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 be
more suitable for nano/biotechnology:
• faster
• more efficiently
• less (or no) damage
Oxidative
hole 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
O
O
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
O
N
H2N NH2
N+
-0.5 V
H
O
O
N
NO
O
O
N
H
OO -
-2.1 V
H
O
O
N
N
N CH3
+ -1.0 V
Part I+II: Photoinduced electron transfer in DNA
Excited state potentials of electron donors
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.
Electron
hopping
Electron
tunneling
Part I. Nucleoside models for electron transfer in DNA
Summary
H
O
O
N
N
HO
OH
O
Py-dU
hν e-
kET : 4.7 ps
pKa = 5.5
O
N
N
HO
OH
O
Py-dC
hν e-
NH2
kET : 40 ps
pKa > 12
Nucleoside model studies:
• T is reduced faster
• exhibits strong basicity•-dC
Implication for DNA:
is the major electron carrierdT -•
Nicole Amann, Elke Mayer-Enthart
In 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, 706
Chem. 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
Strand
break
(HPLC
analysis)
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 1500
0.0
0.5
1.0
0 5 10
0.0
0.5
1.0
Δ
A
485 nm
364 nm
time (ps)
dU
Py
A dU
Br
T T T
*
dU
Py
A dU
Br
T T T
-
+
DNA-ET
Fluorescence Recombination
- Br
Strand Cleavage
Electron injection
2 ps-1 dU
Py
A dU
Br
T T T
-
+several
100 ps-1
-
Py-dU
N
N
O
O
H
HO
HO
O
Nicole Amann
Elke 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 dU
Br
T T T
-
+
DNA-ET
Fluorescence Recombination
- Br
Strand Cleavage
Electron injection
2 ps-1 dU
Py
A dU
Br
T T T
-
+several
100 ps-1
-
Nicole Amann
Elke Mayer-Enthart, Peter Kaden
• Electron injection is independent of
conformational flexibility of DNA
• ET occurs on a manifold of time constants
due to DNA base dynamics
Conformational contribution
of 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 sequence
and distance dependence
0 10 20 30 40 50 60
0
20
40
60
80
100
2C
3C
1C
3T
1T
Pt
z-
D
N
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
A
A
A
A
A
dU
dU
T
Pz
Br
-
T
T
A
A
A
A
A
(H) (-H)
Efficient strand degradation
dU
dU
C
Pz
Br
-
C
C
A
G
G
G
A
-(-H)(H)
dU
dU
C
Pz
Br
C
C
A
G
G
G
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
3T
2C
St
ra
nd
c
le
av
ag
e
Time (min)
3T
2C
Part I. Reductive electron transfer in M-DNA
Thio-dU-Ag(I) base pairs
Janez Barbaric
Based 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
N
HO
OH
O
X = Py-dU
1
Eur. J. Org. Chem. 2008, 64. Nicole Amann
Claudia Wanninger-Weiß
LUMO
Part I. Pyrene as an electron donor
Py*-dU
H
O
O
N
N
HO
OH
O
X = Py'dU
2
Part I: Electron donor placement
Functionalization of DNA
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.
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
O
N
H
N
S
O
DNA
DNA
H
O
O
N
NO
