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Recombinase Polymerase Amplification
Radhika PradhanAidan QuinnZiwei Song
Class 26_2011 updated Dec. 8, 201 12:45 AM
TwistDx Ltd.
qPCR Primer Design
Portable real-time fluorometer
ADVANTAGES AND POTENTIAL APPLICATIONS
Advantages
• From 1 molecule DNA or 10 molecules RNA to detectable levels (billions or trillions) in 5-10 min
• Low cost and simple reagents means practical applications are enormous
• Multiplexing allows simultaneous detection of multiple targets
Potential applications
9
Therapeutic intervention at the level of pre-mRNA splicing
A. Interfere with improper splicing caused by splice site creation or activation
E.g., beta-thalassemia (R. Kole) in which a splice site has been created by a mutation in a hemoglobin gene
Use complementary DNA or RNA (antisense)Natural DNA/RNA rapidly degraded:
Use modified bases, sugars: PNA, morpholino, 2’ OMe,
Normally, DNA-RNA hybrids + endogenous RNase H type activity RNA destruction
Modified antisense DNA circumvents this problem (don’t want mRNA destroyed here, want to correct its splicing.)
PNA = peptide nucleic acids
Class 26_2011 updated Dec. 8, 201 12:45 AM
10
B. Bias alternative splicing ratios
Target the unwanted isoform exon-intron joint.
e.g., BCL-2 isoforms, one is pro-apoptotic, one anti-apoptotic. The latter is increased in many cancers Target the anti-apoptotic isoform in cancer cells.
e.g., GABA-a-gamma-2 receptor (GABA = gamma amino butyric acid, a neurotransmitter) Long and short forms. Long form associated with mental illness.
C. Skip offensive exons
e.g., nonsense truncations in dystrophin --->
11
x
Nonsense mutation truncates protein
Expendable exon (e.g., protein with many repeated domains)
Exon must be multiple of 3 in length to maintain reading frame after skipping
Antisense-induced skipping
Splicing as a target for disease therapy
12
Deoxy, or also can add 2’ MOE
-O-CH2-CH2-O-CH3
Phosphorothioate deoxyoligonucleotides
MOE = methoxyethyl -
RNA modification
13
Morpholino instead of deoxyribose or ribose
Modified phosphate
RNA modification for stabilization
Still base pairs OK!
ase
ase
14
Attached 1 to 4 lysines here
PNA = peptide nucleic acid
Amide bonds,No ribose
B = a nucleic acid baseRNA modification
Even more extreme and more stable: peptide nucleic acids (PNAs)
Base pairs even better than natural nucleic acids (higher melting temperatures)
15
Sazani P, et al. and Kole R.Systemically delivered antisense oligomers upregulate gene expression in mouse tissuesNat Biotechnol. 2002 Dec;20(12):1228-33.
EGFP: Enhanced green fluorescent protein = model system
Actin promoter, universally expressed. Induced exon skipping yields green fluorescence
Mutant globin intron has activated splice sitesAntisense “RNA” injected into tail vein, RNA was modified for stability
A. Interfere with improper splicing caused by splice site creation or activation
16
Antisense treatment incell cultures (ex vivo) from themouse with the mutant EGFP gene
Control oligo (C)(50 nt downstream)was ineffective.
Max. effect = 40%
No antisense:
17
Dystrophin gene 2400 kb, mRNA = 14 kb, 79 exons: a giant geneProtein maintains muscle cell membrane integrityMutation: Duchenne’s muscular dystrophySome cases (~half) are due to stop codons (nonsense) in a repetitious exon (spectrin-like repeat, length = a multiple of 3)
Deliver antisense to the ends of exon with the nonsense mutation in mdx mice (model for Duchenne’s) to promote the skipping of the nonsense-bearing exon and so avoid truncation of the protein .Use AAV (adeno-associated virus) to deliver the antisense gene
Measure:mRNA with skipped exondystrophin proteinmuscle histochemistry for dystrophin
C. Skip offensive exons
18
= 3 X 71
Branch site (consensus = YNYTRAY)
protein
mRNA
79
Use antisense RNA to target the branch point upstream of the offending exon 23 and the donor splice site downstream of the exon.
BP = branch point; SD = splice donor
Sequences targeted by antisense
19
U7 promoter
compl. to splice donor site compl. to branchConsensus binding site for Sm proteins (to target to pre-mRNA)
Double target synergistic (loop?) (Kole)
ITR = inverted terminal repeat, characteristic of AAV
20
0 2 4 6 13 weeks
Expression of U7 antisense construct
Splicing assay (RT-PCR)
Dystrophin protein (Western)
Endog. U7 U7SmOPT-A.S.
RT-PCR
Skip exon 23, after 2-4 wks.
(slow onset =conclude slow mRNA turnover)
normal0 2 4 6 8 13 weeks
transgenic U7
included
21
Top, middle ,and bottom
Normal
Untreated mdx
Treated mdx
dystrophin dystrophin-associated antigensMuscle immuno-histochemistry
intriguing
22
RNAi = RNA interference
Short double stranded RNA molecules trigger thedegradation of the complementary sequence in the cell,and can inhibit translation of the targeted mRNA
Their introduction into a cell can greatly reduce any protein whose mRNA is targeted.
Inhibition is usually incomplete in mammalian cells, but can be considerable (>90%)Thus “gene knockdown” as opposed to knock-out
Alternative technologies:
Antisense RNA: block translation or splicingRibozymes: RNAs that cleave other RNAs, sequence specifically
siRNA = small inhibitory RNAsshRNA = short hairpin RNAs (both strands can be coded by one DNA)asRNA = antisense RNAmiRNA = microRNAsncRNA = noncoding RNA
23
Introduction of long DS RNA into mammalian cells will trigger the “interferon response:
Cessation of protein synthesis via activation of PKR (protein kinase RNA-activated), and phosphorylation of eIF2
Global degradation of mRNA (without any sequence specificity, RNase L activation)
Spread to neighboring cells (induction and secretion of interferon)
Most small DS RNAs do not trigger this response(<30 bp)
24
miRNA synthesis and maturation
25
mRNA degradationInhibits translation of an mRNA
26
Generation of siRNA in vitro
Chemical synthesis, annealing of 22-mers (bypasses dicing by Dicer)
Introduce perfect hairpin RNA into cells, let Dicer make siRNA
T7-mediated in vitro transcription of each complementary strand. Anneal to make long DS RNA and transfer to cells. Let Dicer make siRNA in the cell
Introduce imperfect hairpin RNA into cells(based on mRNA sequence) and let Dicer make miRNA
Also, can use controlled RNase to generatefragments (cheaper)
27
TRE Tet-inducible promoter
rtTA3 Reverse tet-transactivator
UBC promoter Drives expression of rtTA3 and IRES-puro
cPPT Central Polypurine tract. Helps translocation into nucleus of non-dividing cells
WRE Enhances the stability and translation of transcripts
turbo RFP Marker to track inducible shRNAmir expression
Puror Mammalian selectable marker
AMPr Ampicillin bacterial selectable marker
5'LTR 5' long terminal repeat
pUC ori High copy replication and maintenance in e.coli
SIN-LTR 3' Self inactivating long terminal repeat
IRES Internal ribosome entry site
ZEOr Bacterial selectable marker
Generation of si RNA in vivo
Got this far
29
Transient nature of the response (~3 days)
Limitations of siRNA silencing in mammalian cells
Transfection problems (cell type, refractoriness)
Can be cell type specific
Non-renewable nature of siRNAs ($$)
30
siRNA
Incorporation into the RNA-inducing silencing complex (RISC); stability in RISC.Base-pairing with mRNA.Cleavage of mRNA.
mRNA
Base-pairing with siRNA.The position of the siRNA-binding target region.Secondary and tertiary structures in mRNA.Binding of mRNA-associated proteins.The rate of mRNA translation.The number of polysomes that are associated with translating mRNA.The abundance and half-life of mRNA.The subcellular location of mRNA.
DeliveryTransfection (lipofection, electroporation, hydrodynamic injection (mouse))Virus infection (esp. lentivirus (e.g., retrovirus like HIV that can integrate into non-dividing cells)
Potential determinants of efficient siRNA-directed gene silencing
31
Target oncogene Ras V12 (G12V) – silenced mutant ras without silencing the WT allele. Reduced the oncogenic phenotype (soft agar growth, tumor formation in nude mice)
Some applications:
T-lymphocytes infected with anti-CCR5 RNA lower levels of this HIV receptor, and lower levels of infection (5-7X)
Target an enzyme in mouse ES cells with a hairpin vector, Isolate a knockdown, make a mouse. Mouse shows same knockdown phenotype in its cells. So can target the whole mammalian organism,
Just inject a GFP silencer gene into single cell embryos of a GFP mouse:Can find a chimeric GFP mouse with reduced GFP Progeny carry it in the germ line, Get a complete knockdown mouse, without ES cells (easier)
32
Hydrodynamic injection (sudden large volume) of straight siRNA (no vector) into the tail vein of a newborn mouseGet silencing of co-injected luciferase vector in a variety of tissues
C. elegans, 19,000 genes
Make a library 17,000 siRNA genes in plasmids in E. Coli.
Feed the clones of E. coli to the worms.
Look for phenotypes.
1700 genes examined for phenotypes (as of 2005)
(e.g., fat metabolism phenotypes found)
Identify the genes affected from sequnce of the siRNA
High throughput siRNA for gene discovery
Delivery in an intact organism
33NATURE 428. 2004. p. 431
tsSV40LTag inactivates p53 at 32o but not at 39o.Infect with Hu shRNA lentivirus shRNA library;select cells that grow at 39o.Knocked down genes = those necessary for p53-induced growth arrest.
Identified shRNAs
Control Control p16K.D. p53K.D. p533+p16K,K.D.
32o 39o 39o 39o 39o
34
Systemic RNAi: worms, plants, mammals
In plants, get permanent post-transcriptional gene silencing (PTGS, transcriptional level)
Worms: effect can last though several generationsAmplified by reverse transcriptaseInflux/efflux via a specific transmembrane protein (in worms)
Raisons d’etre?
Infection, many viruses go through a DS RNA phase.
Repeat element silencing? (1 million Alus, + others half the human genome)Transcribed in either direction, so could form DS RNA, then RNAi inhibits action of SS ‘mRNA”
35
Nature (1998) 391: 806
Discovered RNAi as they tracked down the effective agent in antisense experiments (DS RNA contaminating their SS antisense preparations had all the inhibitory activity)
Paper characterized by nice controls and variations:Several genes, whole animal phenotype, protein product (GFP), RNA level (in situs)
Phenotype of null mutant is specifically mimicked.
Introns and promoter sequences ineffective.
DS RNA from a different sequence + SS antisense RNA vs. the target: ineffective
DS RNA linked (chimeric molecule) to a single stranded portion vs, the target: ineffective
Transport of DS RNA between cells and amplification implied.
Discovery of RNA interference using double-stranded RNA
36
No RNA injected
In situ hybridizations
No probe
SS antisense RNA
DS RNA
Transcript disappears (RNA degraded)
37Nucleic acid aptamersAptamers: molecules that bind other molecules with good affinity and specificity
Usually these are proteins . . . . But they can also be RNA or DNA.
That is, single stranded RNA or DNA molecules can and will fold up into secondary and tertiary structures depending on their sequence.DNA can be synthesized as very large numbers of different (random sequences)
Aptamers can be selected from among these molecules based on their ability to bind an immobilized ligand. The tiny fraction found by chance to be able to bind to your favorite ligand can by amplified by PCR (along with background molecules).
Re-iteration of the procedure will enrich for the aptamer until they dominate the population. At this point they can be cloned and sequenced.
RNA molecules can be selected by synthesizing them from a randomized DNA population using the T7 promoter appended to each DNA molecule.
This enrichment procedure is just the SELEX method described earlier for finding the RNA substrate for RNA binding proteins. In this case it’s the same procedure, looked from the opposite point of view: not what RNA will the protein bind best, but what RNA binds the protein best.
38SELEX
Have a random 40-mer synthesized, centered between 2 arbitrary 20-mers (PCR sites)
440 = 1024
Practical limit = 1015 = ~ 2 nmoles = ~ 50 ug DNA
1015 is a large number.Very large(e.g., 500,000 times as many as all the unique 40-mers in the human genome.)
These 1015 sequences are known as “sequence space”
Each DNA molecule of these 1015 (or RNA molecule copied from them) can fold into a particular 3-D structure. We know little as yet about these structures.
But we can select the molecules that bind to our target by: AFFINITY CHROMATOGRAPHY
20-merRandom 4020-mer
Previously discussed SELEX in terms of finding the substrate sequence(s) for an RNA binding protein. Here: select an RNA sequence that can bind any particular target of interest (protein, small molecule).
39
Protein:thrombin
(blood protease)
RNA thrombin- binding aptamer
Who’s binding whom?
40
RNA
DNA
RNA
RNA
(1015)
e.g., the soluble form of the immobilized affinity column material
SELEX: Systematic Evolution of Ligands by Exponential Enrichment . . . for RNA (or DNA)
Ligand is immobilized here.Small molecule or large molecule
Essential elements:1) Synthesis of randomized DNA sequences2) In vitro T7-mediated RNA synthesis from DNA3) Affinity chromatography4) RT-PCR
DNA
41
Some examples of aptamer targets
Small molecules
Zn+2
ATPadenosinecyclic AMPGDP FMN (and an RNA aptamer is found
naturally in E.coli)cocainedopamineamino acids (arginine) porphyrinbiotinorganic dyes (cibacron blue, malachite
green) neutral disaccharides (cellobiose, and
cellulose)oligopeptidesaminoglycoside antibiotics (tobramycin)
Proteins
thrombinHIV tatHIV revFactor IX (clotting factor)VEGFPDGFricinlarge glycoproteins such as CD4anthrax spores (?)
42
Electrostatic surface map:
red= - blue = +
Base flap shuts door
Tobramycin
43Hermann, T. and Patel, D.J.2000. Adaptive recognition by nucleic acid aptamers. Science 287: 820-825.
Another anti-Rev aptamer:binds peptide in anextended conformation
One anti-Rev aptamer:binds peptide in alpha-helical conformation
MS2 protein as beta sheet bound via protruding A.A. side chains
44
Rusconi, C.P., Scardino, E., Layzer, J., Pitoc, G.A., Ortel, T.L., Monroe, D., and Sullenger, B.A. 2002.
RNA aptamers as reversible antagonists of coagulation factor IXa. Nature 419: 90-94.
Reading:
Therapeutic use of an aptamer that binds to and inhibits clotting factor IX
Inverted T at 3’ end (3’-3’) slows exonucleolytic degradation( R-3’O-P-O-3’-R-T )
Factor IX acts together with Factor VIIIa to cleave Factor X, thus activating it in a step in the blood coagulation cascade leading to a clot.
Thus inhibition of Factor IX results in inhibition of clot formation. Desirable during an angioplasty, for example.
The usual anti-coagulant used in angioplasty is heparin, which has some toxicity and is difficult to control.
45
Kd for Factor IX = 0.6 nM
F_IXa + F_VIIIa cleaves F_X
4 nM aptamer inhibits this activity
Conjugate to polyethyleneglycol to increase bloodstream lifetime
mutant version
-aptamer == 1
+aptamer-PEG,
Anti-Factor IX RNA aptamer isolated by SELEX
Clotting time increase
PEG = polyethyleneglycol polymer, appended to decrease clearance rate.
+aptamer+PEGylation
46An antidote to stop the anti-clotting action if a patient begins to bleed.Would be an improvement over heparin.Just use the complementary strand (partial) as an antidote. The 2 strands find each other in the bloodstream!
16-fold excess
+Oligomer 5-2 Ratio of anti- to aptamer
An
ti-co
ag
ula
nt
act
ivity
In human plasma duplexedfree aptamer
Antidote 5-2 design = the open squares
Scrambled antidote
47
Antidote acts fast(10 min)
Antidote lasts a long time
Antithrombin aptamer antidotetested in human serum
Need 10X antidote
Ant
i-coa
gula
nt a
ctiv
ityA
nti-c
oagu
lant
act
ivity
Ant
i-coa
gula
nt a
ctiv
ity
Ratio antidote/aptamer
Time (min)
Time (hr)
48
In serum of patients withheparin-induced thrombocytopenia
(heparin can no longer be used)
Reduced clotting
Reversed by antidote
49
R
From the label:
VEGF = vascular endothelial growth factor
Where R is and contains a PEG chain of ~ 450 ethylene glycol units.
The chemical name for pegaptanib sodium is as follows: RNA, ((2'-deoxy-2'-fluoro)C-Gm-Gm-A-A-(2'-deoxy-2'-fluoro)U-(2'-deoxy-2'-fluoro)C-Am-Gm-(2'-deoxy-2′-fluoro)U-Gm-Am-Am-(2'-deoxy-2'-fluoro)U-Gm-(2'-deoxy-2'-fluoro)C-(2'-deoxy-2'-fluoro)U-(2'-deoxy-2'-fluoro)U-Am-(2'-deoxy-2'-fluoro)U-Am-(2'-deoxy-2'-fluoro)C-Am-(2'-deoxy-2'-fluoro)U-(2'-deoxy-2'-fluoro)C-(2'-deoxy-2'-fluoro)C-Gm-(3'→3')-dT), 5'-ester with α,α'-[4,12-dioxo-6-[[[5-(phosphoonoxy)pentyl]amino]carbonyl]-3,13-dioxa-5,11-diaza-1,15-pentadecanediyl]bis[ω-methoxypoly(oxy-1,2-ethanediyl)], sodium salt.The molecular formula for pegaptanib sodium is C294H342F13N107Na28O188P28[C2H4O]n (where n is approximately 900) and the molecular weight is approximately 50 kilodaltons.Macugen is formulated to have an osmolality of 280-360 mOsm/Kg, and a pH of 6–7.
Inverted ribo-T3’-3’ to protect 3’ end
Macugen: an RNA aptamer that binds VEGF andis marketed for adult macular degeneration (wet type)