthesemodificationsinRNAcanbereversedandcouldimpactgeneexpressioninthecentraldogmawasunknownuntiltherecentdiscoveryofN6-methyladenosine(N6-Me-A)asthefirstexampleofreversibleRNAmethylation.1WeoffertheN6-Me-ARNAmonomerwithaphenoxyacetylprotectinggrouptominimizepotentialbranching.WehaveshownN6-Me-A-CEPhosphoramiditetobecompletelycompatiblewithallpopularRNAsynthesisanddeprotectionmethods,fromUltraMildtothemostpopularprocedureusingAMAfordeprotection.


1-Me-A-CEPhosphoramidite 10-3501-95 50µmole 190.00 10-3501-90 100µmole 380.00 10-3501-02 0.25g 975.00

N6-Me-A-CEPhosphoramidite 10-3005-95 50µmole 285.00 10-3005-90 100µmole 550.00 10-3005-02 0.25g 1295.00

RNAmethylationoccursinalargeselectionofRNAnucleosidesandthisposttranscriptionalmodificationofRNA,carriedoutbyavarietyofRNAmethyltransferases,appearsinawidevarietyofRNAspecies-includingtRNA,mRNA,miRNAandRNAviruses.Over90methylatednucleosideshavebeenfoundintRNAandtheseplaymanysignificantrolesintRNAstructure.Inaddition,methylationappearstomarkthetRNAasmature,preventingitsdegradationaswellasdirectinglocalizationwithinthecell.mRNA,modifiedwith1-methylpseudouridine(1-Me-Y)aloneorincombinationwith5-methylcytidine(5-Me-C),significantlyincreasesproteinexpressionincellsandmousemodels.1-Me-YisalsoamodifiednucleobasethatcangreatlyenhancethepropertiesofmRNAbyreducingimmunogenicityandincreasingstability.


1-Me-PseudouridinePhosphoramidite 10-3056-95 50µmole 420.00 10-3056-90 100µmole 820.00 10-3056-02 0.25g 2300.00

1-Me-A

REFERENCE

(1)Y.Fu,D.Dominissini,G.Rechavi,andC.He, Nat Rev Genet, 2014, 15,293-306.

N

N N

N

N

ODMTO

O

P N(iPr)2

O CNEt

OTBDMS

PhO

O

CH3

N6-Me-A

MINOR RNA BASES

ODMTO

O P N(iPr)2

O CNEt

OTBDMS

HN N

O

O

CH3

1-Me-Pseudouridine

SEE ALSO

Pyrrolo-dC on page 68Pyrrolo-C on page 132

SEE ALSO

tCo on page 70

136 137

RNA

AND

2’-O

Me-

RNA

OH

CH 3

N

NO

NH

OO

PO

PO

PHO

O O O

OH OH OH

OH

Pyrrolo-CTP


ThebrightfluorescenttricycliccytosineanaloguestCandtCOstandoutamongfluorescentbasesduetotheirvirtuallyunquenchedfluorescenceinsidesingle-ordouble-strandedDNA. Untilrecently,thisfamilyoftricycliccytosineshadonlybeenstudiedandusedinDNAcontextsand,importantly,introducedaspossibledonorsofthefirstDNAbaseanalogueFRET-pairwithtCnitro.FluorescentbaseanaloguesforRNAarelimitedinnumbercomparedtotheirDNAcounterparts.Tofacilitatetheapplicationofsuchanalogues,characterizationoftheirstructuralanddynamicsbehaviorinRNAcomparedtothecorrespondingnaturalnucleosideisimportant.WenowintroducethetCOribonucleoside,whichhasbeenincorpratedintoarangeofRNAsequences,whereitwasshowntobeaverypotentandusefulfluorophoreinthiscontext.1 Glen ResearchoffersthisusefulfluorescentribonucleosideanalogueincooperationwithModyBaseHB.


Ribo-tC°-CEPhosphoramidite 10-3517-95 50µmole 245.00 10-3517-90 100µmole 470.00 10-3517-02 0.25g 1195.00

MINOR RNA TRIPHOSPHATES

Pyrrolo-dCisafluorescentnucleosidethatcodesasdCandbasepairsefficientlywithdG.Preliminaryevidenceindicatesthatpyrrolo-dCtriphosphateisanexcellentsubstrateforTaq,PfuandVentpolymerasesandisincorporatedspecificallyoppositedG.Pyrrolo-dCTPhasbeenavailableforsometimeandisinuseinbiologicalassays.Pyrrolo-CTPisafluorescentribonucleotidewithfluorescenceexquisitelysensitivetoitsenvironmentandisofgreatinterestforRNAstructuralresearch.Thepyrrolo-CprojectisajointdevelopmentbyBerryandAssociates,Inc.andGlenResearchCorporation.


Pyrrolo-CTP 81-3017-01 100µL 270.00 10mM

REFERENCE

(1)Füchtbauer,A.F.,Preus,S.,Börjesson,K.,McPhee,S.A.,LilleyD.M.J.,Wilhelmsson,L.M.,Sci. Rep., 2017, 7, 2393.


TheseproductsareofferedincollaborationwithModyBaseHB.

O

N

N

O

O P N(iPr)2

O CNEt

O

HN

DMTO

OTBDMS

Ribo-tC° 2’-OMe-Ac-C 2’-OMe-U2’-OMe-G2’-OMe-C2’-OMe-A

2’-OME-RNA PHOSPHORAMIDITES

GlenResearch2’-OMe-RNACE (ß-cyanoethyl)Phosphoramiditesaredesigned toproduce syntheticoligonucleotidescontainingnucleaseresistant2’-O-methylribonucleotidelinkages. Deprotection, isolationandhandlingof2’-O-methyloligonucleotidesareidenticaltotheproceduresforoligodeoxynucleotides. Item Catalog No. Pack Price($)

2’-OMe-A-CEPhosphoramidite 10-3100-90 100µmole 20.00 10-3100-02 0.25g 50.00 10-3100-05 0.5g 100.00 10-3100-10 1.0g 200.00

2’-OMe-C-CEPhosphoramidite 10-3110-90 100µmole 20.00 10-3110-02 0.25g 50.00 10-3110-05 0.5g 100.00 10-3110-10 1.0g 200.00

2’-OMe-Ac-C-CEPhosphoramidite 10-3115-90 100µmole 20.00 10-3115-02 0.25g 50.00 10-3115-05 0.5g 100.00 10-3115-10 1.0g 200.00

2’-OMe-iBu-G-CEPhosphoramidite 10-3120-90 100µmole 20.00 10-3120-02 0.25g 50.00 10-3120-05 0.5g 100.00 10-3120-10 1.0g 200.00

2’-OMe-G-CEPhosphoramidite 10-3121-90 100µmole 20.00 10-3121-02 0.25g 50.00 10-3121-05 0.5g 100.00 10-3121-10 1.0g 200.00

2’-OMe-U-CEPhosphoramidite 10-3130-90 100µmole 20.00 10-3130-02 0.25g 50.00 10-3130-05 0.5g 100.00 10-3130-10 1.0g 200.00

ODMTO

OMeO

NHBz

N

N

N

N

P N(iPr)2O CNEt

ODMTO

OMeO

NHBz

O N

N

P N(iPr)2O CNEt

P N(iPr)2O CNEt

NHAc

O N

N

ODMTO

OMeO

ODMTO

OMeO

(Me)2NN

O

N

N

N

HN

P N(iPr)2O CNEt

ODMTO

OMeO

O

O

N

HN

P N(iPr)2O CNEt

ODMTO

O

P N(iPr)2

O CNEt

OMe

HN

N

N

NNH

O

O

2’-OMe-iBu-G




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MINOR RNA BASES 2’-OME-RNA SYNTHESIS

138 139

RNA

AND

2’-O

Me-

RNA

ULTRAMILD 2’-OME-RNA

TheuseofUltraMildmonomersinoligonucleotidesynthesishasallowedverysensitivedyeslikeTAMRA,HEXandCy5tobeusedvirtuallyroutinely.TheDNAandRNAmonomersarecurrentlyavailableandwealsoprovidethissetof2’-OMe-RNAmonomers.Inourversionofthischemistry,weuseasprotectinggroupsphenoxyacetyl(Pac)forA,acetyl(Ac)forC,andisopropyl-phenoxyacetyl(iPr-Pac)forG.

Ithasbecomeclearthataceticanhydrideintheconventionalcappingmixcancausetransamidationinsituationswhereanamineprotectinggroupisquitelabile.Thisleadstoacetylprotectionontheaminogroupthatmaybeslowtoberemoved.Consequently,ifmanydGresiduesareincludedintheoligonucleotide,werecommendtheuseofphenoxyaceticanhydride(Pac2O)inCapA.ThismodificationremovesthepossibilityofexchangeoftheiPr-PacprotectinggrouponthedGwithacetatefromtheaceticanhydridecappingmix.


2’-OMe-Pac-A-CEPhosphoramidite 10-3601-02 0.25g 62.50 10-3601-05 0.5g 125.00 10-3601-10 1.0g 250.00

2’-OMe-Ac-C-CEPhosphoramidite 10-3115-02 0.25g 50.00 10-3115-05 0.5g 100.00 10-3115-10 1.0g 200.00

2’-OMe-iPr-Pac-G-CEPhosphoramidite 10-3621-02 0.25g 62.50 10-3621-05 0.5g 125.00 10-3621-10 1.0g 250.00




P N(iPr)2O CNEt

NHAc

O N

N

ODMTO

OMeO

O

O P N(iPr)2O CNEt

OMe

O

N

N

N

HN

DMTO

iPr-PhOAcHN

OMe

DMTO

CNEtON(iPr)2PO

O

NHAcOPh

N

N

N

N

2’-OMe-Pac-A 2’-OMe-Ac-C 2’-OMe-iPr-Pac-G

2’-OME-RNA SUPPORTS

ABI-stylecolumnsaresuppliedfor1µmoleand0.2µmolescalesunlessotherwiserequested(seenotebox).


2’-OMe-A-RNA-CPG 20-3600-01 0.1g 40.00 20-3600-02 0.25g 95.00 20-3600-10 1.0g 355.00 1µmolecolumns 20-3700-41 Packof4 100.00 0.2µmolecolumns 20-3700-42 Packof4 75.00 10µmolecolumn(ABI) 20-3700-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3700-14 Packof1 300.00

2’-OMe-C-RNA-CPG 20-3610-01 0.1g 40.00 20-3610-02 0.25g 95.00 20-3610-10 1.0g 355.00 1µmolecolumns 20-3710-41 Packof4 100.00 0.2µmolecolumns 20-3710-42 Packof4 75.00 10µmolecolumn(ABI) 20-3710-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3710-14 Packof1 300.00

2’-OMe-Ac-C-RNA-CPG 20-3615-01 0.1g 40.00 20-3615-02 0.25g 95.00 20-3615-10 1.0g 355.00 1µmolecolumns 20-3715-41 Packof4 100.00 0.2µmolecolumns 20-3715-42 Packof4 75.00 10µmolecolumn(ABI) 20-3715-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3715-14 Packof1 300.00

2’-OMe-G-RNA-CPG 20-3621-01 0.1g 40.00 20-3621-02 0.25g 95.00 20-3621-10 1.0g 355.00 1µmolecolumns 20-3721-41 Packof4 100.00 0.2µmolecolumns 20-3721-42 Packof4 75.00 10µmolecolumn(ABI) 20-3721-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3721-14 Packof1 300.00

2’-OMe-U-RNA-CPG 20-3630-01 0.1g 40.00 20-3630-02 0.25g 95.00 20-3630-10 1.0g 355.00 1µmolecolumns 20-3730-41 Packof4 100.00 0.2µmolecolumns 20-3730-42 Packof4 75.00 10µmolecolumn(ABI) 20-3730-13 Packof1 225.00 15µmolecolumn(Expedite) 20-3730-14 Packof1 300.00




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2’-OME-RNA SYNTHESIS 2’-OME-RNA SYNTHESIS

140 141

RNA

AND

2’-O

Me-

RNA

MINOR 2’-OME-RNA PHOSPHORAMIDITES

Toaid in theevaluationof thestructuresof2’-OMe-RNAcomplexes,weoffer theCEphosphoramidites listedbelow.2’-OMe-Tisusefulintriplexstudieswhilethe2-aminopurinederivativemaybetestedinribozymestudies.Bysupportinganadditionalhydrogenbond,2,6-diaminopurine(2-amino-adenosine)bindsmorestronglywithuridinethandoesadenosine.Oligonucleotides containing2’-OMe-5-Me-Cand2’-OMe-Iwouldbeof interest to researchers involved in triplexandantisensestudiesusing2’-OMe-RNA.Theusesof2’-OMe-5-bromo-Uphosphoramiditerangefromcrystallographicstudiesduetotheheavyatomtocross-linkingbecauseofitsphotolability.5-Fluoro-pyrimidinenucleosideshavebeenusefulastherapeuticagentsandtheireffectonthestructureandactivityofoligonucleotidesmaybeexaminedusingthe2’-OMe-RNAderivatives.The2,4,6-trimethylphenyl(TMP)protected2’-OMe-Uderivativeisaconvertiblenucleosideandreactionwithammonialeadstothe5-fluoro-dCanalogue.2’-OMe-3-deaza-5-aza-C(ReverseC)derivativehasthepotentialtomimicinoligonucleotides5-azacytidine,aDNAmethylaseinhibitor.ItsabilitytobindasaCwilllikelybediminished. ABI-stylevialsaresuppliedunlessotherwiserequested(seenotebox). Item Catalog No. Pack Price($)

2’-OMe-2-Aminopurine- 10-3123-95 50µmole 177.50CEPhosphoramidite 10-3123-90 100µmole 355.00 (N-dmf-AP) 10-3123-02 0.25g 975.00

2’-OMe-2,6-Diaminopurine- 10-3124-95 50µmole 177.50CEPhosphoramidite 10-3124-90 100µmole 355.00 (2-amino-A) 10-3124-02 0.25g 975.00

2’-OMe-5-Me-U-CEPhosphoramidite 10-3131-90 100µmole 150.00 (2’-OMe-T) 10-3131-02 0.25g 360.00

2’-OMe-5-Me-U2’-OMe-2-amino-A2’-OMe-2-AP

2’-OME-RNA SYNTHESIS

O

O

P N(iPr)2O CNEt

DMTO

OMe

Me2NN N

N

N

N

O

O

P N(iPr)2O CNEt

DMTO

OMe

iBuHN N

N

N

N

NNMe 2

P N(iPr)2O CNEt

ODMTO

OMeO

O

O

N

HNCH 3

2’-OMe-5-Br-U2’-OMe-5-Me-C2’-OMe-I

2’-OMe-TMP-5-F-U 2’-OMe-5-F-U 2’-OMe-3-deaza-5-aza-C


O

O

P N(iPr)2O CNEt

DMTO

OMe

O

N

N

N

HN

ODMTON

N

NHAc

O

O

CH3

P N(iPr)2

O CNEt

OMe

O

OP N(iPr)2O CNEt

DMTO

Br

O

O

N

HN

OMe

O N

NF

O

P N(iPr)2O CNEt

O

O

DMTO

OMe

HN

N

O

O

F

P N(iPr)2O CNEt

O

O

DMTO

OMe

ODMTO

O

CNEtON(iPr)2P

OMe

NMe 2N

O

N

N

MINOR 2’-OME-RNA PHOSPHORAMIDITES (CONT.)


2’-OMe-I-CEPhosphoramidite 10-3140-90 100µmole 150.00 10-3140-02 0.25g 360.00

2’-OMe-5-Me-C-CEPhosphoramidite 10-3160-90 100µmole 240.00 10-3160-02 0.25g 675.00

2’-OMe-5-Br-U-CEPhosphoramidite 10-3190-90 100µmole 240.00 10-3190-02 0.25g 675.00

2’-OMe-TMP-5-F-U-CEPhosphoramidite 10-3111-95 50µmole 177.50 (2’-OMe-5-F-CPrecursor) 10-3111-90 100µmole 355.00 10-3111-02 0.25g 975.00

2’-OMe-5-F-U-CEPhosphoramidite 10-3132-95 50µmole 177.50 10-3132-90 100µmole 355.00 10-3132-02 0.25g 975.00

2’-OMe-3-deaza-5-aza-C-CEPhosphoramidite 10-3116 hasbeendiscontinued.




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SEE ALSO

DNA Thiophosphoramidites on page 40

142 143

RNA

AND

2’-O

Me-

RNA


2’-OME-THIOPHOSPHORAMIDITES

Thephosphorodithioatelinkage(PS2)isbothachiralandessentiallyresistanttonucleases.PreviousstudieshaveshownveryinterestingresultswhichincludeobservationsthatDNAwithPS2linkagesactivatesRNaseHin vitro,stronglyinhibitshumanimmunodeficiencyvirus(HIV)reversetranscriptase,inducesB-cellproliferationanddifferentiation,andiscompletelyresistanttohydrolysisbyvariousnucleases.2’-OMe-RNAThiophosphoramiditesareRNAmonomersdesignedtoproduceoligoscombiningthePS2linkagewiththe2’-O-methylribosemodification.ThesePS2-modifiedRNAoligoshavepotentialforuseinsiRNAsanddithiophosphateaptamers(thioaptamers).


2’-OMe-A-Thiophosphoramidite 10-3170-90 100µmole 300.00 10-3170-02 0.25g 720.00

2’-OMe-C-Thiophosphoramidite 10-3171-90 100µmole 300.00 10-3171-02 0.25g 720.00

2’-OMe-G-Thiophosphoramidite 10-3172-90 100µmole 300.00 10-3172-02 0.25g 720.00

2’-OMe-U-Thiophosphoramidite 10-3173-90 100µmole 300.00 10-3173-02 0.25g 720.00

N

N N

N

NHBz

ODMTO

O

PN SCH2CH2S C

O

COCH3

OMe

ODMTO

O

PN SCH2CH2S C

O

PN SCH2CH2S COCH3

N

N

NHAc

O

OMe

ODMTO

O

PN SCH2CH2S C

O

HN

N

N

O

NiBuHN

OMe

ODMTO

O

PN SCH2CH2S C

O

N

HN

O

O

OMe

2'-OMe-C-Thiophosphoramidite2'-OMe-A-Thiophosphoramidite 2'-OMe-U-Thiophosphoramidite2'-OMe-G-Thiophosphoramidite




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2’-F-RNA PHOSPHORAMIDITES

2’-Deoxy-2’-fluoro-nucleosidesadoptanRNA-typesugarconformation,presumablyduetothehighelectronegativityoffluorine.Becauseofthissugarconformation,RNAduplexes(A-form)aregenerallymorethermodynamicallystablethanDNAduplexes(B-form).Asexpected,theadditionof2’-F-RNAresiduestooligodeoxynucleotidesprogressivelyincreasesthethermalstabilityoftheirduplexeswithRNA.Thestabilizationisadditiveatapproximately2°perresidue.Thiscomparesfavorablywith2’-OMe-RNAataround1.5°andRNAat1.1°perresidue.Inthemeantime,basepairspecificityremainsintact.

2’-F-RNAphosphodiesterlinkagesarenotnucleaseresistant,althoughthecorrespondingphosphorothioatelinkagesarehighlyresistant.ResearchersusuallydesignantisenseoligonucleotidestoformduplexeswithRNA,whicharethensubstratesforRNaseH.Uniformlymodified2’-F-RNA/RNAduplexesarenotsubstratesforRNaseH.However,itisstraightforwardtopreparechimeric2’-F-RNA/DNAphosphorothioateoligonucleotideswhichexhibitenhancedbindingtotheRNAtarget,aresubstratesforRNaseH,andarehighlynucleaseresistant.


2'-F-A-CEPhosphoramidite 10-3400-02 0.25g 100.00 10-3400-05 0.5g 200.00

2'-F-Ac-C-CEPhosphoramidite 10-3415-02 0.25g 50.00 10-3415-05 0.5g 100.00

2'-F-G-CEPhosphoramidite 10-3420-02 0.25g 100.00 10-3420-05 0.5g 200.00

2'-F-U-CEPhosphoramidite 10-3430-02 0.25g 50.00 10-3430-05 0.5g 100.00

2’-F-U

2’-F RNA SYNTHESIS

O

O P N(iPr)2O CNEt

DMTO

F

NHAc

O N

N

O

O P N(iPr)2O CNEt

DMTO

F

O

O

N

HNN

N

N

N

NHBz

O

O P N(iPr)2O CNEt

DMTO

F

HN

N

N

N

O

iBuHN

F

DMTO

CNEtON(iPr)2PO

O

2’-F-G2’-F-Ac-C2’-F-A

STABILITY NOTE

Syntheticoligonucleotidescontaining2’-F-RNAlinkagesmaybedeprotectedwithammoniumhydroxideasnormal.DeprotectionusingAMAat65°Cleadstosomedegradationandsowerecommend the use of AMA at room temperaturefor2hours.




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SEE ALSO

DNA PACE on page 37DCI on page 30UniCap on page 320.5M CSO on page 32

144 145

RNA

AND

2’-O

Me-

RNA

2’-F ANA SYNTHESIS

2’-F-ARABINONUCLEIC ACID (2’-F-ANA)

Arabinonucleosidesareepimersofribonucleosideswiththechiralswitchbeingatthe2’positionofthesugarresidue.2’-F-ANAadoptsamoreDNA-likeB-typehelixconformation,notthroughthetypicalC2’-endoconformationbut,rather,throughanunusualO4’-endo(east)pucker.However,thepresenceoftheelectronegativefluorineleadstoastillsignificantincrease (DTm1.2°C/mod)inmeltingtemperaturepermodification.12’-F-ANA-containingoligonucleotidesexhibitveryhighbindingspecificitytotheirtargets.Indeed,asinglemismatchina2’-F-ANA–RNAduplexleadstoaDTmof-7.2°Candina2’-F-ANA-DNAduplexaDTmof-3.9°C.

2

Thepresenceoffluorineatthe2’positionin2’-F-ANAleadstoincreasedstabilitytohydrolysisunderbasicconditionsrelativetoRNAandeven2’-F-RNA.1,3Thestabilityof2’-F-ANAtonucleasesalsomakesthisausefulmodificationforenhancingthestabilityofoligonucleotidesinbiologicalenvironments.22’-F-ANAhybridizesstronglytotargetRNAand,unlikemost2’modifications,inducescleavageofthetargetbyRNaseH.Phosphorothioate(PS)2’-F-ANAisroutinelyusedintheseapplicationsdueto its increasednucleaseresistance. Alternating2’-F-ANAandDNAunitsprovideamongthehighestpotencyRNaseH-activatingoligomers. Boththe“altimer”and“gapmer”strandarchitecturesconsistentlyoutperformPS-DNAandDNA/RNAgapmers.4

siRNAoligoswere found to tolerate thepresenceof 2’-F-ANA linkages verywell. Highpotency gene silencingwasdemonstrated5 withsiRNAchimerascontaining2’-F-RNAand/orLNAand2’-F-ANA.ThehighefficacyofthesechimeraswasattributedtothecombinationoftherigidRNA-likepropertiesof2’-F-RNAandLNAwiththeDNA-likepropertiesof2’-F-ANA.


2’-F-A-ANACEPhosphoramidite 10-3800-90 100µmole 150.00 10-3800-02 0.25g 375.00

2’-F-Bz-C-ANACEPhosphoramidite 10-3810-02 0.25g 200.00 10-3810-05 0.5g 400.00

2’-F-Ac-C-ANACEPhosphoramidite 10-3815-02 0.25g 200.00 10-3815-05 0.5g 400.00

2’-F-G-ANACEPhosphoramidite 10-3820-90 100µmole 165.00 10-3820-02 0.25g 425.00

2’-F-U-ANACEPhosphoramidite 10-3830-02 0.25g 125.00 10-3830-05 0.5g 250.00

ODMTO

N

HN

O

O

O P N(iPr)2

O CNEt

F

N

N N

N

NHBz

O

O P N(iPr)2

O

F

CNEt

DMTO ODMTON

N

NHBz

O

O P N(iPr)2

O CNEt

F

HN

N

N

O

N

ODMTO

O P N(iPr)2

O CNEt

iBuHN

F

REFERENCES

1. E.Viazovkina,M.M.Mangos,M.I.Elzagheid,andM.J.Damha,Curr Protoc Nucleic Acid Chem, 2002, Chapter 4, Unit415.

2. J.K.Watts,andM.J.Damha,Can. J. Chem., 2008, 86,641-656.

3. J.K.Watts,A.Katolik,J.Viladoms,andM.J.Damha,Org Biomol Chem, 2009, 7,1904-10.

4. A.Kalota,et al., Nucleic Acids Res., 2006, 34,451.

5. G.F.Deleavey, et al., Nucleic Acids Res., 2010, 38,4547-4557,J.K.Watts,et al., Nucleic Acids Res., 2007, 35,1441-1451,T.Dowler,et al., Nucleic Acids Res., 2006, 34,1669-1675.

STABILITY NOTE

Syntheticoligonucleotidescontaining2’-F-RNAlinkagesmaybedeprotectedwithammoniumhydroxideasnormal.DeprotectionusingAMAat65°Cleadstosomedegradationandsowerecommend the use of AMA at room temperaturefor2hours.


2’-F-ANAiscoveredbyintellectualproperty.KeypatentscoveringsiRNAandantisenseapplicationsareasfollows:

WO/2009/146556(siRNA);WO03064441 and WO 0220773 (antisense).

2'-F-A-ANA 2'-F-U-ANA 2'-F-G-ANA 2'-F-Bz-C-ANA 2'-F-Ac-C-ANA

ODMTON

N

NHAc

O

O P N(iPr)2

O CNEt

F

Chemical Formula: C41H49FN5O8PExact Mass: 789.33

Molecular Weight: 789.83m/z: 789.33 (100.0%), 790.33 (46.5%), 791.34 (10.0%), 791.33 (2.5%), 792.34 (2.2%)

Elemental Analysis: C, 62.35; H, 6.25; F, 2.41; N, 8.87; O, 16.21; P, 3.92


Theseproductsarecoveredbypatents,US 6,693,187 and 7,067,641, and patentspendingownedbyMetasenseTechnologies.Purchaseofalloranyof these products includes a limited licensetousetheproductssolelyforthemanufactureofoligonucleotidesforresearchuseonly.Thislicensespecificallyexcludestheuseoftheproductoroligonucleotidescontainingtheproductfor:(a)therapeuticordiagnosticapplications(includingkits,pools,librariesandotherproducts or services that incorporate oligonucleotidescontainingtheproduct),(b)anyinvivotoxicity/safetystudyinsupportofaninvestigationalnewdrugapplication(orforeigncounterpart),or(c)resale(includingsaleofkits,pools,librariesandotherproducts or services that incorporate theproductoroligonucleotidescontainingtheproduct).Ifsuchactivitieshavecommercialapplication,aseparatelicenseisrequiredfromMetasenseTechnologies.Neithertheproductnoranyproductcreatedthroughitsusemaybeusedinhumanclinicaltrials.

Asimpleagreementmustbesignedbeforeend-usersandcustomoligoservicesmaypurchasetheseproductsforuseasdefinedabove.


2’-OME-RNA-PACE SYNTHESIS

REFERENCES

1. A.Hendel, et al., Nat Biotechnol, 2015, 33,985-989.

2. D.E.Ryan, et al., Nucleic Acids Res, 2018, 46,792-803.

N

N N

N

NHBz

ODMTO

O P N(iPr)2

OCN

O

OMe

ODMTO

O P N(iPr)2

OCN

O

OMe

N

N

NHAc

O

ODMTO

O P N(iPr)2

OCN

O

OMe

HN

N

N

O

NiBuHN

ODMTO

O P N(iPr)2

OCN

O

OMe

N

HN

O

O

2’-OMe-A-PACE 2’-OMe-U-PACE2’-OMe-Ac-C-PACE 2’-OMe-G-PACE

2’-OME-RNA-PACE PHOSPHORAMIDITES

PACEmodifications have enjoyed a resurgence in interest as applied to the field of CRISPR gene editing. In aninitial publication, itwas shown that single guideRNAs (sgRNA)provided significantly higher activity in cellswhen2‘-O-methylthiophosphonoacetateswereincorporatedontheendsoftheguideRNAtoprotectagainstcellularnucleases.1 Insubsequentstudies,2’-OMePACEmodifiedsgRNAswerealsoshowntosignificantlyincreaseon-targetspecificityoftheCRISPR-Cas9DNAcleavageineukaryoticcells.Inarecentpaper,theincorporationof2’-OMePACEmodifiednucleotidesinthe20-nucleotideguideregionofthesgRNAwasshowntodecreaseoff-targetcuttingbyoveranorderofmagnitudewhileinmostcasesincreasingtheoverallon-targetefficiencyascomparedtounmodifiedsingleguideRNA.2

Asanoptimalcycle,werecommendusingDCIasanactivator(30-3150-XX)anda15minutecouplingtime.Followingcoupling,capusingUnicap(10-4410-XX)witharegularcouplingtimeandthenoxidizeusing0.5MCSOfor3minutes.Alternatively,a33minutecouplingtimeusing0.45Mtetrazole,oxidationusinglow-wateriodine(40-4032-XX)followedbycappingwith6.5%DMAPasCapBwillgiveacceptableresults.Fordeprotection,pre-treatthesynthesiscolumnwith1.5%DBUinanhydrousacetonitrilefor60minutesatroomtemperaturetoremove1,1-dimethyl-2-cyanoethylprotectinggroups.Rinsethecolumnwithacetonitrile,dryunderargonandcompletethedeprotectionwith40%aqueousmethylaminefor2hoursatroomtemperature.


2’-OMe-A-PACEPhosphoramidite 10-3150-02 0.25g 110.00 10-3150-05 0.5g 220.00 10-3150-10 1.0g 440.00

2’-OMe-Ac-C-PACEPhosphoramidite 10-3151-02 0.25g 110.00 10-3151-05 0.5g 220.00 10-3151-10 1.0g 440.00

2’-OMe-G-PACEPhosphoramidite 10-3152-02 0.25g 110.00 10-3152-05 0.5g 220.00 10-3152-10 1.0g 440.00

2’-OMe-U-PACEPhosphoramidite 10-3153-02 0.25g 110.00 10-3153-05 0.5g 220.00 10-3153-10 1.0g 440.00



SEE ALSO

Poly-Pak Reagents on page 149

146 147

MIS

CELL

ANEO

US

GLEN-PAK™ PURIFICATION

Glen-Pak™DNAandRNAcartridgeshaveadvantagesoverPoly-Pakcartridgesinthatasingleloadingofthedilutedcrudedeprotectionsolutionisallthatisnecessary.Also,therangeofpurificationhasbeenextendedto100+usingDMT-ONoligos.Inaddition,Glen-Pakcartridgesallowpurificationofvirtuallythecompleterangeofdyesandmodifiers.

TheGlen-PakDNACartridge3gisalargecartridgecapableofpurifying10-20µmoleoligonucleotidesynthesesusingthestandardDMT-ONprocedureandGlen-PakDNA30mg96-WellPlatesareforparallelpurificationofupto50nmolescalesyntheses.TheGlen-PakDNA3mg384-WellPlateisdesignedforusewith384-wellplatecompatiblevacuummanifoldsystemsandcanpurifyuptoa20nmolescalesynthesis.Eachwellcontains3mgofGlen-PakDNAresin,whichbindsabout15nmolesoffulllength40-merDMT-ONoligo.

ScalesuggestionsfortheGlen-PakDNAproductlineareshownbelow:

Glen-Pak DNA Product Catalog Number Synthesis Scale Compatibility

Glen-PakDNA50mgPurificationCartridge 60-5000-96 10nmole–200nmoleGlen-PakDNAPurificationCartridge 60-5100-XXand60-5200-XX 10nmole–1.0µmoleGlen-PakDNACartridge3G 60-5300-01 5µmole–20µmoleGlen-PakDNA30mg96-WellPlate 60-5400-01 10nmole–50nmoleGlen-PakDNA3mg384-WellPlate 60-5500-XX upto20nmole

A User Guide to Glen-Pak™ PurificationdescribesindetailtheprocessandseveralapplicationsforDNAandRNApurification.Thisbookletisavailableonlineat:http://www.glenresearch.com/Technical/GlenPak_UserGuide.pdf.


DNA Purification CartridgesGlen-Pak™50mgDNAPurificationCartridge 60-5000-96 Packof96 415.00 (For use in vacuum manifolds andhigh-throughputdevices)

Glen-Pak™DNAPurificationCartridge 60-5100-10 Packof10 80.00 (Foruseinvacuummanifolds 60-5100-30 Packof30 200.00 andhigh-throughputdevices) 60-5100-96 Packof96 475.00

Glen-Pak™DNAPurificationCartridge 60-5200-01 each 8.00 (Forusewithdisposablesyringes) 60-5200-10 Packof10 80.00

Glen-Pak™DNACartridge3g 60-5300-01 Packof1 150.00

Glen-Pak™DNA30mg96-WellPlate 60-5400-01 Packof1 475.00

Glen-Pak™DNA3mg384-WellPlate 60-5500-01 Packof1 675.00 60-5500-10 Packof10 6750.00

PURIFICATION

Poly-Pak™ and Glen-Pak™ are trademarks of Glen Research Corporation

Thispageisintentionallyleftblank.

http://www.glenresearch.com/Technical/GlenPak_UserGuide.pdf

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GLEN-PAK™ PURIFICATION (CONT.)


RNA Purification CartridgesGlen-Pak™RNAPurificationCartridge 60-6100-10 Packof10 95.00 (Foruseinvacuummanifolds 60-6100-30 Packof30 225.00 andhigh-throughputdevices) 60-6100-96 Packof96 575.00

Glen-Pak™RNAPurificationCartridge 60-6200-01 each 9.50 (Forusewithdisposablesyringes) 60-6200-10 Packof10 95.00

ReagentsRNAQuenchingBuffer 60-4120-82 250mL 80.00 60-4120-80 1L 200.00

Racks and Seals AdapterRack 60-0010-01 each 20.00 (Forusewith96wellmanifolds)SealforAdapterRack 60-0020-01 each 30.00 (Foruseon96welladapterrack)

PURIFICATION

Poly-Pak Cartridge Used Manually

POLY-PAK™ PURIFICATION

TheuseofPoly-Pak™packingsincartridgesorbarrelsovercomesseveraldisadvantagesusuallyassociatedwithreversephase(RP)cartridges.ThepackingisstableinthepHrange1-13,thustheammoniumhydroxidesolution,dilutedwithwater,isloadeddirectlyontothepacking.Also,afterelutionoffailuresequences,thetritylgroupisremovedandwashedfromthesupport-boundoligonucleotide.Thefullydeprotectedproductcanthenbeelutedandisolatedbylyophilization.Poly-Pak™Cartridgesmayalsobeusedfordesaltingnormalorlabeledoligonucleotides.TheoriginalPoly-Pakcartridgeandbarrelaredesignedfor0.2µmolesynthesesorless.Poly-PakIIcartridgesandbarrelsaredesignedforusewith1µmolesyntheses.Abooklet,User Guide To Poly-Pak™ Cartridge Purification,describesindetailtheprocessandseveralapplications.Thisbookletisavailableonlineat:http://www.glenresearch.com/Technical/PolyPakBooklet.pdf.


Packing, Cartridges and Barrels

Poly-Pak™Packing 60-1000-05 5g 70.00 60-1000-25 25g 350.00

Poly-Pak™Cartridge 60-1100-01 each 8.00 60-1100-10 Packof10 80.00

Poly-Pak™IICartridge 60-3100-01 each 12.00 60-3100-10 Packof10 120.00

Reagents

2.0MTriethylamineAcetate(TEAA) 60-4110-52 200mL 60.00HPLCGrade 60-4110-57 450mL 120.00 60-4110-60 960mL 200.00 60-4110-62 2L 400.00 2%AqueousTrifluoroaceticAcid 60-4040-57 450mL 36.00

PURIFICATION

Poly-Pak™ is a trademark of Glen Research Corporation

http://www.glenresearch.com/Technical/PolyPakBooklet.pdf

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PURIFICATION

GLEN GEL-PAK™ DESALTING

TheprincipleoftheGlenResearchgelfiltrationcolumn,GlenGel-Pak™,isbasedonsizeexclusionchromatographythatseparatesmoleculesaccordingtothehydrodynamicvolumeofthemoleculeinaqueoussolutions.Ingelfiltration,themobilephaseforsizeexclusionisanaqueoussolutionandthestationaryphaseisaporousresin.Theporesoftheresinaresizedsuchthattheyallowsmallmoleculestoenterthepores,yetexcludelargermoleculesfromthepores.Thesmallmolecules,suchassaltsandhydrolyzedprotectinggroups,diffuseintotheporesoftheresinandmoveslowlythroughthecolumn.Thelargermolecules,suchasDNAorproteins,areexcludedfromtheporesandmovequicklythroughthecolumn.Theendresultisthatthelargermoleculeselutefirstinthecolumnvoidvolumewhilethesmallmoleculesarestillflowingthroughtheresinofthecolumn.GlenGel-Pakcolumnsare ideal fordesaltingandreactioncleanup. Theycanbeusedforremovalof theammoniumhydroxidedeprotectionsolutionandhydrolyzedprotectinggroupsafterdeprotection.ThecolumnscanalsobeusedforthecleanupofNHS-labelingreactionstoseparatethelabeledoligoandunlabeledoligofromtheunreactedNHSester,thehydrolyzedlabel,andn-hydroxysuccinimide,therebygreatlysimplifyingthedownstreampurificationsteps.

TherearemanybenefitstoGlenGel-Pakcolumns:

Versatility:

• Ability to directly desalt oligonucleotides deprotected ineither 30% ammonium hydroxideOR 50:50 ammoniumhydroxide/40%aqueousmethylamine(AMA)

• Easilyexchangebuffers• Simpleclean-upoflabelingreactions• Mildmethodforpurificationfromsaltsandsolventssuchas

DMSO and DMF

Capacity:

• Multiplecolumnsizes(0.2mL,1.0mLand2.5mL)areavailabletomatchsynthesisscale

• Abilitytoefficientlydesaltshortandlongoligosatdifferentscalesusingthesameprotocol• Suitableforoligos>10merinlength


GlenGel-Pak™0.2DesaltingColumn 61-5002-05 Packof5 30.00 (0.2mLCapacity) 61-5002-50 Packof50 300.00GlenGel-Pak™1.0DesaltingColumn 61-5010-05 Packof5 35.00 (1.0mLCapacity) 61-5010-50 Packof50 350.00GlenGel-Pak™2.5DesaltingColumn 61-5025-05 Packof5 45.00 (2.5mLCapacity) 61-5025-25 Packof25 225.00

Glen Gel-Pak 0.2 Glen Gel-Pak 2.5 Glen Gel-Pak 1.0

Glen Gel-Pak™ is a trademark of Glen Research Corporation

PURIFICATION

OLIGO-AFFINITY SUPPORT

Oligo-affinitysupports(OAS)shouldideallybecompatiblewithautomatedsynthesis,shouldbenon-friable,shouldnotshrinkorswell,andshouldhavelownon-specificbindingoftheproteinsorDNA.OnthesupportshownbelowisanAdenosineresidueattachedthroughtheexocyclicaminogroup.Inthisway,synthesisprogressesregularlyonremovalofthe5’-DMTgroup.However,ontreatmentwithammoniumhydroxide,theoligoisnotcleavedfromthesupport.ThismatrixcanthenbeusedasanaffinitysupportforacomplementarysegmentofDNAorRNA.Alternatively,thecomplementarystrandcanbeannealedtothesupportandthedoublestrandedDNAcanbeusedasanaffinitysupportforpurifyingDNAbindingproteins.

WeexpectthatOASPSwillbeusedforpurificationofcomponentsfrombiologicalfluids.


Oligo-AffinitySupport(PS) 26-4001-01 0.1g 180.00 (OASPS) 26-4001-02 0.25g 425.00 26-4001-10 1.0g 1590.00

Oligo-AffinitySupport(PS) 1µmoleTWISTcolumns 26-4101-41 Packof4 300.00

OAS PS

O

ODMTO

OAc OAc

NH

N

N

N

N

PS




Expedite EMerMade M




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PHYSICAL DATA

PHYSICAL DATA

Thephysicaldatatablecontainsinformationwhichisuniquetoeachmonomerphosphoramidite.Themolecularweight(MW)istheformulaweightofthefully-protectedmonomerphosphoramidite.TheMWisusedtocalculatethevolumeofsolventrequiredtodilute0.25gofthemonomertogiveafinal0.1Mconcentration.Thisfigureisalsoshowninthetable.Theunitmolecularweight(UnitFW)istheformulaweightofeachmonomeronceinsertedintoanoligonucleotidewithallprotectinggroupsremoved.Toobtainthemolecularweightofaspecificoligonucleotide,thefollowingformulaisused:

OligonucleotideMW=SumofUnitFW-61.96

Cat. No. Item Phosphoramidite MW Unit FW Dilution I0.1M)

10-0001 dA-5’-CEPhosphoramidite 857.95 313.21 0.25g/2.91mL10-0101 dC-5’-CEPhosphoramidite 833.93 289.18 0.25g/3.00mL10-0301 dT-5’-CEPhosphoramidite 744.83 304.2 0.25g/3.36mL10-1000 dA-CEPhosphoramidite 857.95 313.21 0.25g/2.91mL10-1001 7-Deaza-dA-CEPhosphoramidite 856.96 312.22 0.25g/2.92mL10-1003 N6-Me-dA-CEPhosphoramidite 767.86 327.24 0.25g/3.26mL10-1004 3’-dA-CEPhosphoramidite 857.95 313.21 0.25g/2.91mL10-1006 Etheno-dA-CEPhosphoramidite 777.86 337.23 0.25g/3.21mL10-1007 8-Br-dA-CEPhosphoramidite 887.81 392.11 0.25g/2.82mL10-1008 8-oxo-dA-CEPhosphoramidite 873.95 329.21 0.25g/2.86mL10-1010 dC-CEPhosphoramidite 833.93 289.18 0.25g/3.00mL10-1014 pdC-CEPhosphoramidite 907.1 327.23 0.25g/2.76mL10-1015 Ac-dC-CEPhosphoramidite 771.85 289.18 0.25g/3.24mL10-1016 TMP-F-dU-CEPhosphoramidite 866.97 307.18 0.25g/2.88mL10-1017 Pyrrolo-dC-CEPhosphoramidite 767.85 327.23 0.25g/3.26mL10-1018 5-Me-dCBrancherPhosphoramidite 942.1 402.36 0.25g/2.65mL10-1019 Amino-ModifierC6dC 1049.14 457.42 0.25g/2.38mL10-1020 dG-CEPhosphoramidite 839.92 329.21 0.25g/2.98mL10-1021 7-deaza-dG-CEPhosphoramidite 823.93 328.22 0.25g/3.03mL10-1027 8-Br-dG-CEPhosphoramidite 903.9 408.1 0.25g/2.77mL10-1028 8-oxo-dG-CEPhosphoramidite 855.93 345.21 0.25g/2.92mL10-1029 dmf-dG-CEPhosphoramidite 824.92 329.21 0.25g/3.03mL10-1030 dT-CEPhosphoramidite 744.83 304.2 0.25g/3.36mL10-1031 5’-OMe-dT-CEPhosphoramidite 456.48 318.22 0.25g/5.48mL10-1032 O4-Me-dT-CEPhosphoramidite 758.85 318.22 0.25g/3.29mL10-1034 4-Thio-dT-CEPhosphoramidite 813.95 320.26 0.25g/3.07mL10-1035 Carboxy-dT 814.88 360.22 0.25g/3.07mL10-1036 2-Thio-dT-CEPhosphoramidite 879.02 320.26 0.25g/2.84mL10-1037 Amino-ModifierC2dT 938.94 402.3 0.25g/2.66mL10-1038 Biotin-dT 1285.55 684.7 0.25g/1.94mL10-1039 Amino-ModifierC6dT 995.05 458.41 0.25g/2.51mL10-1040 dI-CEPhosphoramidite 754.79 314.19 0.25g/3.31mL10-1041 2’-DeoxyNebularine-CEPhosphoramidite(Purine) 738.82 298.19 0.25g/3.38mL10-1042 O6-Phenyl-dI-CEPhosphoramidite 830.92 Varies 0.25g/3.01mL10-1044 5-Nitroindole-CEPhosphoramidite 780.86 340.23 0.25g/3.20mL10-1046 2-Aminopurine-CEPhosphoramidite 809.01 313.21 0.25g/3.09mL10-1047 dP-CEPhosphoramidite 771.85 330.23 0.25g/3.24mL10-1048 dK-CEPhosphoramidite 853.96 358.25 0.25g/2.93mL10-1050 dU-CEPhosphoramidite 730.8 290.17 0.25g/3.42mL10-1051 O4-Triazolyl-dU-CEPhosphoramidite 781.84 varies 0.25g/3.20mL10-1052 4-Thio-dU-CEPhosphoramidite 799.93 306.23 0.25g/3.13mL10-1053 5-OH-dU-CEPhosphoramidite 788.83 306.17 0.25g/3.17mL10-1054 pdU-CEPhosphoramidite 768.85 328.22 0.25g/3.25mL


10-1055 2’-deoxypseudoU-CEPhosphoramidite 730.8 290.17 0.25g/3.42mL10-1056 Fluorescein-dTPhosphoramidite 1425.57 815.71 0.25g/1.75mL10-1057 TAMRA-dT 1311.48 870.85 0.25g/1.91mL10-1058 Dabcyl-dT 1150.32 709.7 0.25g/2.17mL10-1059 EDTA-C2-dT-CEPhosphoramidite 1201.32 676.53 0.25g/2.08mL10-1060 5-Me-dC-CEPhosphoramidite 847.9 303.21 0.25g/2.95mL10-1061 5-Me-2’-deoxyZebularine-CEPhosphoramidite 728.82 288.19 0.25g/3.43mL10-1062 5-Hydroxymethyl-dC-CEPhosphoramidite 917 319.21 0.25g/2.73mL10-1063 5-OH-dC-CEPhosphoramidite 954.03 305.18 0.25g/2.62mL10-1064 3’-dC-CEPhosphoramidite 833.92 289.18 0.25g/3.00mL10-1065 dmf-5-Me-isodC-CEPhosphoramidite 798.91 303.21 0.25g/3.13mL10-1066 5-Carboxy-dC-CEPhosphoramidite 905.97 333.19 0.25g/2.76mL10-1068 N4-Et-dC-CEPhosphoramidite 757.87 317.42 0.25g/3.30mL10-1070 O6-Me-dG-CEPhosphoramidite 853.97 343.24 0.25g/2.93mL10-1072 6-thio-dG-CEPhosphoramidite 934.97 345.26 0.25g/2.67mL10-1073 7-Deaza-8-aza-dG-CEPhosphoramidite(PPG) 824.91 329.2 0.25g/3.03mL10-1074 3’-dG-CEPhosphoramidite 824.92 329.21 0.25g/3.03mL10-1076 7-deaza-dX-CEPhosphoramidite 769.83 329.21 0.25g/3.25mL10-1078 dmf-isodG-CEPhosphoramidite 1020.13 329.21 0.25g/2.45mL10-1079 8-Amino-dG-CEPhosphoramidite 895.01 344.22 0.25g/2.79mL10-1080 5-Br-dC-CEPhosphoramidite 912.82 368.08 0.25g/2.74mL10-1081 5-I-dC-CEPhosphoramidite 959.83 415.08 0.25g/2.60mL10-1082 2-F-dI-CEPhosphoramidite 921.96 varies,2F=332.18 0.25g/2.71mL10-1083 7-deaza-8-aza-dA-CEPhosphoramidite 808.91 313.2 0.25g/3.09mL10-1084 3’-dT-CEPhosphoramidite 744.83 304.2 0.25g/3.36mL10-1085 2-Amino-dA-CEPhosphoramidite 1047.33 328.22 0.25g/2.39mL10-1086 8-Amino-dA-CEPhosphoramidite 879.01 328.22 0.25g/2.84mL10-1088 3-deaza-dA-CEPhosphoramidite 856.95 312.22 0.25g/2.92mL10-1089 Amino-ModifierC6dA 1068.14 427.4 0.25g/2.34mL10-1090 5-Br-dU-CEPhosphoramidite 809.69 369.07 0.25g/3.09mL10-1091 5-I-dU-CEPhosphoramidite 856.69 416.07 0.25g/2.92mL10-1092 5-F-dU-CEPhosphoramidite 748.79 308.16 0.25g/3.34mL10-1093 5-Hydroxymethyl-dU-CEPhosphoramidite 802.86 320.19 0.25g/3.11mL10-1096 ThymidineGlycolCEPhosphoramidite 1007.36 338.21 0.25g/2.48mL10-1097 AP-dC-CEPhosphoramidite 974.97 438.33 0.25g/2.56mL10-1098 8,5’-Cyclo-dACEPhosphoramidite 855.92 311.19 0.25g/2.92mL10-1100 dA-MePhosphonamidite 802.91 311.24 0.25g/3.11mL10-1115 Ac-dC-MePhosphonamidite 716.81 287.21 0.25g/3.49mL10-1120 dG-MePhosphonamidite 784.89 327.24 0.25g/3.19mL10-1130 dT-MePhosphonamidite 689.79 302.23 0.25g/3.62mL10-1140 dA-PACEPhosphoramidite 928.02 354.24 0.25g/2.69mL10-1150 Ac-dC-PACEPhosphoramidite 841.93 330.21 0.25g/2.97mL10-1160 dG-PACEPhosphoramidite 910.01 370.24 0.25g/2.75mL10-1170 dT-PACEPhosphoramidite 814.9 345.22 0.25g/3.07mL10-1200 dA-H-Phosphonate,TEASalt 822.9 313.21 0.25g/3.04mL10-1210 dC-H-Phosphonate,DBUSalt 849.35 289.18 0.25g/2.94mL10-1220 dG-H-Phosphonate,TEASalt 804.88 329.21 0.25g/3.11mL10-1230 dT-H-Phosphonate,TEASalt 709.78 304.2 0.25g/3.52mL10-1301 Pac-dA-MePhosphoramidite 848.93 327.23(Methyltriester) 0.25g/2.94mL10-1315 Ac-dC-MePhosphoramidite 732.81 303.21(Methyltriester)0.25g/3.41mL10-1321 iPr-Pac-dG-MePhosphoramidite 907.01 343.23(Methyltriester) 0.25g/2.76mL10-1330 dT-MePhosphoramidite 705.79 318.22(Methyltriester) 0.25g/3.54mL

PHYSICAL DATA

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10-1440 CleanAmp™-Pac-dA-CEPhosphoramidite 1045.25 523.56(triester) 0.25g/2.39mL10-1450 CleanAmp™-Ac-dC-CEPhosphoramidite 929.13 499.54(triester) 0.25g/2.69mL10-1460 CleanAmp™-Pac-dG-CEPhosphoramidite 1061.25 539.56(triester) 0.25g/2.36mL10-1470 CleanAmp™-dT-CEPhosphoramidite 902.11 514.55(triester) 0.25g/2.77mL10-1501 1-Me-dA-CEPhosphoramidite 814.31 328.24 0.25g/3.07mL10-1503 N6-Ac-N6-Me-dA-CEPhosphoramidite 809.89 327.23 0.25g/3.09mL10-1504 def-dA-CEPhosphoramidite 836.97 313.21 0.25g/2.99mL10-1510 5-Hydroxymethyl-dCII-CEPhosphoramidite 785.82 319.21 0.25g/3.18mL10-1511 5-aza-5,6-dihydro-dC-CEPhosphoramidite 787.89 292.18 0.25g/3.17mL10-1513 N4-Ac-N4-Et-dC-CEPhosphoramidite 799.89 317.24 0.25g/3.13mL10-1514 5-Formyl-dC-CEPhosphoramidite 915.96 317.19(formyl) 0.25g/2.73mL 349.23(diol)10-1516 tC-CEPhosphoramidite 835.95 395.33 0.25g/2.99mL10-1517 tC°-CEPhosphoramidite 819.88 379.26 0.25g/3.05mL10-1518 tCnitro-CEPhosphoramidite 880.94 440.32 0.25g/2.84mL10-1529 N2-Amino-ModifierC6dG 965.01 428.38 0.25g/2.59mL10-1530 5,6-Dihydro-dT-CEPhosphoramidite 746.84 306.21 0.25g/3.35mL10-1531 N3-Cyanoethyl-dT 797.88 357.26 0.25g/3.13mL10-1532 5’-Dabsyl-dT-CEPhosphoramidite 729.78 591.53 0.25g/3.43mL10-1534 N-POMCaged-dT-CEPhosphoramidite 967.99 527.38(N-POM-dT) 0.25g/2.58mL10-1535 NHS-Carboxy-dT 897.91 varies,-CO2H=360.22 0.25g/2.78mL10-1536 FmocAmino-ModifierC6dT 1121.28 458.41(NH2) 0.25g/2.23mL10-1537 dX-CEPhosphoramidite 1069.1 330.19 0.25g/2.34mL10-1538 S-Bz-Thiol-ModifierC6-dT 1091.26 546.53 0.25g/2.29mL10-1539 DBCO-dT-CEPhosphoramidite 1214.57 773.77 0.25g/2.06mL10-1540 C8-Alkyne-dT-CEPhosphoramidite 834.94 394.32 0.25g/2.99mL10-1541 C8-TIPS-Alkyne-dC-CEPhosphoramidite 1094.4 393.33 0.25g/2.28mL10-1542 C8-TMS-Alkyne-dC-CEPhosphoramidite 1010.24 393.33 0.25g/2.47mL10-1543 C8-Alkyne-dC-CEPhosphoramidite 938.06 393.33 0.25g/2.67mL10-1544 C8-TIPS-Alkyne-dT-CEPhosphoramidite 991.28 394.32 0.25g/2.52mL10-1545 C8-TMS-Alkyne-dT-CEPhosphoramidite 907.12 394.32 0.25g/2.76mL10-1550 5,6-Dihydro-dU-CEPhosphoramidite 732.81 292.19 0.25g/3.41mL10-1554 5-Ethynyl-dU-CEPhosphoramidite 754.81 314.19 0.25g/3.31mL10-1555 TIPS-5-Ethynyl-dU-CEPhosphoramidite 911.15 314.19 0.25g/2.74mL10-1560 Ac-5-Me-dC-CEPhosphoramidite 785.86 303.21 0.25g/3.18mL10-1564 5-FormyldCIIICEPhosphoramidite 950.02 317.19 0.25g/2.63mL 375.27(acetal)10-1576 Ferrocene-dT-CEPhosphoramidite 1125.07 684.45 0.25g/2.22mL10-1585 Pac-2-Amino-dA-CEPhosphoramidite 1042.21 328.22 0.25g/2.40mL10-1590 Pyrene-dU-CEPhosphoramidite 955.04 514.42 0.25g/2.62mL10-1591 Perylene-dU-CEPhosphoramidite 1005.1 564.48 0.25g/2.49mL10-1598 8,5’-Cyclo-dG-CEPhosphoramidite 619.65 327.19 0.25g/4.03mL10-1601 Pac-dA-CEPhosphoramidite 887.97 313.21 0.25g/2.82mL10-1621 iPr-Pac-dG-CEPhosphoramidite 946.05 329.21 0.25g/2.64mL10-1700 dA-Thiophosphoramidite 955.09 345.34(dithioate) 0.25g/1.75mL10-1710 dC-Thiophosphoramidite 931.07 321.31(dithioate) 0.25g/1.79mL10-1720 dG-Thiophosphoramidite 937.07 361.34(dithioate) 0.25g/1.78mL10-1730 dT-Thiophosphoramidite 841.97 336.32(dithioate) 0.25g/1.98mL10-1900 ChemicalPhosphorylationReagent 656.77 79.98 0.25g/3.81mL10-1901 ChemicalPhosphorylationReagentII 722.82 79.98 0.25g/3.46mL10-1902 SolidChemicalPhosphorylationReagentII 692.79 79.98 0.25g/3.61mL10-1905 5’-Amino-Modifier5 577.71 167.1 0.25g/4.33mL

PHYSICAL DATA


10-1906 5’-Amino-ModifierC6 589.76 179.16 0.25g/4.24mL10-1907 5’-DMS(O)MT-Amino-ModifierC6 681.34 179.16 0.25g/3.67mL10-1908 5’-HexynylPhosphoramidite 298.36 160.11 0.25g/8.38mL10-1909 SpacerPhosphoramidite9 652.77 212.14 0.25g/3.83mL10-1910 1-Ethynyl-dSpacerCEPhosphoramidite 644.74 204.12 0.25g/3.88mL10-1912 5’-Amino-ModifierC12 673.92 263.32 0.25g/3.71mL10-1913 SpacerPhosphoramiditeC3 578.69 138.06 0.25g/4.32mL10-1914 dSpacerCEPhosphoramidite 620.73 180.1 0.25g/4.03mL10-1915 Pyrrolidine-CEPhosphoramidite 841.97 178.1 0.25g/2.97mL10-1916 5’-Amino-ModifierC6-TFA 413.42 179.16 0.25g/6.05mL10-1917 5’-Amino-ModifierTEGCE-Phosphoramidite 489.47 255.21 0.25g/5.11mL10-1918 SpacerPhosphoramidite18 784.93 344.3 0.25g/3.18mL10-1919 5’-Aminooxy-Modifier-11-CEPhosphoramidite 711.82 271.21 0.25g/3.51mL10-1920 SymmetricDoublerPhosphoramidite 1095.32 351.31 0.25g/2.28mL10-1922 TreblerPhosphoramidite 1417.72 370.33 0.25g/1.76mL10-1923 5’-Amino-ModifierC3-TFA 371.34 137.08 0.25g/6.73mL10-1925 LongTreblerPhosphoramidite 1475.78 428.41 0.25g/1.69mL10-1926 5’-Thiol-ModifierC6 576.78 196.2 0.25g/4.33mL10-1927 AbasicIIPhosphoramidite 750.98 196.1 0.25g/3.33mL10-1928 SpacerC12CEPhosphoramidite 704.93 264.3 0.25g/3.55mL10-1931 5’-I-dT-CEPhosphoramidite 552.35 414.09 0.25g/4.53mL10-1932 5’-Amino-dT-CEPhosphoramidite 713.81 303.21 0.25g/3.50mL10-1933 5’-Aldehyde-ModifierC2Phosphoramidite 480.58 228.14 0.25g/5.20mL10-1934 5-Formylindole-CEPhosphoramidite 763.86 323.24 0.25g/3.27mL10-1935 5’-Carboxy-ModifierC10 485.56 varies,-CO2H=250.23 0.25g/5.15mL10-1936 Thiol-ModifierC6S-S 769.05 328.4(disulfide) 0.25g/3.25mL 196.2(thiol)10-1938 5’-Maleimide-ModifierPhosphoramidite 437.47 299.22(pre-retro-DA) 0.25g/5.71mL 203.09(maleimide)10-1939 SperminePhosphoramidite 1233.17 408.52 0.25g/2.03mL10-1941 5’-DBCO-TEGPhosphoramidite 708.82 570.57 0.25g/3.53mL10-1945 5’-Carboxy-ModifierC5 595.11 180.1 0.25g/4.20mL10-1946 5’-BromohexylPhosphoramidite 381.29 243.04(bromide) 0.25g/6.56mL 205.15(azide)10-1947 5’-Amino-ModifierC6-PDA 478.57 179.15 0.25g/5.22mL10-1948 5’-Amino-ModifierC12-PDA 562.7 263.32 0.25g/4.44mL10-1949 5’-Amino-ModifierTEGPDA 554.62 255.21 0.25g/4.51mL10-1952 DesthiobiotinTEGPhosphoramidite 980.19 539.56 0.25g/2.55mL10-1953 BiotinPhosphoramidite 876.1 435.48 0.25g/2.85mL10-1955 BiotinTEGPhosphoramidite 1010.24 569.61 0.25g/2.47mL10-1963 FluoresceinPhosphoramidite 1207.5 598.56 0.25g/2.07mL10-1964 6-FluoresceinPhosphoramidite 1176.35 566.48 0.25g/2.13mL10-1973 AcridinePhosphoramidite 891.53 450.86 0.25g/2.80mL10-1974 5’-GalNAcC3Phosphoramidite 1206.38 609.61 0.25g/2.07mL10-1975 Cholesteryl-TEGPhosphoramidite 1196.6 755.97 0.25g/2.09mL10-1976 5’-Cholesteryl-TEGPhosphoramidite 820.13 682.89 0.25g/3.05mL10-1977 a-Tocopherol-TEGPhosphoramidite 1139.56 698.91 0.25g/2.19mL10-1979 StearylPhosphoramidite 470.71 332.46 0.25g/5.31mL10-1981 AsymmetricDoubler(Lev)Phosphoramidite 891.04 352.32 0.25g/2.81mL10-1982 PsoralenC2Phosphoramidite 502.55 364.29 0.25g/4.97mL10-1983 PsoralenC6Phosphoramidite 558.65 420.4 0.25g/4.48mL10-1985 DNP-TEGPhosphoramidite 950.00 509.41 0.25g/2.63mL

PHYSICAL DATA

156 157

MIS

CELL

ANEO

US

PHYSICAL DATA


10-1986 5’-TrimethoxystilbeneCapPhosphoramidite 571.65 433.39 0.25g/4.37mL10-1987 5’-PyreneCapPhosphoramidite 501.6 363.35 0.25g/4.98mL10-1991 DithiolSerinolPhosphoramidite 853.08 412.46 0.25g/2.93mL10-1992 Alkyne-ModifierSerinolPhosphoramidite 758.88 318.26 0.25g/3.29mL10-1993 ProtectedBiotinSerinolPhosphoramidite 1051.28 450.45 0.25g/2.38mL10-1994 6-FluoresceinSerinolPhosphoramidite 1191.3 582.45 0.25g/2.10mL10-1995 ProtectedBiotinLCSerinolPhosphoramidite 1298.57 697.74 0.25g/1.93mL10-1996 COTSerinolPhosphoramidite 822.97 382.35 0.25g/3.04mL10-1997 Amino-ModifierSerinolPhosphoramidite 887.01 224.15 0.25g/2.82mL10-1998 DBCO-SerinolPhosphoramidite 909.08 468.45 0.25g/2.75mL10-2000 Bz-A-LA-CEPhosphoramidite 885.96 341.22 0.25g/2.82mL10-2011 5-Me-Bz-C-LA-CEPhosphoramidite 875.96 331.22 0.25g/2.85mL10-2029 dmf-G-LA-CEPhosphoramidite 852.93 357.22 0.25g/2.93mL10-2030 T-LA-CEPhosphoramidite 772.84 332.20 0.25g/3.23mL10-3000 Pac-A-CEPhosphoramidite 1018.23 329.21 0.25g/2.46mL10-3003 Bz-A-CEPhosphoramidite 988.21 329.21 0.25g/2.53mL10-3004 A-TOM-CEPhosphoramidite 998.24 329.21 0.25g/2.50mL10-3005 N6-Methyl-A-CEPhosphoramidite 1032.25 343.23 0.25g/2.42mL10-3011 Zebularine-CEPhosphoramidite 845.05 290.17 0.25g/2.96mL10-3012 Pyridin-2-one-CEPhosphoramidite 844.06 289.18 0.25g/2.96mL10-3014 C-TOM-CEPhosphoramidite 974.22 305.18 0.25g/2.57mL10-3015 Ac-C-CEPhosphoramidite 902.11 305.18 0.25g/2.77mL10-3017 Pyrrolo-C-TOM-CEPhosphoramidite 970.23 343.27 0.25g/2.58mL10-3021 iPr-Pac-G-CEPhosphoramidite 1076.31 345.21 0.25g/2.32mL10-3024 G-TOM-CEPhosphoramidite 1014.24 345.21 0.25g/2.46mL10-3025 Ac-G-CEPhosphoramidite 941.43 345.21 0.25g/2.66mL10-3030 U-CEPhosphoramidite 861.06 306.17 0.25g/2.90mL10-3034 U-TOM-CEPhosphoramidite 933.17 306.17 0.25g/2.68mL10-3039 Amino-ModifierC6-UPhosphoramidite 1197.41 474.4 0.25g/2.09mL10-3040 I-CEPhosphoramidite 885.08 330.19 0.25g/2.82mL10-3050 5-Me-U-CEPhosphoramidite 875.08 320.19 0.25g/2.86mL10-3052 4-Thio-U-TOM-CEPhosphoramidite 1002.29 322.22 0.25g/2.49mL10-3055 PseudoUridine-CEPhosphoramidite 861.05 306.17 0.25g/2.90mL10-3056 1-Methyl-PseudoUridinePhosphoramidite 875.07 320.19 0.25g/2.86mL10-3064 5-Me-C-TOM-CEPhosphoramidite 988.25 319.21 0.25g/2.53mL10-3070 2-Aminopurine-TBDMS-CEPhosphoramidite 954.19 329.21 0.25g/2.62mL10-3072 6-Thio-G-CEPhosphoramidite 1039.31 361.26 0.25g/2.41mL10-3083 8-Aza-7-deaza-A-CEPhosphoramidite 939.16 329.21 0.25g/2.66mL10-3085 2,6-Diaminopurine-TOM-CEPhosphoramidite 1113.36 344.22 0.25g/2.25mL10-3090 Br-U-CEPhosphoramidite 939.96 385.06 0.25g/2.66mL10-3091 5-I-U-CEPhosphoramidite 986.96 432.07 0.25g/2.53mL10-3100 2’-OMe-A-CEPhosphoramidite 887.97 343.24 0.25g/2.82mL10-3110 2’-OMe-C-CEPhosphoramidite 863.95 319.21 0.25g/2.89mL10-3111 2’-OMe-TMP-5-F-U-CEPhosphoramidite 897.08 337.2 0.25g/2.79mL10-3115 2’-OMe-Ac-C-CEPhosphoramidite 801.88 319.21 0.25g/3.12mL10-3116 2’-OMe-3-deaza-5-aza-C-CEPhosphoramidite 816.91 319.21 0.25g/3.06mL10-3120 2’-OMe-ibu-G-CEPhosphoramidite 869.97 359.24 0.25g/2.87mL10-3121 2’-OMe-G-CEPhosphoramidite 854.93 359.24 0.25g/2.92mL10-3123 2’-OMe-2-Aminopurine-CEPhosphoramidite 839.04 343.24 0.25g/2.98mL10-3124 2’-OMe-2,6-Diaminopurine-CEPhosphoramidite 924.05 358.25 0.25g/2.71mL10-3130 2’-OMe-U-CEPhosphoramidite 760.82 320.2 0.25g/3.29mL10-3131 2’-OMe-5-Me-U-CEPhosphoramidite 774.84 334.22 0.25g/3.23mL


10-3132 2’-OMe-5-F-U-CEPhosphoramidite 778.78 338.19 0.25g/3.21mL10-3140 2’-OMe-I-CEPhosphoramidite 784.85 344.22 0.25g/3.19mL10-3150 2’-OMe-A-PACEPhosphoramidite 958.07 385.27 0.25g/2.61mL10-3151 2’-OMe-Ac-C-PACEPhosphoramidite 871.97 361.25 0.25g/2.87mL10-3152 2’-OMe-G-PACEPhosphoramidite 940.05 401.27 0.25g/2.66mL10-3153 2’-OMe-U-PACEPhosphoramidite 830.92 362.23 0.25g/3.01mL10-3160 2’-OMe-5-Me-C-CEPhosphoramidite 815.9 333.24 0.25g/3.06mL10-3170 2’-OMe-A-Thiophosphoramidite 985.12 375.36 0.25g/1.69mL10-3171 2’-OMe-C-Thiophosphoramidite 899.02 351.34 0.25g/1.85mL10-3172 2’-OMe-G-Thiophosphoramidite 967.1 391.36 0.25g/1.72mL10-3173 2’-OMe-U-Thiophosphoramidite 857.97 352.32 0.25g/1.94mL10-3190 2’-OMe-5-Br-U-CEPhosphoramidite 839.72 399.09 0.25g/2.98mL10-3400 2’-F-A-CEPhosphoramidite 875.93 331.2 0.25g/2.85mL10-3415 2’-F-Ac-C-CEPhosphoramidite 789.84 307.18 0.25g/3.17mL10-3420 2’-F-G-CEPhosphoramidite 857.91 347.19 0.25g/2.91mL10-3430 2’-F-U-CEPhosphoramidite 748.79 308.16 0.25g/3.34mL10-3501 1-Me-A-CEPhosphoramidite 944.57 344.24 0.25g/2.65mL10-3517 Ribo-tC°Phosphoramidite 950.16 395.26 0.25g/2.63mL10-3601 2’-OMe-Pac-A-CEPhosphoramidite 917.99 343.24 0.25g/2.72mL10-3621 2’-OMe-iPr-Pac-G-CEPhosphoramidite 976.07 359.24 0.25g/2.56mL10-3800 2’-FANA-A-CEPhosphoramidite 875.93 331.2 0.25g/2.85mL10-3815 2’-FANA-Ac-C-CEPhosphoramidite 789.83 307.17 0.25g/3.16mL10-3820 2’-FANA-G-CEPhosphoramidite 857.91 347.19 0.25g/2.91mL10-3830 2’-FANA-U-CEPhosphoramidite 748.79 308.16 0.25g/3.34mL10-3914 rSpacerCEPhosphoramidite 823.09 196.09 0.25g/3.04mL10-3915 rSpacerTBDMSCEPhosphoramidite 750.99 196.09 0.25g/3.33mL10-4410 UniCapPhosphoramidite 334.39 0.25g/7.48mL10-4906 PCAmino-ModifierPhosphoramidite 605.59 371.32 0.25g/4.13mL10-4913 PCSpacerPhosphoramidite 784.88 344.26 0.25g/3.19mL10-4920 PCLinkerPhosphoramidite 699.78 259.15 0.25g/3.57mL10-4950 PCBiotinPhosphoramidite 1038.25 597.62 0.25g/2.41mL10-4960 3-CyanovinylcarbazolePhosphoramidite(CNVK) 836.95 396.33 0.25g/2.99mL10-5800 AzobenzenePhosphoramidite 815.94 375.32 0.25g/3.06mL10-5901 5’-FluoresceinPhosphoramidite 843.95 537.46 0.25g/2.96mL10-5902 5’-Hexachloro-FluoresceinPhosphoramidite 1050.62 744.13 0.25g/2.38mL10-5903 5’-Tetrachloro-FluoresceinPhosphoramidite 981.73 675.24 0.25g/2.55mL10-5905 SIMA(HEX)Phosphoramidite 1065.02 759.54 0.25g/2.35mL10-5906 5’-Dichloro-dimethoxy-FluoresceinPhosphoramiditeII972.88 666.4 0.25g/2.57mL10-5912 5’-DabcylPhosphoramidite 568.69 430.18 0.25g/4.40mL10-5913 Cyanine3Phosphoramidite 953.64 507.59 0.25g/2.62mL10-5914 Cyanine3.5Phosphoramidite 1053.76 607.7 0.25g/2.37mL10-5915 Cyanine5Phosphoramidite 979.68 533.63 0.25g/2.55mL10-5916 Cyanine5.5Phosphoramidite 1171.25 633.74 0.25g/2.13mL10-5920 RedmondRed®Phosphoramidite 971.09 445.34 0.25g/2.57mL10-5921 YakimaYellow®Phosphoramidite 1023.81 718.33 0.25g/2.44mL10-5923 5’-AquaPhluor®593CEPhosphoramidite 1239.17 787.82 0.25g/2.02mL10-5924 5’-CDPI3MGB™Phosphoramidite 1323.42 872.96 0.25g/1.89mL10-5925 Eclipse®QuencherPhosphoramidite 978.5 537.89 0.25g/2.55mL10-5931 5’-BHQ-1Phosphoramidite 676.75 538.49 0.25g/3.69mL10-5932 5’-BHQ-2Phosphoramidite 678.72 540.47 0.25g/3.68mL10-5934 5’-BBQ-650®-CEPhosphoramidite 802.9 665.65 0.25g/3.11mL10-5941 BHQ-1-dT 1401.56 960.93 0.25g/1.78mL

PHYSICAL DATA

158 159

MIS

CELL

ANEO

US


10-5942 BHQ-2-dT 1403.53 962.91 0.25g/1.78mL10-5944 BBQ-650®-dT-CEPhosphoramidite 1441.57 1000.95 0.25g/1.73mL10-5945 SIMA(HEX)-dTPhosphoramidite 1646.64 1037.79 0.25g/1.52mL10-5950 5’-BiotinPhosphoramidite 846.08 405.45 0.25g/2.95mL10-5961 MethyleneBlueIIPhosphoramidite 967.67 489.57 0.25g/2.58mL10-7001 2’,3’-ddA-CEPhosphoramidite 574.7 297.21 0.25g/4.35mL10-7101 2’,3’-ddC-CEPhosphoramidite 550.68 273.18 0.25g/4.54mL10-7201 2’,3’-ddG-CEPhosphoramidite 506.54 313.2 0.25g/4.94mL10-7301 2’,3’-ddT-CEPhosphoramidite 426.45 288.19 0.25g/5.86mL10-9201 dmf-dG-5’-CEPhosphoramidite 824.92 329.21 0.25g/3.03mL11-1330 Cis-synThymineDimerPhosphoramidite 1024.01 608.39 0.25g/2.44mL13-1000 AAATrimerPhosphoramidite 1911.5 0.25g/1.31mL13-1001 AACTrimerPhosphoramidite 1887.5 0.25g/1.32mL13-1011 ACCTrimerPhosphoramidite 1863.5 0.25g/1.34mL13-1013 ACTTrimerPhosphoramidite 1774.5 0.25g/1.41mL13-1020 AGATrimerPhosphoramidite 1893.5 0.25g/1.32mL13-1031 ATCTrimerPhosphoramidite 1774.5 0.25g/1.41mL13-1032 ATGTrimerPhosphoramidite 1780.5 0.25g/1.40mL13-1102 CAGTrimerPhosphoramidite 1869.5 0.25g/1.34mL13-1103 CATTrimerPhosphoramidite 1774.5 0.25g/1.41mL13-1110 CCATrimerPhosphoramidite 1863.5 0.25g/1.34mL13-1112 CCGTrimerPhosphoramidite 1845.5 0.25g/1.35mL13-1122 CGGTrimerPhosphoramidite 1851.5 0.25g/1.35mL13-1123 CGTTrimerPhosphoramidite 1756.5 0.25g/1.42mL13-1132 CTGTrimerPhosphoramidite 1756.5 0.25g/1.42mL13-1200 GAATrimerPhosphoramidite 1893.5 0.25g/1.32mL13-1201 GACTrimerPhosphoramidite 1869.5 0.25g/1.34mL13-1203 GATTrimerPhosphoramidite 1780.5 0.25g/1.40mL13-1210 GCATrimerPhosphoramidite 1869.5 0.25g/1.34mL13-1212 GCGTrimerPhosphoramidite 1851.5 0.25g/1.35mL13-1213 GCTTrimerPhosphoramidite 1756.5 0.25g/1.42mL13-1223 GGTTrimerPhosphoramidite 1762.5 0.25g/1.42mL13-1230 GTATrimerPhosphoramidite 1780.5 0.25g/1.40mL13-1233 GTTTrimerPhosphoramidite 1667.5 0.25g/1.50mL13-1301 TACTrimerPhosphoramidite 1774.5 0.25g/1.41mL13-1313 TCTTrimerPhosphoramidite 1661.4 0.25g/1.50mL13-1321 TGCTrimerPhosphoramidite 1756.5 0.25g/1.42mL13-1322 TGGTrimerPhosphoramidite 1762.5 0.25g/1.42mL13-1331 TTCTrimerPhosphoramidite 1661.4 0.25g/1.50mL13-1333 TTTTrimerPhosphoramidite 1572.4 0.25g/1.59mL20-0002 dA-5’-CPG 313.2120-0102 dC-5’-CPG 289.1820-0202 dG-5’-CPG 329.2120-0302 dT-5’-CPG 304.220-2000 dA-CPG500 313.2120-2001 dA-CPG1000 313.2120-2002 dA-CPG2000 313.2120-2004 3’-dA-CPG 313.2120-2010 dC-CPG500 289.1820-2011 dC-CPG1000 289.1820-2012 dC-CPG2000 289.1820-2013 Ac-dC-CPG500 289.1820-2015 Ac-dC-CPG1000 289.18

PHYSICAL DATA


20-2017 2’,3’-ddC-CPG 273.1920-2019 3’-Amino-ModifierC6dCCPG 457.4220-2020 dG-CPG500 329.2120-2021 dG-CPG1000 329.2120-2022 dG-CPG2000 329.2120-2029 dmf-dG-CPG 329.2120-2030 dT-CPG500 304.220-2031 dT-CPG1000 304.220-2032 dT-CPG2000 304.220-2040 dI-CPG500 314.1920-2041 dI-CPG1000 314.1920-2050 dU-CPG500 290.1720-2051 dU-CPG1000 290.1720-2056 3’-Fluorescein-dTCPG 815.7120-2064 3’-dC-CPG 289.1820-2074 3’-dG-CPG 329.2120-2084 3’-dT-CPG 304.220-2090 5-Br-dU-CPG 369.0720-2101-61 dA-CPG1000 313.2120-2101-62 dA-CPG1000 313.2120-2101-65 dA-CPG1000 313.2120-2115-61 Ac-dC-CPG1000 289.1820-2115-62 Ac-dC-CPG1000 289.1820-2115-65 Ac-dC-CPG1000 289.1820-2129-61 dmf-dG-CPG 329.2120-2129-62 dmf-dG-CPG 329.2120-2129-65 dmf-dG-CPG 329.2120-2131-61 dT-CPG1000 304.220-2131-62 dT-CPG1000 304.220-2131-65 dT-CPG1000 304.220-2601 Pac-dA-CPG 313.2120-2621 iPr-Pac-dG-CPG 329.2120-2900 3’-PhosphateCPG 79.9820-2902 3’-GlycerylCPG 154.0620-2903 3’-CPRIICPG 79.9820-2913 3’-SpacerC3CPG 138.0620-2933 3’-Thiol-ModifierC3S-SCPG 154.12(thiol),244.27(disulfide)20-2938 3’-Thiol-Modifier6S-SCPG 198.18(thiol),332.37(disulfide)20-2952 DesthiobiotinTEG-CPG 539.5620-2954 3’-PT-Amino-ModifierC3CPG 137.0720-2955 3’-BiotinTEGCPG 569.6120-2956 3’-PT-Amino-ModifierC6CPG 179.1520-2958 3’-Amino-ModifierC7CPG1000 209.1820-2961 3’-(6-FAM)CPG 569.4620-2963 3’-FluoresceinCPG 598.5620-2964 3’-(6-Fluorescein)CPG 566.4820-2973 3’-AcridineCPG 450.8620-2974 GalNAcC3CPG 609.6120-2975 3’-Cholesteryl-TEGCPG 755.9720-2980 3’-UaqCapCPG 539.3920-2981 3’-Amino-dTCPG 303.2120-2982 3’-Propargyl-5-Me-dCCPG 341.2620-2991 3’-DithiolSerinolCPG 412.46

PHYSICAL DATA

160 161

MIS

CELL

ANEO

US


20-2992 3’-Alkyne-ModifierSerinolCPG 334.2620-2993 3’-ProtectedBiotinSerinolCPG 450.4520-2994 3’-6-FluoresceinSerinolCPG 584.4720-2995 3’-ProtectedBiotinLCSerinolCPG 697.7420-2997 3’-Amino-ModifierSerinolCPG 224.1520-3300 Pac-A-RNA-CPG 329.2120-3303 Bz-A-RNA-CPG 329.2120-3304 Ac-A-RNA-CPG 329.2120-3315 Ac-C-RNA-CPG 305.1820-3321 iPr-Pac-G-RNA-CPG 345.2120-3324 Ac-G-RNA-CPG 345.2120-3330 U-RNA-CPG 306.1720-3600 2’-OMe-A-RNA-CPG 343.2420-3610 2’-OMe-C-RNA-CPG 319.2120-3615 2’-OMe-Ac-C-RNA-CPG 319.2120-3621 2’-OMe-G-RNA-CPG 359.2420-3630 2’-OMe-U-RNA-CPG 320.220-4040 Puromycin-CPG 533.4820-5910 3’-TAMRACPG 623.620-5911 3’-DabsylCPG 498.4920-5912 3’-DabcylCPG 462.4420-5913 Cyanine3CPG 507.5920-5915 Cyanine5CPG 533.6320-5920 RedmondRed®CPG 445.3420-5921 YakimaYellow®CPG 718.3320-5923 AquaPhluor®593CPG 900.9320-5924 CDPI3MGB™CPG 831.8720-5925 Eclipse®QuencherCPG 537.8920-5931 3’-BHQ-1CPG 554.4920-5932 3’-BHQ-2CPG 556.4720-5933 3’-BHQ-3CPG 597.6320-5934 BBQ-650®CPG 667.6321-2000 dA-Q-CPG500 313.2121-2010 dC-Q-CPG500 289.1821-2013 Ac-dC-Q-CPG500 305.1821-2029 dmf-dG-Q-CPG500 329.2121-2030 dT-Q-CPG500 304.225-2000 dA-HighLoad-CPG 313.2125-2010 dC-HighLoad-CPG 289.1825-2020 dG-HighLoadCPG 329.2125-2030 dT-HighLoad-CPG 304.225-2900 3’-PhosphateCPG(HighLoad) 79.9826-2600 dAPS 313.2126-2610 dCPS 289.1826-2629 dmf-dGPS 329.2126-2630 dT-PS 304.226-2900 3’-PhosphatePS 79.9826-2955 3’-BiotinTEGPS 569.6126-2956 3’-PT-Amino-ModifierC6PS 179.1526-2961 3’-(6-FAM)PS 569.4626-5910 3’-TAMRAPS 623.626-5912 3’-DabcylPS 462.44

PHYSICAL DATA PHYSICAL DATA

Cat. No. Item MW Unit FW

50-1904 AzidobutyrateNHSEster 226.19 113.1250-1905 Alkyne-NHSEster 225.2 110.1150-1941 DBCO-sulfo-NHSEster 532.5 316.3750-2000 BiotinTEGAzide 444.55 50-2001 DesthiobiotinTEGAzide 414.5 50-2002 Dipivaloyl6-FAM-TEGAzide 744.79 50-2003 6-FAM-TEGAzide 576.55 50-2004 CoumarinAzide 203.15 50-2005 6-HEXAzide 665.09 50-2006 6-TETAzide 596.2 50-2007 TEMPOAzide 197.26 50-2008 TEMPO-TEGAzide 373.47 50-2009 PsoralenAzide 283.28 50-2010 Disulfo-Cyanine7Azide 829.08 50-5910 TAMRANHSEster 527.53 413.45

Index

Symbols2’-5’ Linkages3’-dA-CEPhosphoramidite653’-dA-CPG653’-dC-CEPhosphoramidite653’-dC-CPG653’-dG-CEPhosphoramidite653’-dG-CPG663’-dT-CEPhosphoramidite653’-dT-CPG66

2’-5’ Linked Oligonucleotides 64, 665’ -> 3’ SYNTHESIS5’-CEPhosphoramidites34

AA1-Me-A-CEPhosphoramidite1351-Me-dA-CEPhosphoramidite662’,3’-ddA562’-F-A-ANACEPhosphoramidite1442’-F-A-CEPhosphoramidite1432’-OMe-A-CEPhosphoramidite1372’-OMe-A-PACEPhosphoramidite1452’-OMe-A-RNA1392’-OMe-Pac-A-CEPhosphoramidite1383’-dA-CEPhosphoramidite653’-dA-CPG55, 667-Deaza-dA-CEPhosphoramidite578-Amino-dA-CEPhosphoramidite598-Br-dA-CEPhosphoramidite608-Oxo-dA-CEPhosphoramidite61Ac-A-RNA-CPG126Amino-ModifierC6dA77A-TOM-CEPhosphoramidite126Bz-A-CEPhosphoramidite128Bz-A-LNA-CEPhosphoramidite41Bz-A-RNA-CPG125, 129dA-CEPhosphoramidite8, 12, 15, 16, 18, 20dA-H-Phosphonate39dA-MePhosphonamidite36dA-MePhosphoramidite38dA-PACEPhosphoramidite37dA-Thiophosphoramidite40, 142def-dA-CEPhosphoramidite22dma-dA-CEPhosphoramidite22N6-Ac-N6-Me-dA-CEPhosphoramidite47, 66N6-Me-A-CEPhosphoramidite135N6-Me-dA-CEPhosphoramidite47, 66Pac-A-CEPhosphoramidite129Pac-A-RNA-CPG129Pac-dA-CEPhosphoramidite23

A-2-Amino2-Amino-A-TOM-CEPhosphoramidite1312-Amino-dA-CEPhosphoramidite47

2’-OMe-2-Amino-A-CEPhosphoramidite140Pac-2-Amino-dA-CEPhosphoramidite47

Abasic Site 62, 84AbasicIIPhosphoramidite62dSpacer Phosphoramidite 62Pyrrolidine-CEPhosphoramidite63

Acridine Labelling3’-AcridineCPG114Acridine Phosphoramidite 114

Activator (Powder)4,5-Dicyanoimidazole305-Benzylthio-1H-tetrazole305-Ethylthio-1H-tetrazole26, 30, 70, 110, 112Saccharin1-Methylimidazole30

Adamantane Carbonyl Chloride 39Affinity Chromatography 151ÄKTA oligopilot 18, 19Aldehyde Modifier5’-Aldehyde-ModifierC2Phosphoramidite835-Formyl-dC-CEPhosphoramidite50FormylindoleCEPhosphoramidite83

Alternative Solvents and Reagents 30Amino-dA8-Amino-dA-CEPhosphoramidite59

Amino-dG8-Amino-dG-CEPhosphoramidite62

Amino-Modifiers3’-Amino-ModifierC6dCCPG813’-Amino-ModifierC6dTCPG813’-Amino-ModifierSerinolCPG793’-PT-Amino-ModifierC3CPG793’-PT-Amino-ModifierC6CPG793’-PT-Amino-ModifierC6PS795’-Amino-dT-CEPhosphoramidite555’-Amino-Modifier5745’-Amino-ModifierC3-TFA74, 755’-Amino-ModifierC674, 755’-Amino-ModifierC6-PDA755’-Amino-ModifierC6-TFA74, 755’-Amino-ModifierC12745’-Amino-ModifierC12-PDA755’-Amino-ModifierTEG745’-Amino-Modifier-TEG-PDA755’-DMS(O)MT-Amino-ModifierC674Amino-ModifierC2dT77Amino-ModifierC6dA77Amino-ModifierC6dC77Amino-ModifierC6dT77Amino-ModifierC6-UPhosphoramidite132Amino-ModifierSerinolPhosphoramidite78Fmoc-Amino-ModifierC6dT78N2-Amino-ModifierC6dG77PCAmino-ModifierPhosphoramidite76, 86, 95

AminoOxy-Modifier5’-AminoOxy-Modifier1176

Aminopurine2’-OMe-2-Aminopurine-CEPhosphoramidite140

Anthraquinone3’-UaqCapCPG49

Applied Biosystems InstrumentsAB39001000ÅCPGColumns10AB3900PolystyreneColumns10AB3900PolystyreneModifierColumns11CE Phosphoramidites 8Solvents/Reagents 8Supports and Columns 9

Aptamer Development 73AquaPhluor® 5935’-AquaPhluor®593Phosphoramidite108AquaPhluor®593CPG109

Aza-dC5-Aza-5,6-dihydro-dC-CEPhosphoramidite71

Azidobutyrate NHS Ester 89AzobenzeneAzobenzenePhosphoramidite122

BBenzylthio-1H-tetrazole 30Biocompatible Chemical Ligation 64Biotin Labelling3’-BiotinTEGCPG1013’-BiotinTEGPS1013’-ProtectedBiotinLCSerinolCPG96, 1013’-ProtectedBiotinSerinolCPG95, 1015’-BiotinPhosphoramidite100Biotin-dT100BiotinPhosphoramidite99BiotinTEGAzide92BiotinTEGPhosphoramidite99DesthiobiotinTEGAzide92DesthiobiotinTEG-CPG101DesthiobiotinTEGPhosphoramidite100PCBiotinPhosphoramidite86, 100ProtectedBiotinLCSerinolPhosphoramidite95, 99ProtectedBiotinSerinolPhosphoramidite94, 99

BlackBerry® Quencher3’-BBQ-650®CPG1125’-BBQ-650®Phosphoramidite112BBQ-650®-dT112

Black Hole Quencher™ Dyes3’-BHQ-1CPG1113’-BHQ-2CPG1113’-BHQ-3CPG111, 1125’-BHQ-1Phosphoramidite1105’-BHQ-2Phosphoramidite70, 110, 112BHQ-1-dT110, 112BHQ-2-dT110

Brancher PhosphoramiditedC Brancher Phosphoramidite 85

Br-dA8-Br-dA-CEPhosphoramidite60

Br-dC5-Br-dC-CEPhosphoramidite60

Br-dG8-Br-dG-CEPhosphoramidite60

Br-dU5-Br-dU-CEPhosphoramidite605-Br-dU-CPG60

Bromohexyl Phosphoramidite 89Br-U2’-OMe-5-Br-U-CEPhosphoramidite1415-Br-U-CEPhosphoramidite133

CC2’,3’-ddC562’,3’-ddC-CPG562’-F-Bz-C-ANACEPhosphoramidite1442’-OMe-5-Me-C-CEPhosphoramidite1412’-OMe-Ac-C-CEPhosphoramidite137, 1382’-OMe-Ac-C-PACEPhosphoramidite1452’-OMe-Ac-C-RNA1392’-OMe-C-CEPhosphoramidite1372’-OMe-C-RNA1393’-Amino-ModifierC6dCCPG813’-dC-CEPhosphoramidite653’-dC-CPG55, 655-Br-dC-CEPhosphoramidite605-Carboxy-dC-CEPhosphoramidite505-Formyl-dC-CEPhosphoramidite505-Hydroxymethyl-dC-CEPhosphoramidite505-Hydroxymethyl-dCII-CEPhosphoramidite505-I-dC-CEPhosphoramidite605-Me-Bz-C-LNA-CEPhosphoramidite415-Me-dC-CEPhosphoramidite465-OH-dC-CEPhosphoramidite61Ac-C-CEPhosphoramidite128Ac-C-RNA-CPG125, 127, 130Ac-dC-CEPhosphoramidite8, 12, 15, 16, 18, 20, 23Ac-dC-MePhosphonamidite36Ac-dC-PACEPhosphoramidite37Amino-ModifierC6dC77AP-dC68AP-dC-CEPhosphoramidite46C8-Alkyne-dC-CEPhosphoramidite87, 90C8-TIPS-Alkyne-dC-CEPhosphoramidite87C8-TMS-Alkyne-dC-CEPhosphoramidite87C-TOM-CEPhosphoramidite126dC Brancher Phosphoramidite 85dC-CEPhosphoramidite8, 12, 15, 16, 18, 20dC-H-Phosphonate39dC-MePhosphoramidite38dC-Thiophosphoramidite40, 142N4-Et-dC-CEPhosphoramidite47pdC-CEPhosphoramidite46Pyrrolo-dCTP68

162 163

MIS

CELL

ANEO

US

INDEX INDEX

tC-CEPhosphoramidite70tC°-CEPhosphoramidite70

Camphorsulfonyloxaziridine (CSO) 32Cap CPG3’-UaqCapCPG49, 64

Cap Phosphoramidite5’-PyreneCapPhosphoramidite495’-TrimethoxystilbeneCapPhosphoramidite49

Capping ReagentUniCap Phosphoramidite 32

Carboxy-dC5-Carboxy-dC-CEPhosphoramidite50

Carboxy-Modifiers5’-Carboxy-ModifierC5765’-Carboxy-ModifierC1076Carboxy-dT77

Chain Terminators 56ChelatesEDTA-C2-dT-CEPhosphoramidite118

Chemical Phosphorylation 82Cholesterol Labelling3’-Cholesteryl-TEGCPG1155’-Cholesteryl-TEGPhosphoramidite115Cholesteryl-TEGPhosphoramidite75, 115

CleanAmp™ TechnologyCleanAmp™ Primers 54

Click Chemistry 871,2,3-triazoles871-Ethynyl-dSpacerCEPhosphoramidite903’-Alkyne-ModifierSerinolCPG80, 89, 973’-Propargyl-5-Me-dCCPG645’-BromohexylPhosphoramidite895-Ethynyl-dU-CEPhosphoramidite885’-HexynylPhosphoramidite895’-I-dT-CEPhosphoramidite89Alkyne-ModifierSerinolPhosphoramidite89, 95Alkyne-NHSEster89Azides 89AzidobutyrateNHSEster89baseclickOligo-Click-M-Biotin90baseclickOligo-Click-M-Fluorescein90baseclickOligo-Click-M-Reload90baseclickOligo-Click-M-TAMRA90C8-Alkyne-dC-CEPhosphoramidite87, 90C8-Alkyne-dT-CEPhosphoramidite87C8-TIPS-Alkyne-dC-CEPhosphoramidite87, 88C8-TIPS-Alkyne-dT-CEPhosphoramidite88C8-TMS-Alkyne-dC-CEPhosphoramidite87, 88C8-TMS-Alkyne-dT-CEPhosphoramidite88ClickDNAandRNALigation64Copper-freeClickChemistry89THPTA Ligand 88TIPS-5-Ethynyl-dU-CEPhosphoramidite88

Convertible 2-dG2-F-dI-CEPhosphoramidite67

Convertible dAO6-Phenyl-dI-CEPhosphoramidite67

Convertible dUO4-Triazolyl-dU-CEPhosphoramidite67

Convertible F-dCTMP-F-dU-CEPhosphoramidite67

Convertible Nucleosides 67Copper-free Click Chemistry 905’-DBCO-TEGPhosphoramidite91DBCO-dT-CEPhosphoramidite91DBCO-sulfo-NHSEster91

Cross-linking 22, 58, 60, 93, 118, 123Custom Doping 51Cyanine LabellingCyanine3.5Phosphoramidite106Cyanine3CPG107Cyanine3Phosphoramidite106Cyanine5.5Phosphoramidite106Cyanine5CPG107Cyanine5Phosphoramidite106Disulfo-Cyanine7Azide93, 107

Cyanovinylcarbazole3-CyanovinylcarbazolePhosphoramidite123CNVK 123

Cyclo-dA5’,8-Cyclo-dACEPhosphoramidite63

Cyclo-dG5’,8-Cyclo-dGCEPhosphoramidite63

CyclooctatetraeneCOT Serinol Phosphoramidite 97

Cytosine Arabanoside 71

DDabcyl Labelling3’-DabcylCPG983’-DabcylPS983’-DabsylCPG70, 98, 110, 1125’-DabcylPhosphoramidite98Dabcyl-dT98

DBCO5’-DBCO-TEGPhosphoramidite91DBCO-dT-CEPhosphoramidite91DBCO-SerinolPhosphoramidite91DBCO-sulfo-NHSEster91

DCI (4,5-Dicyanoimidazole) 30Deaza-5-aza-C2’-OMe-3-deaza-5-aza-C-CEPhosphoramidite141

Deaza-8-aza-A7-deaza-8-Aza-A-CEPhosphoramidite1347-Deaza-8-aza-dA-CEPhosphoramidite57

Deaza-8-aza-G7-deaza-8-Aza-dG-CEPhosphoramidite57

Deaza-A3-Deaza-dA-CEPhosphoramidite577-Deaza-dA-CEPhosphoramidite57

Deaza-G7-Deaza-dG-CEPhosphoramidite57

Deaza-X7-Deaza-dX-CEPhosphoramidite5057

DendrimersAsymmetricDoubler(LEV)Phosphoramidite85LongTreblerPhosphoramidite85SymmetricDoublerPhosphoramidite85TreblerPhosphoramidite85

Depurination Resistant CE Phosphoramidites 22DesthiobiotinDesthiobiotinTEG-CPG101DesthiobiotinTEGPhosphoramidite100

Deuterated Nucleosides 60Diaminopurine 47, 131, 140Dicyanoimidazole 30Dideoxynucleoside, 2’,3’- 55Dideoxynucleosides2’,3’-ddA-CEPhosphoramidite562’,3’-ddC-CEPhosphoramidite562’,3’-ddC-CPG562’,3’-ddG-CEPhosphoramidite562’,3’-ddT-CEPhosphoramidite56

Dihydro-dT5,6-Dihydro-dT-CEPhosphoramidite61

Dihydro-dU5,6-Dihydro-dU-CEPhosphoramidite61

Distributors 6Dithiol3’-DithiolSerinolCPG80Dithiol Serinol Phosphoramidite 76

DNA Damage/Repair 62–63, 63DNA Methylation5-Carboxy-dC-CEPhosphoramidite505-Formyl-dC-CEPhosphoramidite505-Me-dC-CEPhosphoramidite46

DNA Methyltransferases 71DNP LabellingDNP-TEGPhosphoramidite114

Doubler PhosphoramiditeSymmetric85

Dr. Oligo SynthesizersCE Phosphoramidites 20Solvents and Reagents 20Supports and Columns 21

Duplex Stabilization 46, 47, 48, 49

EEclipse® QuencherEclipse®QuencherCPG109Eclipse®QuencherPhosphoramidite108

EDTA-dTEDTA-C2-dT-CEPhosphoramidite118

EdU5-Ethynyl-dU-CEPhosphoramidite88TIPS-5-Ethynyl-dU-CEPhosphoramidite88

ELITechGroup Dyes and Quencher 108Epigenetics 50, 135Et-dC-CE Phosphoramidite 47Etheno-AEtheno-dA-CEPhosphoramidite68

Ethylthiotetrazole 30Excimers 120Expedite™ Instruments

CE Phosphoramidites 12Solvents and Reagents 12Supports and Columns 13

FFAM3’-(6-FAM)CPG1043’-(6-FAM)PS1046-FAM1026-FAM-TEGAzide92Dipivaloyl6-FAM-TEGAzide92

F-ANA Monomers2’-F-A-ANACEPhosphoramidite1442’-F-Ac-C-ANACEPhosphoramidite1442’-F-Bz-C-ANACEPhosphoramidite1442’-F-G-ANACEPhosphoramidite1442’-F-U-ANACEPhosphoramidite144

F-C2’-F-Ac-C-CEPhosphoramidite492’-OMe-5-F-CPrecursor141F-dCPrecursor67

F-dI2-F-dI-CEPhosphoramidite67

F-dU5-F-dU-CEPhosphoramidite605-Fluoro-dU60

Ferrocene LabellingFerrocene-dT-CEPhosphoramidite119

Fluorescein Labelling3’-(6-FAM)CPG1043’-(6-FAM)PS1043’-(6-Fluorescein)CPG104, 1073’-6-FluoresceinSerinolCPG96, 1043’-FluoresceinCPG104

164 165

MIS

CELL

ANEO

US

INDEX INDEX

3’-Fluorescein-dTCPG1045’-Dichloro-dimethoxy-Fluorescein1025’-FluoresceinPhosphoramidite1025’-Hexachloro-Fluorescein1025’-Tetrachloro-Fluorescein1026-FluoresceinPhosphoramidite1036-FluoresceinSerinolPhosphoramidite94, 103Dichloro-diphenyl-fluorescein105Fluorescein-dTPhosphoramidite103SIMA(HEX)105

Fluorescent Nucleosides 682-Aminopurine-CEPhosphoramidite585-Me-2’-deoxyZebularine-CEPhosphoramidite71AP-dC-CEPhosphoramidite46Etheno-dA-CEPhosphoramidite68Perylene-dU-CEPhosphoramidite69Pyrrolo-C-TOM-CEPhosphoramidite132Pyrrolo-dC-CEPhosphoramidite68Pyrrolo-dCTP68tC-CEPhosphoramidite70tC°-CEPhosphoramidite70

Formyl-dC5-Formyl-dC-CEPhosphoramidite505-Formyl-dCIII-CEPhosphoramidite50

Formylindole CE Phosphoramidite 83Free Radicals 61F-RNA Monomers2’-F-Ac-C-CEPhosphoramidite1432’-F-A-CEPhosphoramidite1432’-F-G-CEPhosphoramidite1432’-F-U-CEPhosphoramidite143

F-U2’-OMe-5-F-U-CEPhosphoramidite1412’-OMe-TMP-5-F-U-CEPhosphoramidite141

GG2’,3’-ddG562’-F-G-ANACEPhosphoramidite1442’-F-G-CEPhosphoramidite1432’-OMe-G-CEPhosphoramidite1372’-OMe-G-PACEPhosphoramidite1452’-OMe-G-RNA1392’-OMe-iPr-Pac-G-CEPhosphoramidite1383’-dG-CEPhosphoramidite653’-dG-CPG55, 666-Thio-dG-CEPhosphoramidite586-Thio-G-CEPhosphoramidite1337-Deaza-8-aza-dG-CEPhosphoramidite577-Deaza-dG-CEPhosphoramidite578-Amino-dG-CEPhosphoramidite628-Br-dG-CEPhosphoramidite608-Oxo-dG-CEPhosphoramidite61Ac-G-CEPhosphoramidite128Ac-G-RNA-CPG127, 130dG-CEPhosphoramidite8, 12, 15, 16, 18, 20

dG-H-Phosphonate39dG-MePhosphonamidite36dG-MePhosphoramidite38dG-PACEPhosphoramidite37dG-Thiophosphoramidite40, 142dmf-dG-5’-CEPhosphoramidite34dmf-dG-CEPhosphoramidite8, 12, 15, 16, 18, 20dmf-G-LNA-CEPhosphoramidite41G-TOM-CEPhosphoramidite126iPr-Pac-dG-CEPhosphoramidite23iPr-Pac-G-RNA-CPG130N2-Amino-ModifierC6dG77O6-Me-dG-CEPhosphoramidite66

GalNAc5’-GalNAcC3Phosphoramidite116GalNAc C3 CPG 116

G-Clamp 46, 68GE Healthcare LIfe Sciences Instruments

CE Phosphoramidite 18Solvents and Reagents 19

Glen Gel-Pak™ PurificationGlenGel-Pak™150

Glen-Pak™ PurificationAdapter Rack 148Glen-Pak™DNAPurificationCartridge147Glen-Pak™RNAPurificationCartridge148RNAQuenchingBuffer148Seal for Adapter Rack 148

Glen UnySupport™GlenUnySupportCPG24, 25GlenUnySupportFCCPG25GlenUnySupportPS24, 25

Glyceryl CPG 80GoldConjugationtogoldsurfaces94

G-Quadruplex 72

HHalogenated Nucleosides2’-OMe-5-F-U-CEPhosphoramidite1412’-OMe-TMP-5-F-U-CEPhosphoramidite1415-Br-dC-CEPhosphoramidite605-Br-dU-CEPhosphoramidite605-Br-dU-CPG605-Br-U-CEPhosphoramidite1335-F-dU-CEPhosphoramidite605-I-dC-CEPhosphoramidite605-I-dU-CEPhosphoramidite605-I-U-CEPhosphoramidite1338-Br-dA-CEPhosphoramidite608-Br-dG-CEPhosphoramidite60

HEX 1026-HEXAzide92, 93

Hexynyl Phosphoramidite 89

High Load CPG 29H-Phosphonate Chemistry

Monomers 39ReagentsforABIsynthesizers39

Hydrogen Bonding 57Hydroxy-C5-OH-dC-CEPhosphoramidite61

Hydroxymethyl-dC5-Hydroxymethyl-dC-CEPhosphoramidite505-Hydroxymethyl-dCII-CEPhosphoramidite50

Hydroxymethyl-dU5-Hydroxymethyl-dU-CEPhosphoramidite61

Hydroxy-U5-OH-dU-CEPhosphoramidite61

II2-F-dI-CEPhosphoramidite672’-OMe-I-CEPhosphoramidite141, 142dI-CEPhosphoramidite51dI-CPG51I-CEPhosphoramidite133O6-Phenyl-dI-CEPhosphoramidite67

I-dC5-I-dC-CEPhosphoramidite60

I-dT5’-I-dT-CEPhosphoramidite89

I-dU5-I-dU-CEPhosphoramidite60

i-Motif DNA structures 72Introduction 1, 3, 5, 6, 8, 10, 12, 14, 16, 18, 20Ionizing Radiation 61isodCdmf-5-Me-isodC-CEPhosphoramidite53

isodGdmf-isodG-CEPhosphoramidite53

Isopropyl Phosphite 39I-U5-I-U-CEPhosphoramidite133

JJOE5’-Dichloro-dimethoxy-FluoresceinPhosphoramiditeII102

KKdK-CEPhosphoramidite52

LLabelling of MicroRNAs 64Large Scale SynthesisN3-Cyanoethyl-dT71

Locked Analog Phosphoramidites5-Me-Bz-C-LA-CEPhosphoramidite41Bz-A-LA-CEPhosphoramidite41dmf-G-LA-CEPhosphoramidite41T-LA-CEPhosphoramidite41

Locked Nucleic Acid (LNA) 41

MMaleimide-Modifier5’-Maleimide-ModifierPhosphoramidite76

Me-C2’-OMe-5-Me-C-CEPhosphoramidite1413’-Propargyl-5-Me-dCCPG645-Me-C-TOM-CEPhosphoramidite1315-Me-dC-CEPhosphoramidite46Ac-5-Me-dC-CEPhosphoramidite46

MerMade InstrumentsCE Phosphoramidites 16Solvents and Reagents 16Supports and Columns 17

Methylated Nucleosides1-Me-A-CEPhosphoramidite1351-Me-dA-CEPhosphoramidite661-Me-PseudouridinePhosphoramidite135N6-Ac-N6-Me-dA-CEPhosphoramidite47, 66N6-Me-A-CEPhosphoramidite135N6-Me-dA-CEPhosphoramidite47, 66O4-Me-dT-CEPhosphoramidite47, 66O6-Me-dG-CEPhosphoramidite66

Methylene BlueMethyleneBlueIIPhosphoramidite119MethyleneBlueNHSEster119

Methyl Phosphonamidites 36Me-U2’-OMe-5-Me-U-CEPhosphoramidite1405-Me-U-CEPhosphoramidite133

MGB3’-CDPI3MGB™CPG485’-CDPI3MGB™Phosphoramidite48, 117CDPI3 MGB™ CPG 117

MicroRNA 64Minor 2’-OMe-RNA Phosphoramidites 140–142Minor Groove 58Minor Groove Binder (MGB) 117Mixed Base Combinations 51Modifiers 74, 75, 78Mutagenesis 66

166 167

MIS

CELL

ANEO

US

INDEX INDEX

NNebularine2’-DeoxyNebularine-CEPhosphoramidite51

Nitroindole5-Nitroindole-CEPhosphoramidite52

Non-canonical Structures 72

OOligo-Affinity Support

OAS PS 151

OMe-RNA Synthesis2’-OMe-RNAPhosphoramidites1372’-OMe-RNASupports139Minor2’-OMe-RNAPhosphoramidites140, 141

OMe-T 140Oxo-dA8-Oxo-dA-CEPhosphoramidite61

Oxo-dG8-Oxo-dG-CEPhosphoramidite61

PPdP-CEPhosphoramidite52, 54

PACE Phosphoramidites2’-OMe-RNA-PACEPhosphoramidites145DNA PACE phosphoramidites 37

PCR/Sequencing Utilities 51PerylenePerylene-dU-CEPhosphoramidite69, 120

PhenothiazinetC-CEPhosphoramidite70

PhenoxazinetC°-CEPhosphoramidite70

Phosphonocarboxylate Monomers 37Phosphorylation3’-CPRIICPG823’-PhosphateCPG823’-PhosphateCPG-HighLoad823’-PhosphatePS82ChemicalPhosphorylationReagent82ChemicalPhosphorylationReagentII82CPR II 82Solid CPR II 82

Photoaffinity Labelling 58Photocleavable MonomersPCAmino-ModifierPhosphoramidite76, 86, 95PCBiotinPhosphoramidite86, 100PC Linker Phosphoramidite 86PC Spacer Phosphoramidite 84, 86

Photo cross-linking 58, 123

Photo-Regulation of DNA Function 70NPOM-Caged-dT-CEPhosphoramidite70

Photo-responsive DNAAzobenzenePhosphoramidite122

Phthalimide (PT)3’-PT-Amino-ModifierC3CPG793’-PT-Amino-ModifierC6CPG793’-PT-Amino-ModifierC6PS79

Poly-Pak™ PurificationPoly-Pak™Cartridge149Poly-Pak™IICartridge149Poly-Pak™Packing148, 149Reagents 148, 149

Polystyrene Supports3’-(6-FAM)PS1043’-BiotinTEGPS1013’-DabcylPS983’-PhosphatePS823’-PT-Amino-ModifierC6PS793’-TAMRAPS113GlenUnySupportPS24Universal Support III PS 26

PPG 57Propyne DerivativespdC-CEPhosphoramidite46pdU-CEPhosphoramidite46

Protein-DNA Interaction 58PseudoU1-Me-PseudouridinePhosphoramidite1352’-deoxypseudoU-CEPhosphoramidite58PseudoUridine-CEPhosphoramidite134

Psoralen LabellingPsoralen Azide 22, 93, 118Psoralen C2 Phosphoramidite 118Psoralen C6 Phosphoramidite 118

PurificationGlen-Pak™Purification147, 148Poly-Pak™Purification149

PurinePurine 52

PuromycinPuromycinCPG121

Pyrene5’-PyreneCapPhosphoramidite49Pyrene-dU-CEPhosphoramidite69, 70, 120

Pyridin-2-one-CE Phosphoramidite 134Pyrrolidine-CE Phosphoramidite 63Pyrrolo-CPyrrolo-C-TOM-CEPhosphoramidite132Pyrrolo-dC-CEPhosphoramidite68Pyrrolo-dCTP68

QQ-Supports 27, 28Quenched Autoligation (QUAL) Probes 1215’-Dabsyl-dT-CEPhosphoramidite121

RRedmond Red®RedmondRed®CPG109RedmondRed®Phosphoramidite108

Repair Enzyme 61Reverse Synthesis 34Rhodamine 113RNA Supportsfor3’DNAModification125

RNA SynthesisMinor RNA Phosphoramidites 130, 135RNA Phosphoramidites 128, 129RNA Supports 129, 130RNASupportsforTOM-RNASynthesis126, 127TOM-ProtectedMinorRNAPhosphoramidites127, 131,

132, 133TOM-ProtectedRNAPhosphoramidites126

SSaccharin 1-Methylimidazole 30SBC Oligos 48Sequence Modifiers 78Serinol Backbone3’-6-FluoresceinSerinolCPG96, 1043’-Alkyne-ModifierSerinolCPG80, 89, 973’-Amino-ModifierSerinolCPG79, 963’-DithiolSerinolCPG80, 973’-ProtectedBiotinLCSerinolCPG96, 1013’-ProtectedBiotinSerinolCPG95, 1016-FluoresceinSerinolPhosphoramidite94, 103Alkyne-ModifierSerinolPhosphoramidite89, 96Amino-ModifierSerinolPhosphoramidite78, 95COT Serinol Phosphoramidite 97Dithiol Serinol Phosphoramidite 76, 95ProtectedBiotinLCSerinolPhosphoramidite95, 100ProtectedBiotinSerinolPhosphoramidite94, 100

SIMASIMA(HEX)-dTPhosphoramidite105SIMA(HEX)Phosphoramidite105

SMI 30Spacer Modifiers1-Ethynyl-dSpacerCEPhosphoramidite903’-SpacerC3CPG84dSpacer CE Phosphoramidite 84PC Spacer Phosphoramidite 84, 86rSpacer CE Phosphoramidite 132rSpacer TBDMS CE Phosphoramidite 134Spacer C12 CE Phosphoramidite 84

Spacer Phosphoramidite 9 84Spacer Phosphoramidite 18 84Spacer Phosphoramidite C3 84

Spermine Phosphoramidite 48Spin Labels

TEMPO Azide 93TEMPO-TEGAzide93

Stearyl Labelling 1155’-StearylPhosphoramidite115

SterlingIntroduction7

Structural Studies 57Structure/Activity Relationship 57Sulfurizing Reagent 33Sulfurizing Reagent II 33

TT2’,3’-ddT562-Thio-dT-CEPhosphoramidite583’-Amino-dTCPG643’-Amino-ModifierC6dTCPG813’-dT-CEPhosphoramidite653’-dT-CPG55, 663’-Fluorescein-dTCPG1044-Thio-dT-CEPhosphoramidite585,6-Dihydro-dT-CEPhosphoramidite615’-Amino-dT-CEPhosphoramidite555’-Dabsyl-dT1215’-I-dT-CEPhosphoramidite895’-OMe-dT-CEPhosphoramidite55Amino-ModifierC2dT77Amino-ModifierC6dT77C8-Alkyne-dT-CEPhosphoramidite87C8-TIPS-Alkyne-dT-CEPhosphoramidite88C8-TMS-Alkyne-dT-CEPhosphoramidite88DBCO-dT-CEPhosphoramidite91dT-CEPhosphoramidite8, 12, 15, 16, 18, 20dT-H-Phosphonate39dT-MePhosphonamidite36dT-MePhosphoramidite38dT-PACEPhosphoramidite37dT-Thiophosphoramidite40EDTA-C2-dT-CEPhosphoramidite118Ferrocene-dT-CEPhosphoramidite119Fluorescein-dT103N3-Cyanoethyl-dT71NPOM-Caged-dT70O4-Me-dT-CEPhosphoramidite47, 66S-Bz-Thiol-ModifierC6-dT78TAMRA-dT113ThymidineGlycolCEPhosphoramidite62T-LNA-CEPhosphoramidite41

TAMRA Labelling3’-TAMRACPG1133’-TAMRAPS113

168 169

MIS

CELL

ANEO

US

INDEX INDEX

TAMRA-dT113TAMRA NHS Ester 113

tCtC-CEPhosphoramidite70

tCnitrotCnitro-CEPhosphoramidite70

tCoRibo-tC°-CEPhosphoramidite136tC°-CEPhosphoramidite70

TEMPOTEMPO Azide 93TEMPO-TEGAzide93

Termination, 3’2’,3’-ddA562’,3’-ddC562’,3’-ddC-CPG562’,3’-ddG562’,3’-ddT563’-3’linkage35, 553’-dA-CPG553’-dC-CPG553’-dG-CPG553’-dT-CPG553’-SpacerC3CPG84

Termination, 5’5’-OMe-dT-CEPhosphoramidite55

Terminus Modifiers 74TET 1026-TETAzide92, 93

Thio-dT2-Thio-dT-CEPhosphoramidite584-Thio-dT-CEPhosphoramidite58

Thio-dU4-Thio-dU-CEPhosphoramidite58

Thio-G6-Thio-dG-CEPhosphoramidite586-Thio-G-CEPhosphoramidite133

Thiol-Modifiers3’-DithiolSerinolCPG803’-Thiol-Modifier6S-SCPG805’-Thiol-ModifierC676Dithiol Serinol Phosphoramidite 76S-Bz-Thiol-ModifierC6-dT78Thiol-ModifierC6S-S76

Thiophosphoramidites2’-OMe-RNAThiophosphoramidites142DNA Thiophosphoramidites 40

Thio-U4-Thio-U-TOM-CEPhosphoramidite131

Thymidine GlycolThymidineGlycolCEPhosphoramidite62

Thymine DimerCis-synThymineDimerPhosphoramidite63

Tm Modulation 53Tocopherola-Tocopherol-TEGPhosphoramidite115

TOM-Protecting-GroupAc-A-RNA-CPG126Ac-C-RNA-CPG127Ac-G-RNA-CPG127A-TOM-CEPhosphoramidite126C-TOM-CEPhosphoramidite126G-TOM-CEPhosphoramidite126U-RNA-CPG127U-TOM-CEPhosphoramidite126

Trebler PhosphoramiditeTrebler85

Trimer phosphoramidites 42Trimethoxystilbene5’-TrimethoxystilbeneCapPhosphoramidite49

Triphosphate NucleotidesPyrrolo-dCTP68

Triplex 57Triplex-forming oligonucleotides 72

UU2’-F-U-ANACEPhosphoramidite1442’-OMe-5-Br-U-CEPhosphoramidite1412’-OMe-5-F-U-CEPhosphoramidite1412’-OMe-5-Me-U-CEPhosphoramidite1402’-OMe-TMP-5-F-U-CEPhosphoramidite1412’-OMe-U-CEPhosphoramidite1372’-OMe-U-PACEPhosphoramidite1452’-OMe-U-RNA1393’-UaqCapCPG49, 644-Thio-dU-CEPhosphoramidite585,6-Dihydro-dU-CEPhosphoramidite615-Br-dU-CEPhosphoramidite605-Br-dU-CPG605-Ethynyl-dU-CEPhosphoramidite885-F-dU-CEPhosphoramidite605-Hydroxymethyl-dU-CEPhosphoramidite615-I-dU-CEPhosphoramidite605-I-U-CEPhosphoramidite1335-OH-dU-CEPhosphoramidite61Amino-ModifierC6-UPhosphoramidite132Br-U-CEPhosphoramidite133dU-CEPhosphoramidite51dU-CPG50051dU-CPG100051O4-Triazolyl-dU-CEPhosphoramidite67pdU-CEPhosphoramidite46Perylene-dU-CEPhosphoramidite69Pyrene-dU-CEPhosphoramidite69, 70TIPS-5-Ethynyl-dU-CEPhosphoramidite88TMP-F-dU-CEPhosphoramidite67

U-CEPhosphoramidite128, 129U-RNA-CPG125, 127, 130U-TOM-CEPhosphoramidite126

UltraMILD Deprotection2’-OMe-Ac-C-CEPhosphoramidite1382’-OMe-iPr-Pac-G-CEPhosphoramidite1382’-OMe-Pac-A-CEPhosphoramidite138Ac-C-CEPhosphoramidite129Ac-dC-CEPhosphoramidite23CapMixA23, 38, 130, 138iPr-Pac-dG-CEPhosphoramidite23iPr-Pac-G-CEPhosphoramidite129Pac-A-CEPhosphoramidite129Pac-dA-CEPhosphoramidite23PotassiumCarbonateinMethanol23, 38, 130, 138

UniCap Phosphoramidite 32Universal Support III

Universal Support III PS 26

Unnatural base pairs 48Unnatural Base Pairs5-Me-isodC53isodG 53

VVitamin E 115

XX2’-dX-CEPhosphoramidite597-deaza-dX-CEPhosphoramidite57

X-ray crystallography 60

YYakima Yellow®YakimaYellow®CPG109YakimaYellow®Phosphoramidite108

ZZebularine5-Me-2’-deoxyZebularine-CEPhosphoramidite71Zebularine-CEPhosphoramidite134

Zip Nucleic Acid 48Spermine Phosphoramidite 48

ZNA® 48Spermine Phosphoramidite 48

170 171

MIS

CELL

ANEO

US

INDEX INDEX

172

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Documents

Products for DNA Research · 2019. 4. 24. · Company awarded patents for a chemical phosphorylation reagent compatible with DMT-ON purification. 2002 . Company made an agreement