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
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.
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
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
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
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.
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
Part II: Charge transfer in ethidium-modified DNA
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
Part II: Charge transfer in ethidium-modified DNA
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.
Part III: DNA base substitutions
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
Part III: DNA base substitutions
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.
Part III: DNA base substitutions
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'
Part III: DNA base substitutions
Interstrand perylenebisimide-zippers
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
Part III: DNA base substitutions
Interstrand perylenebisimide-zippers
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
Part III: DNA base modifications
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.
Part III: DNA base modifications
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