Download pdf - Functional DNA architectures: Photoinduced …dnatec09/presentations/2009_05...Part I. Nucleoside models for electron transfer in DNA Summary H O O N N HO OH O Py-dU hν e-k ET : 4.7

Functional DNA architectures: Photoinduced electron transfer and

switchable optical properties

Hans-Achim Wagenknecht

Part I+II: Photoinduced charge transfer in DNA

Part I+II: Photoinduced charge transfer in DNA

Hole transfer vs. electron transfer

H.-A. Wagenknecht (Ed.), Charge Transfer in DNA, Wiley-VCH, 2005, 1.Angew. Chem. Int. Ed. 2003, 42, 2454; Curr. Org. Chem. 2004, 8, 251; Nat. Prod. Rep. 2006, 23, 973.

Proposed to bemore suitable for nano/biotechnology:• faster• more efficiently• less (or no) damage

Oxidativehole transfer

Reductive(excess)electron transfer

X X Do

X X X

X X X Ac

X X X X

X X

X X

*+

HOMO

LUMO

Do* B

ET

Hole injection

X X Do

X X X

X X X Ac

X X X X

X X

X X

*-

HOMO

LUMO

Do* B

ET

Electron injection

• Superexchange• Hopping

OO

N

N

O

O

H

S

N

O

O

O N

N

O

O

H

H3C

O

O

O

-2.3 V

-2.0 V

-1.8 V

-2.15 V

-1.80 V

-1.10 V

C, T

C(H), T(H) ?

- -

H

O

ON

H2N NH2

N+

-0.5 V

HO

O

N

NO

O

O

NH

OO -

-2.1 V

H

O

ON

NN CH3

+ -1.0 V

Part I+II: Photoinduced electron transfer in DNA

Excited state potentials of electron donors


Electronhopping

Electrontunneling

Part I. Nucleoside models for electron transfer in DNA

Summary

H

O

O

N

NHO

OH

O

Py-dU

hν e-

kET : 4.7 pspKa = 5.5

O

N

NHO

OH

O

Py-dC

hν e-

NH2

kET : 40 pspKa > 12

Nucleoside model studies:

• T is reduced faster

• exhibits strong basicity•-dC

Implication for DNA:

is the major electron carrierdT -•

Nicole Amann, Elke Mayer-EnthartIn collaboration with Torsten Fiebig, Boston

Synlett 2002, 687.Angew. Chem. Int. Ed. 2002, 41, 2978.Chem. Commun. 2003, 1878 .Synthesis 2003, 2335.

ChemPhysChem 2004, 5, 706Chem. Phys. Lett. 2005, 409, 277.

Redox potentials:

C and T as electron carriers in DNA

Part I. Reductive electron transfer in DNA

Angew. Chem. Int. Ed. 2003, 42, 2454.

Chem. Eur. J. 2005, 22, 1871.

Angew. Chem. Int. Ed. 2005, 44, 1636.

Proc. Natl. Acad. Sci. USA 2006, 103, 10192

DNA studies

Electron injection studies

Chem. Eur. J. 2002, 8, 4877-4883.

Eur. J. Org. Chem. 2003, 2498.

Angew. Chem. Int. Ed. 2004, 43, 1845.

-• 3'

5'

5'

3'

X

X A A

dU T

R

X

X

X

X

X

X

C

XG

X

hν

Part I. Reductive electron transfer in DNA

Angew. Chem. Int. Ed. 2003, 42, 2454.

Chem. Eur. J. 2005, 22, 1871.

Angew. Chem. Int. Ed. 2005, 44, 1636.

Proc. Natl. Acad. Sci. USA 2006, 103, 10192

DNA studies

Chemical electron acceptor

X

X X

X

dU XBr •-Br-

•

X

X X

X

dU X

Strandbreak

(HPLCanalysis)

ET

Br-dU

Br

N

N

O

O

H

O

HO

HO

Part I. Reductive electron transfer in pyrene-modified DNA

Time-resolved spectroscopy

Chem. Eur. J. 2002, 8, 4877.Angew. Chem. Int. Ed. 2005, 44, 1636.

150 ps

1500 ps

Time-resolved transient absorption spectra

0 500 1000 15000.0

0.5

1.0

0 5 100.0

0.5

1.0

ΔA

485 nm 364 nm

time (ps)

dU

Py

A dU

Br

T T T

*dU

Py

A dUBr

T T T

-+

DNA-ET

Fluorescence Recombination

- Br

Strand Cleavage

Electron injection

2 ps-1dU

Py

A dUBr

T T T

-+several

100 ps-1

-

Py-dU

N

N

O

O

H

HO

HO

O

Nicole AmannElke Mayer-Enthart, Peter Kaden

A A A A

Part I. Reductive electron transfer in pyrene-modified DNA

Influence of DNA dynamics

Chem. Eur. J. 2002, 8, 4877.Angew. Chem. Int. Ed. 2005, 44, 1636.

dU

Py

A dU

Br

T T T

*dU

Py

A dUBr

T T T

-+

DNA-ET

Fluorescence Recombination

- Br

Strand Cleavage

Electron injection

2 ps-1dU

Py

A dUBr

T T T

-+several

100 ps-1

-

Nicole AmannElke Mayer-Enthart, Peter Kaden

• Electron injection is independent of conformational flexibility of DNA

• ET occurs on a manifold of time constantsdue to DNA base dynamics

Conformational contributionof the DNA(„Conformational gating“)

A A A A A A

Part I. Reductive electron transfer in phenothiazine-modified DNA

Chemical experiments

Chem. Eur. J. 2005, 11, 1871.

3C

2C

1C

3T

2T

1T

A dU C

T A G

Ptz

C

G

C

G

TdU

A A

Br

5'3'

3'5'

-•

A dU C

T A G

Ptz

C

Br

AA

dU T

G 5'3'

3'5'

•-

5' 3'

3' 5'

TA dU C dU

T A G A A

Ptz Br•-

•-5' 3'

3' 5'

A dU T

T A A

Ptz

T

A

T

A

TdU

A A

Br

-•

5' 3'

3' 5'

A dU T

T A A

Ptz

T

Br

AA

dU T

A

-•TA dU T dU

T A A A A

Ptz Br

5'3'

3'5'

DNA base sequenceand distance dependence

0 10 20 30 40 50 60

0

20

40

60

80

100

2C3C

1C3T

1T

Ptz-

DN

A (%

)

Irradiation time (min)

2T

Clemens Wagner

Part I: Reductive electron transfer in DNA

Mechanism of electron hopping

Clemens Wagner

PCETNo PCET

• Each base pair can participate• Question of long range ET in G-C rich DNA?

Chem. Eur. J. 2005, 11, 1871.

dU

dU

T

Pz

Br

-T

T

AA

AA

A

dU

dU

T

Pz

Br

-T

T

AA

AA

A

(H) (-H)

Efficient strand degradation

dU

dU

C

Pz

Br

-C

C

AG

GG

A

-(-H)(H)

dU

dU

C

Pz

Br

C

C

AG

GG

A

Less efficient strand degradation

Part I. Reductive electron transfer in phenothiazine-modified DNA

Directionality

3T

A dU C

T A G

Ptz

C

Br

AA

dU T

G 5'3'

3'5'

•- •-5' 3'

3' 5'

A dU T

T A A

Ptz

T

A

T

A

TdU

A A

Br

Clemens Wagner

5‘ 3‘

3‘ 5‘

2C

0 10 20 30 40 50 60

0.0

0.2

0.4

0.6

0.8

1.0

3T2C

Stra

nd c

leav

age

Time (min)

3T

2C

Part I. Reductive electron transfer in M-DNA

Thio-dU-Ag(I) base pairs

Janez BarbaricBased on metallated base pair by Simone Peters in the group of Elmar Weinhold, Aachen

Photochemistry of pyrene-modified DNA bases

(Py•+ dU•-)*

H

O

O

N

NHO

OH

O

X = Py-dU

1

Eur. J. Org. Chem. 2008, 64. Nicole AmannClaudia Wanninger-Weiß

LUMO

Part I. Pyrene as an electron donor

Py*-dU

H

O

O

N

NHO

OH

O

X = Py'dU

2

Part I: Electron donor placement

Functionalization of DNA


DNA base substitutionDNA base modification

Part I. Electron donor placement

DNA Base substitution vs. base modification: Phenothiazine

Clemens WagnerOrg. Biomol. Chem. 2008, 6, 48.

DNA base substitution DNA base modification

ONH

N

S

O

DNA

DNA

H

O

O

N

NO

O

O

CH3

S

N

DNA

DNA

Tm values (17mer DNA)

CounterbaseA 50 °CC 50 °CG 50 °CT 49 °C

Tm values (17 mer DNA)

CounterbaseA 60 °CC 56 °CG 55 °CT 55 °C

1600 1400 1200 1000 800 600 400 200-2.5

-2.0

-1.5

-1.0

-0.5

0.0

0.5

1.0

I / a

.u.

U / mV

400 600 8000.0

0.2

0.4

0.6

0.8

1.0

ΔAno

rm

λ / nm

CV

Spectroelectrochemistry

OO

N

N

O

O

H

S

N

O

O

O N

N

O

O

H

H3C

O

O

O

-2.3 V

-2.0 V

-1.8 V

-2.15 V

-1.80 V

-1.10 V

C, T

C(H), T(H) ?

- -

H

O

ON

H2N NH2

N+

-0.5 V

HO

O

N

NO

O

O

NH

OO -

-2.1 V

H

O

ON

NN CH3

+ -1.0 V

Part II: Photoinduced electron transfer in DNA

Electron donors


Electronhopping

Electrontunneling

Part II: Charge transfer with cyanines

Non-intercalative mode: Cyanine dyes as the charge donor

J. Org. Chem. 2008, 73, 4263.

X

G

CTG C

A

CTCA

ANIT

C AX

CG

5'

3'

A NITElectron

transfer No ET

Low f luorescence High fluorescence

Florian MenacherMoritz Rubner

N N

O OP

O

O

OCy3

ON

NO2

OP

O

OO

O

NI

550 600 650 7000,0

0,2

0,4

0,6

0,8

1,0

Flu

ores

cenc

e in

tens

ity

λ / nm

without NI

Part II: Charge transfer in ethidium-modified DNA

Hole vs. electron transfer with ethidium

β=0.4 Å-1

β=0.3 Å-1

E

+ N

NH2H2N

N

O

OH

Proc. Natl. Acad. Sci. USA 2006, 103, 10192. Nicole Amann, Robert Huber, Linda ValisIn collaboration with Torsten Fiebig, Boston

+ •5'3'

3'5'

5' 3'

3' 5'

•

+AC A C

E T T Z

5' 3'

3' 5'

•

+AC

E T

G

ZT

CA

C

AC

E T Z

C AC

E T N

C

AC

E T

G

NT

CA

C

•

5'3'

3'5'

AC A C

E T T N

•

5'3'

3'5'

5' 3'

3' 5'

•-

-

-

Z

O

O

O NH2

O

N

NN N

NO2

O

O

O

N

3.4 6.8 10.2 13.6 17.05.8

6.0

6.2

6.4

6.6

6.8

7.0

7.2

7.4

7.6

7.8

Logk

ET

Distance(Angstrom)

β = 0.32

β = 0.42

β

= 0.32 Å-1

β

= 0.42 Å-1


Intercalative mode: Ethidium as a charge donor

β=0.4 Å-1

β=0.3 Å-1

E

+ N

NH2H2N

N

O

OH

Proc. Natl. Acad. Sci. USA 2006, 103, 10192. Nicole Amann, Robert Huber, Linda ValisIn collaboration with Torsten Fiebig, Boston

+ •5'3'

3'5'

5' 3'

3' 5'

•

+AC A C

E T T Z

5' 3'

3' 5'

•

+AC

E T

G

ZT

CA

C

AC

E T Z

C AC

E T N

C

AC

E T

G

NT

CA

C

•

5'3'

3'5'

AC A C

E T T N

•

5'3'

3'5'

5' 3'

3' 5'

•-

-

-

Z

O

O

O NH2

O

N

NN N

NO2

O

O

O

N


Conformational gating

β=0.4 Å-1

β=0.3 Å-1

Proc. Natl. Acad. Sci. USA 2006, 103, 10192.

rigid flexiblevs.

Nicole Amann, Robert Huber, Linda ValisIn collaboration with Torsten Fiebig, Boston

Inflence ofbase mismatch ?

Part II. Charge transfer in ethidium-modified DNA

Single base mismatch detection

Org. Biomol. Chem. 2005, 3, 36. Nicole AmannLinda Valis

G

CAGCATZCTEATGCTG

ACYA T C AC A G C T G C T

5'3'

3'5'+

550 600 650 700 750 8000

2

4

6

8

10

12

14

F/F 0

λ / nm

With charge transfer A, C, T, S

Y = G

ss

Strongmatch/mismatchdiscrimination

E

+ N

NH2H2N

N

O

OH

Z

O

O

O NH2

O

N

NN

Part II. Charge transfer in ethidium-modified DNA

Single base mismatch detection

550 600 650 700 750 8000

2

4

6

8

10

12

14

16

18

F/F 0

λ / nm

No significantmatch/mismatchdiscrimination

Control: without charge transfer

G

CAGCATGCTEATGCTG

ACYA T C AC A G C T G C T

5'3'

3'5'

Y = GA, C, T, S

ss

E

+ N

NH2H2N

N

O

OH

Org. Biomol. Chem. 2005, 3, 36. Nicole AmannLinda Valis

Part III: DNA architectures for switchable optical properties

Part III: DNA base substitutions

Interstrand thiazole orange dimers

Angew. Chem. Int. Ed. 2009, accepted. Sina Berndl

OO

NH

O

O SN

N

TO

G T C A G T T G C A5' 3'T GAC A C C

C A G T C A A C G T3' 5'A CTO T T G G

G T C A G T C T G C5' 3'A TAC A A G

C A G T C A G A C G3' 5'T ATO TO T T C

C A G T C A A C G T3' 5'A CTO T T G G

G T C A G T T G C A5' 3'T GTOT A C C

500 550 600 650 7000.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

λ / nm

I / a.u.


Interstrand thiazole orange excimers

Sina BerndlAngew. Chem. Int. Ed. 2009, accepted.

500 550 600 650 700 750 8000.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

λ / nm

DNA5

DNA5 + 4.9 equiv. DNA6

I / a.u.

G T C A A C CG

T A

TO T T G

C

C A G T T G G

T

5'

C A

TOT A C

G

GT

C

T TG

A3'

A A C T G G C A G5' AC T G TGACCAACT 3'T GCA

T T G A C C G T CA G T C A G T T G A C T G G T C ATOACTG TO T T G A C 5'3'

Part III. DNA base substitutions

Aggregation of perylenebisimide-capped DNA

Org. Lett. 2006, 8, 4191. Clemens Wagner

NN

O

OO

OODNA

ODNA

550 600 650 700 750 8000

1

2

3

4

10 °C 20 °C 30 °C 40 °C 50 °C 60 °C 70 °C 80 °C

Fluo

resc

ence

inte

nsity

Wavelength (nm)

C A T T T T

G T A A A A

3'

5'

CATTTT

GTAAAA

3'

5'

C A T T T T

G T A A A A

3'

5'

+

Tm

DNA DNA


Interstrand perylenebisimide dimers

Daniela Baumstark

Match: X = TMismatches: X = C, A, G

GTGAGTCXCTGCATGCA

CAGTCAAACGTACGT5'

3'

3'

5'

550 600 650 700 750 800 850 9000.0

0.2

0.4

0.6

0.8

1.0

1.2

0 20 40 60 80 1000.0

0.5

1.0

1.5

2.0

2.5

Wavelength (nm)

Match:

Flu

ores

cenc

e in

tens

ity

0 % 5 % 10 % 20 % 40 % 60 % 80 %100 %

[Match] / %

I558/I603

I603/I660

Angew. Chem. Int. Ed. 2008, 47, 2612.


Interstrand perylenebisimide-zippers

Daniela Baumstark

GTGCATATTATGCACG

CACGTATTATACGTGC G

C

5'

3'

3'

5'

550 600 650 700 750 800 850 9000.0

0.2

0.4

0.6

0.8

1.0

1.2

Fluo

resc

ence

Inte

nsity

Wavelength / nm

10°C 20°C 30°C 40°C 50°C 60°C 70°C 80°C 90°C

CACGTATTATACGTGC G5' 3'

ΔT

Chem. Eur. J. 2008, 14, 6640.

GTGCATTTTGCACG

CACGTTTTACGTGC G

C

5'

3'

3'

5'

550 600 650 700 750 800 850 9000.0

0.5

1.0

1.5

2.0

2.5

Fluo

resc

ence

Inte

nsity

Wavelength / nm

10°C 20°C 30°C 40°C 50°C 60°C 70°C 80°C 90°CΔT

CACGTTT

TACGTGC G5' 3'



Daniela Baumstark

GTGCATTTTGCACG

CACGTTTTACGTGC G

C

5'

3'

3'

5'

GTGCATATTATGCACG

CACGTATTATACGTGC G

C

5'

3'

3'

5'

Chem. Eur. J. 2008, 14, 6640.

GTGCASSSTGCACG

CACGTSSSACGTGC G

C

5'

3'

3'

5'

OO

O

S

PO

OO

450 500 550 600 650-6

-4

-2

0

2

4

6

8

Θ /

mde

g cm

2

λ / nm

Left-handed helix?

CD spectra



Daniela Baumstark

GTGCATTTTGCACG

CACGTTTTACGTGC G

C

5'

3'

3'

5'

Chem. Eur. J. 2008, 14, 6640.

Left-handed helix?

450 500 550 600 650-6

-4

-2

0

2

4

6

8

Θ /

mde

g cm

2

λ / nm

35-45 ° left85-95 °C right

85-95 °C right35-45 ° left

35-45 ° left

Δε

= f(sin(2λ))

CD spectra

Part III: DNA base modifications

Multifluorophores based on DNA base modifications

Reji Varghese

together with fs-resolved microarray readout

BB

BB

B

B

B

B

B

B

BB

BB= chromophores

B = DNA base

Genetic codonB

BB

BBB

B

Single base mutations

DNA hybridization

Random coil single strand

Helical chromophoreassembly


Multiple Py-≡-dU-labels

Org. Biomol. Chem. 2006, 4, 2088. Janez Barbaric

CD

250 300 350 400 450 500

-6

-4

-2

0

2

4

6

8C

D /

mde

g

λ / nm

350 400

0

5

10 °C

90 °Cθ

/ mde

gcm

2

Manuscript submitted.


Multiple Py-dU-labels

Angew. Chem. Int. Ed. 2006, 45, 3372. Elke Mayer-Enthart

Fluorescence

ds/ss = 22

400 450 500 550 6000.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

Flu

ores

cenc

e in

tens

ityWavelength (nm)

PydU5/PydU1 = 11

Vielberth-Symposium

on Functional Nucleic

Acids

(IV. Nucleinsäurechemie-Treffen)

10. –

11. September 2009

University of Regensburg (Germany)

Header

picture: Karsten Dörre, GFD-Licence: www.gnu.org/licenses/fdl-1.2.html

Lectures:

Hiroyuki

Asanuma

(Nagoya, JP)

Shankar Balasubramanian

(Cambridge, UK)

Tom Brown (Southampton, UK)

Alexander Deiters

(Raleigh, North Carolina, USA)

Alexander Heckel (Frankfurt, D)

Christian Leumann

(Bern, CH)

Jens Müller (Münster, D)

Floyd Romesberg

(Scripps

La Jolla, USA)

Poster session

including

short

poster

talks

Header

picture: Karsten Dörre, GFD-Licence: www.gnu.org/licenses/fdl-1.2.html

Acknowledgements

Fonds derChemischenIndustrie