Crossover from superexchange to hopping as the mechanism for photoinduced charge transfer in DNA hairpin conjugates

Article abstract of DOI:10.1021/ja0540831

The mechanism and dynamics of photoinduced charge separation and charge recombination have been investigated in synthetic DNA hairpins possessing donor and acceptor stilbenes separated by one to seven A:T base pairs. The application of femtosecond broadband pump-probe spectroscopy, nanosecond transient absorption spectroscopy, and picosecond fluorescence decay measurements permits detailed analysis of the formation and decay of the stilbene acceptor singlet state and of the charge-separated intermediates. When the donor and acceptor are separated by a single A:T base pair, charge separation occurs via a single-step superexchange mechanism. However, when the donor and acceptor are separated by two or more A:T base pairs, charge separation occurs via a multistep process consisting of hole injection, hole transport, and hole trapping. In such cases, hole arrival at the electron donor is slower than hole injection into the bridging A-tract. Rate constants for charge separation (hole arrival) and charge recombination are dependent upon the donor-acceptor distance; however, the rate constant for hole injection is independent of the donor-acceptor distance. The observation of crossover from a superexchange to a hopping mechanism provides a "missing link" in the analysis of DNA electron transfer and requires reevaluation of the existing literature for photoinduced electron transfer in DNA.

Full text of DOI:10.1021/ja0540831

Published on Web 12/27/2005
Crossover from Superexchange to Hopping as the Mechanism
for Photoinduced Charge Transfer in DNA Hairpin Conjugates
Frederick D. Lewis,*,† Huihe Zhu,† Pierre Daublain,† Torsten Fiebig,*,‡
Milen Raytchev,‡ Qiang Wang,‡ and Vladimir Shafirovich*,§
Contribution from the Department of Chemistry, Northwestern UniVersity,
EVanston, Illinois 60201, Department of Chemistry, Boston College, Chestnut Hill,
Massachusetts 02467, and Department of Chemistry, New York UniVersity,
New York, New York 10003
Received June 20, 2005; E-mail: lewis@chem.northwestern.edu; fiebig@bc.edu; vs5@nyu.edu
Abstract: The mechanism and dynamics of photoinduced charge separation and charge recombination
have been investigated in synthetic DNA hairpins possessing donor and acceptor stilbenes separated by
one to seven A:T base pairs. The application of femtosecond broadband pump-probe spectroscopy,
nanosecond transient absorption spectroscopy, and picosecond fluorescence decay measurements permits
detailed analysis of the formation and decay of the stilbene acceptor singlet state and of the charge-
separated intermediates. When the donor and acceptor are separated by a single A:T base pair, charge
separation occurs via a single-step superexchange mechanism. However, when the donor and acceptor
are separated by two or more A:T base pairs, charge separation occurs via a multistep process consisting
of hole injection, hole transport, and hole trapping. In such cases, hole arrival at the electron donor is
slower than hole injection into the bridging A-tract. Rate constants for charge separation (hole arrival) and
charge recombination are dependent upon the donor-acceptor distance; however, the rate constant for
hole injection is independent of the donor-acceptor distance. The observation of crossover from a
superexchange to a hopping mechanism provides a “missing link” in the analysis of DNA electron transfer
and requires reevaluation of the existing literature for photoinduced electron transfer in DNA.
Introduction
led to the proposal that photoinduced electron transfer might
occur via either superexchange or hopping mechanisms, de-
The mechanism and dynamics of charge-transfer processes
in DNA continue to attract the attention of both experimentalists
and theoreticians.1 We and others proposed that photoinduced
charge transfer in systems possessing an excited acceptor
separated from a guanine or deazaguanine donor by a small
number of A:T base pairs occurs via a single-step superexchange
process.2-5 However, in the case of intercalated ethidium as
the acceptor, multistep hopping followed by irreversible trapping
was suggested as the mechanism for charge separation.6
Theoretical analyses of DNA bridge-mediated electron transfer
pending on the donor-bridge-acceptor energetics, endergonic
bridge oxidation favoring a superexchange mechanism (Scheme
1a) and exergonic bridge oxidation favoring a hopping mech-
anism (Scheme 1b).7 Because the superexchange process is
expected to be strongly distance dependent and the hopping
process weakly distance dependent, crossover from super-
exchange to hopping as the mechanism for charge separation
in DNA is expected to occur at intermediate distances, as has
been observed for charge separation in several donor-bridge-
acceptor systems.8-10 Following hole injection, hole transport
can occur over both short and long distances in DNA.11 Hole
transport has been proposed to occur via a superexchange
mechanism at short distances and via a hopping mechanism at
† Northwestern University.
‡ Boston College.
§ New York University.
(1) (a) Lewis, F. D. In Electron Transfer in Chemistry; Balzani, V., Ed.; Wiley-
VCH: Weinheim, Germany, 2001; Vol. 3, pp 105-175. (b) Schuster, G.
B., Ed. Long-Range Charge Transfer in DNA, I and II; Springer: New
York, 2004; Vols. 236, 237. (c) Wagenknecht, H. A., Ed. Charge Transfer
in DNA; Wiley-VCH: Weinheim, 2005.
(6) Wan, C.; Fiebig, T.; Kelley, S. O.; Treadway, C. R.; Barton, J. K.; Zewail,
A. H. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6014-6019.
(7) (a) Felts, A. K.; Pollard, W. T.; Friesner, R. A. J. Phys. Chem. 1995, 99,
2929-2940. (b) Jortner, J.; Bixon, M.; Langenbacher, T.; Michel-Beyerle,
M. E. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 12759-12765.
(8) Abdel Malak, R.; Gao, Z.; Wishart, J. F.; Isied, S. S. J. Am. Chem. Soc.
2004, 126, 13888-13889.
(2) Lewis, F. D.; Wu, T.; Zhang, Y.; Letsinger, R. L.; Greenfield, S. R.;
Wasielewski, M. R. Science 1997, 277, 673-676.
(3) Lewis, F. D.; Wu, T.; Liu, X.; Letsinger, R. L.; Greenfield, S. R.; Miller,
S. E.; Wasielewski, M. R. J. Am. Chem. Soc. 2000, 122, 2889-2902.
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Fukui, K.; Tanaka, K.; Fujitsuka, M.; Watanabe, A.; Ito, O. J. Photochem.
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B.; Michel-Beyerle, M. E. J. Am. Chem. Soc. 2001, 123, 10046-10055.
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E.; Ernsting, N. P.; Kovalenko, S. A.; Lustres, J. L. P. ChemPhysChem
2002, 3, 452-455.
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2005, 127, 4860-4868.
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Wasielewski, M. R. J. Am. Chem. Soc. 2005, 127, 11842-11850.
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Nature 2001, 412, 318-320. (b) Giese, B. Acc. Chem. Res. 2000, 33, 631-
636. (c) Schuster, G. B. Acc. Chem. Res. 2000, 33, 253-260. (d) O’Neil,
M. A.; Barton, J. K. J. Am. Chem. Soc. 2004, 126, 11471-11483. (e) Lewis,
F. D.; Liu, J.; Zuo, X.; Hayes, R. T.; Wasielewski, M. R. J. Am. Chem.
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9
10.1021/ja0540831 CCC: $33.50 © 2006 American Chemical Society
J. AM. CHEM. SOC. 2006, 128, 791-800
791

A R T I C L E S
Lewis et al.
Scheme 1. (a) Superexchange and (b) Hopping Mechanisms for Photoinduced Charge Separation between an Excited Acceptor and
Ground-State Donor Separated by Three A:T Base Pairs
Chart 1. Structures of (a) Stilbene Linkers, (b) Donor-Acceptor Capped Hairpins, and (c) Stilbene-Linked Hairpins
longer distances (alternatively viewed as polaron motion).12
However, a crossover in mechanism has not been directly
observed for photoinduced charge transfer in DNA.
serves as the electron acceptor and either guanine or Sd serves
as the electron donor.3,15 We have for the first time disentangled
the various kinetic processes that are involved in photoinduced
electron transfer in DNA: hole injection, hole arrival, and charge
recombination. Furthermore, we have shown that each of these
processes exhibits a characteristic distance dependence, resulting
in the observation of a crossover from superexchange to
interbase hopping as the mechanism for charge separation at a
donor-acceptor plane-to-plane distance of ca. 10 Å (two base
pairs) and at longer distances for charge recombination. Previous
experimental studies of DNA charge separation and charge
recombination dynamics can be analyzed in terms of these two
limiting mechanisms.
We report here the results of our collaborative investigation
of the dynamics and mechanism of charge separation and charge
recombination in DNA hairpin conjugates possessing donor and
acceptor stilbene chromophores (Sa and Sd, respectively, Chart
1a) separated by (A:T)n base pair domains (1-7, Chart 1b).
The combination of femtosecond (fs) broadband pump-probe
spectroscopy with an expanded spectral range,13 nanosecond (ns)
transient absorption,14 and picosecond (ps) fluorescence decay
measurements permits more detailed analysis of electron-transfer
dynamics than was possible in previous studies in which Sa*
(12) (a) Berlin, Y. A.; Burin, A. L.; Ratner, M. A. J. Phys. Chem. A 2000, 104,
443-445. (b) Berlin, Y. A.; Burin, A. L.; Ratner, M. A. J. Am. Chem.
Soc. 2001, 123, 260-268. (c) Bixon, M.; Giese, B.; Wessely, S.;
Langenbacher, T.; Michel-Beyerle, M. E.; Jortner, J. Proc. Natl. Acad. Sci.
U.S.A. 1999, 96, 11713-11716. (d) Bixon, M.; Jortner, J. Chem. Phys.
2002, 281, 393-408. (e) Conwell, E. M.; Rakhmanova, S. V. Proc. Natl.
Acad. Sci. U.S.A. 2000, 97, 4556-4560. (f) Conwell, E. M.; Park, J.-H.;
Choi, H.-Y. J. Phys. Chem. B 2005, 109, 9760-9763.
(13) (a) Raytchev, M.; Mayer, E.; Amann, N.; Wagenknecht, H. A.; Fiebig, T.
Chem. Phys. Chem. 2004, 5, 706-712. (b) Kaden, P.; Mayer-Enthart, E.;
Trifonov, A.; Fiebig, T.; Wagenknecht, H.-A. Angew. Chem., Int. Ed. 2005,
44, 1636-1639.
(14) Shafirovich, V. Y.; Courtney, S. H.; Ya, N.; Geacintov, N. E. J. Am. Chem.
Soc. 1995, 117, 4920-4929.
(15) Lewis, F. D.; Wu, Y.; Zhang, L.; Zuo, X.; Hayes, R. T.; Wasielewski, M.
R. J. Am. Chem. Soc. 2004, 126, 8206-8215.
9
792 J. AM. CHEM. SOC. VOL. 128, NO. 3, 2006

Crossover from Superexchange to Hopping
A R T I C L E S
Experimental Section
Sample Preparation. Stilbene-4,4′-dicarboxylic acid was obtained
from toluic acid by treatment with sulfur powder at high temperature.16
The bis(3-hydroxypropyl)amide of stilbene-4,4′-dicarboxylic acid and
the bis(2-hydroxyethyl)stilbene 4,4′-diether (Sa and Sd, respectively,
in Chart 1a) were prepared and converted to their mono-DMT
derivatives by reaction with 4,4′-dimethoxytrityl chloride.17,18 The
mono-DMT derivatives were reacted with 2-cyanoethyl diisopropyl-
chlorophosphoramidite to afford the monoprotected, monoactivated
diols. Hairpins Sa-AT, Sd-AT, and capped hairpins 1-7 (Chart 1) were
prepared by means of conventional phosphoramidite chemistry using
a Millipore Expedite oligonucleotide synthesizer. The conjugates were
first isolated as trityl-on derivatives by reverse phase HPLC, and then
detritylated in 80% acetic acid for 30 min. The presence of the stilbene
linker was confirmed by absorption and fluorescence spectroscopy.
Molecular weights were determined by using a Voyager DE-Pro
MALDI-TOF mass spectrometer.
All samples were prepared in 0.1 M NaCl and 10 mM sodium
phosphate, pH 7.2 (standard buffer). Hairpin concentrations were
adjusted to provide absorbances of ca. 0.2 at the excitation wavelength
for fluorescence measurements and ca. 0.3 for pump-probe measure-
ments. Fluorescence quantum yields for 1-7 were determined using
355 nm excitation by comparing the fluorescence intensity at the
emission maximum with that for Sa-AT.
Figure 1. UV spectra of conjugates Sa-AT, Sd-AT, and 6 in aqueous buffer
(0.1 M NaCl and 10 mM sodium phosphate, pH 7.2, concentrations of Sa-
AT and Sd-AT adjusted to provide similar absorbance at 325 nm).
with magic angle (54.7°) setting for the polarization of pump with
respect to the polarization of the probe pulse. A sample cell with 1.25
mm fused silica windows and an optical path of 1 mm was used for all
measurements. A wire stirrer was used to ensure fresh sample volume
was continuously used during the measurement.
Fluorescence Decay Measurements. In the picosecond single
photon counting system, the sample is excited by a Coherent Mira 900
fs Ti:Sp laser that is pumped by an Innova 310 argon ion laser. The
output of the Ti:Sp laser (700 nm) is passed through a Conoptics
electrooptic light modulator system consisting of a model 350-160
Modulator, a model 25D Digital Amplifier, and a M305 Synchronous
countdown device, to reduce the laser pulse frequency from 76 to 12
MHz, which is then doubled to provide excitation at 350 nm.
Fluorescence emission is registered at 390 nm using an Aries FF250
monochromator. A Time Harp 100 PC card (PicoQuant, Germany)
controlled by an IBM PC computer provides registration of the counts
with rates of up to 80 MHz. After deconvolution (PicoQuant FluoFit
software), the time resolution of this apparatus is ca. 35 ps. All
experiments, including data collection and analysis, are controlled by
an IBM PC computer using PicoQuant software.
Nanosecond Transient Absorption Spectra. The transient absorp-
tion spectra and kinetics of the radical ions were monitored directly
using a fully computerized kinetic spectrometer system (∼7 ns response
time). The excitation source was a nanosecond Nd:YAG laser (Con-
tinuum Surelite II, ca. 6 ns pulse width, 10 Hz repetition rate, ∼10 mJ
pulse-1 cm-2, 355 nm excitation). The sample excitation frequency was
reduced to 1 Hz by an electromechanical shutter and used to excite
sample solutions (0.25 mL) of the oligonucleotides saturated with argon.
The transient absorbance was probed along a 1 cm optical path by light
from a pulsed 75 W xenon arc lamp with its light beam oriented
perpendicular to the laser beam. The signal was recorded by a Tektronix
TDS 5052 oscilloscope operating in its high-resolution mode. Satisfac-
tory signal/noise ratios were obtained even after a single laser shot.
Femtosecond Broadband Pump-Probe Spectroscopy. A detailed
description of our experimental setup has been given elsewhere.19 The
pump wavelength was set to 355 nm for hairpins 1 and 2 and to 333
nm for hairpins 3 and 4. The changes in optical density were probed
by a femtosecond white-light continuum (WLC) generated by tight
focusing of a small fraction of the output of a commercial Ti:Sp based
pump laser (CPA-2010, Clark-MXR) into a 3 mm calcium fluoride
(CaF2) plate. The WLC provides a usable probe source between 300
and 750 nm. The WLC was split into two beams (probe and reference)
and focused into the sample using reflective optics. After passing
through the sample, both probe and reference beams were spectrally
dispersed and simultaneously detected on a CCD sensor. The pump
pulse (1 kHz, 400 nJ) was generated by frequency doubling of the
compressed output of a home-built NOPA system (from 666 to 708
nm respectively, 7 µJ, 40 fs). To compensate for group velocity
dispersion in the UV-pulse, an additional prism compressor was used.
The overall time resolution of the setup is determined by the cross
correlation function between pump and probe pulses, which is typically
120-150 fs (fwhm, assuming a Gaussian line shape). A spectral
resolution of 7-10 nm was obtained. All measurements were performed
Results
Absorption and Fluorescence Spectra. The syntheses and
characterization of the stilbene derivatives Sa and Sd, the dyad
Sa-An, and the hairpins Sa-AT and Sd-AT (Chart 1a,c) have
previously been described.15,18,20 The capped hairpins 1-7
(Chart 1b) were prepared, purified, and characterized by methods
employed for the preparation of capped hairpins with Sa linkers
and capping groups.15 Capped hairpins possessing one or more
base pair are known to form folded structures that are stable at
room temperature.21,22
The UV absorption spectra of Sa, Sd, Sa-An, Sa-AT, and
Sd-AT have been reported.3,23 The spectra of Sa-AT, Sd-AT,
and 6 are shown in Figure 1. The 260 nm bands of all three
conjugates are dominated by base pair absorption, and the long-
wavelength bands are dominated by the stilbene absorption. The
long-wavelength bands of 1-7 are superimposable. The Sa-
(20) Lewis, F. D.; Liu, X.; Wu, Y.; Miller, S. E.; Wasielewski, M. R.; Letsinger,
R. L.; Sanishvili, R.; Joachimiak, A.; Tereshko, V.; Egli, M. J. Am. Chem.
Soc. 1999, 121, 9905-9906.
(16) Khalaf, A. I.; Pitt, A. R.; Scbie, M.; Suckling, C. J.; Urwin, J.; Waigh, R.
D.; Young, S. C.; Fishleigh, R. V.; Fox, K. Tetrahedron 2000, 56, 5225-
5239.
(17) Letsinger, R. L.; Wu, T. J. Am. Chem. Soc. 1995, 117, 7323-7328.
(18) Lewis, F. D.; Wu, Y.; Liu, X. J. Am. Chem. Soc. 2002, 124, 12165-12173.
(19) Raytchev, M.; Pandurski, E.; Buchvarov, I.; Modrakowski, C.; Fiebig, T.
J. Phys. Chem. A 2003, 107, 4592-4600.
(21) Lewis, F. D.; Liu, X.; Wu, Y.; Zuo, X. J. Am. Chem. Soc. 2003, 125,
12729-12731.
(22) Lewis, F. D.; Zhang, L.; Liu, X.; Zuo, X.; Tiede, D. M.; Long, H.; Schatz,
G. S. J. Am. Chem. Soc. 2005, 127, 14445-14453.
(23) Lewis, F. D.; Wasielewski, M. R. In Charge Transfer in DNA; Wagen-
knecht, H.-A., Ed.; Wiley-VCH: Weinheim, Germany, 2005.
9
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A R T I C L E S
Lewis et al.
Table 1. Fluorescence Quantum Yields and Decay Dataa
conjugate
Φfb
τ
1 (amp), psc
τ
2 (amp), nsc
τ
3 (amp), nsc
Sad
0.11
0.32
280, 362f
350, 379f
45 (71)
Sde
Sa-AT
0.38d
<0.01
0.033
0.15
0.86 (8)
2.2 (21)
1
2
3
4
5
6
7
38 (73)
66 (76)
40 (75)
81 (75)
95 (71)
43 (82)
1.7 (25)
g
0.37 (20)
0.58 (12)
1.24 (20)
1.26 (19)
0.89 (6)
1.4 (3)
1.4 (11)
2.0 (10)
2.0 (12)
1.9 (12)
0.26
0.29
0.31
0.37
a Data for Sa and Sd in methanol solution. Data for Sa-AT and 1-7 in
aqueous solution (standard buffer). b Quantum yield data for 1-7 determined
using 355 nm excitation by comparison of the peak intensity with that for
Sa-AT. Estimated error (10%. c Decays and amplitudes for Sa-AT and
1-7 determined from triple exponential fits of the 390 nm fluorescence
decay obtained using 350 nm excitation. d Data from ref 24. e Data from
ref 25. f Data from transient absorption measurements. g The third compo-
nent (τ3 ) 12.7 ns) is not considered to be significant.
AT stilbene band extends to a slightly longer wavelength than
that of Sd-AT as a consequence of extended conjugation
provided by the amide groups. The long-wavelength band of 6
and the other donor-acceptor hairpins appears as the sum of
the Sa and Sd absorption bands. Excitation at 355 nm is
absorbed predominantly by Sa, whereas excitation at 333 nm
is absorbed comparably by Sa and Sd.
The fluorescence properties of Sa and Sd in methanol have
been reported.24,25 They have emission maxima at 386 and 374
nm, respectively, and fluorescence quantum yields of 0.11 and
0.32 in methanol. Their fluorescence decays are single expo-
nential with decay times of 0.28 and 0.35 ns, respectively. Sa-
An is nonfluorescent in methanol. The fluorescence maximum
for Sa-AT is at 389 nm, and its fluorescence quantum yield is
0.38.3 A fluorescence decay time of 2.0 ns was determined using
a stroboscopic instrument with a time resolution of ca. 0.2 ns.
Sd-AT is nonfluorescent in aqueous solution (Φf < 10-5).25
The fluorescence spectra of 1-7 have band shapes identical
to that of Sa-AT, which are independent of the excitation
wavelength (333 or 355 nm), in accord with the absence of
fluorescence from Sd-AT. Fluorescence quantum yields were
determined by comparison of the peak intensity obtained with
355 nm excitation to that for Sa-AT. Values of Φf reported in
Table 1 increase as the separation between Sa and Sd increases.
Picosecond Time-Resolved Fluorescence. Fluorescence
decays for Sa-AT and 2-7 were determined using a Ti-Sp
based laser system having a time resolution of ca. 35 ps. A
sample fluorescence decay for 3 is shown in the Supporting
Information (Figure S1) with fits to double and triple exponential
functions. Superior fits were achieved with triple exponential
functions, particularly in the short time domain (<2 ns). Decay
times and amplitudes obtained from triple exponential fits are
summarized in Table 1. In all cases, the decays are dominated
by short-lived components having decay times of 38-95 ps and
amplitudes of 71-82%. The long-lived components for Sa-AT
and 5-7 are similar to those previously determined with 0.2 ns
instrument resolution for Sa-AT and for other Sa-linked hairpins
having poly(T:A) base pairs domains with four or more T:A
base pairs adjacent to Sa.3 Fluorescence decays were not
Figure 2. Temporal evolution of the pump-probe spectra of (a) Sa-An
and (b) Sa-AT in the time range of -0.1 ps to 150 ps after excitation at
333 nm. Early spectra are shown in blue/green, and late spectra are shown
in orange/red colors.
determined for Sa-An, Sd-AT, and 1, all of which are essentially
nonfluorescent.
Femtosecond Pump-Probe Experiments: Reference Com-
pounds. Femtosecond time-resolved transient absorption spectra
with a spectral range of 450-750 nm have previously been
reported for Sa, Sd, Sa-An, Sa-AT, and Sd-AT.3,25 We have
repeated these measurements using a Ti-Sp based system with
a white-light continuum, which provides a usable probe source
between 350 and 750 nm with a time resolution of ca. 150 fs
and a spectral resolution of ca. 10 nm.13 The temporal evolution
of the 350-750 nm pump-probe spectra of Sa and Sd obtained
with 333 nm excitation and kinetic analysis of the 570 nm decay
is provided as Supporting Information (Figure S2). In agreement
with previous studies, their spectra display broad maxima at
ca. 575 nm, which rise within ca. 3 ps, and decay components
of 362 and 379 ps, respectively, similar to their fluorescence
decay times (Table 1). The spectra of both Sa and Sd also
display negative bands at 380 and 360 nm, respectively (Figure
S2), which were not observed in previous studies using a
narrower spectra detection range. These bands have minima near
the fluorescence maxima of Sa and Sd and are assigned to
stimulated emission from their singlet excited states. The decay
times of these bands are similar to those of the 575 nm bands.
The temporal evolution of the 350-750 nm pump-probe
spectra of Sa-An and Sa-AT obtained with excitation at 333
nm is shown in Figure 2. Both spectra display rapid growth
(24) Lewis, F. D.; Wu, T.; Burch, E. L.; Bassani, D. M.; Yang, J.-S.; Schneider,
S.; Jaeger, W.; Letsinger, R. L. J. Am. Chem. Soc. 1995, 117, 8785-8792.
(25) Lewis, F. D.; Liu, X.; Miller, S. E.; Hayes, R. T.; Wasielewski, M. R. J.
Am. Chem. Soc. 2002, 124, 11280-11281.
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794 J. AM. CHEM. SOC. VOL. 128, NO. 3, 2006

Crossover from Superexchange to Hopping
A R T I C L E S
Table 2. Femtosecond Pump-Probe Transient Dataa
reference compounds. Both Sa and Sd absorb at this wavelength
(Figure 1). However, because Sd-AT is nonfluorescent and
rapidly forms a short-lived 525 nm band (Table 2), it is possible
to dissect the transient components arising from excitation of
Sa and Sd. Simplification of the spectra at short delay times
can be accomplished by excitation of the red-edge of the steady-
state absorption spectra, where Sa absorbs more strongly than
Sd. Pump-probe spectra in the time range 0.1-150 ps for
hairpins 1-4 obtained using 355 nm excitation for 1 and 2 and
333 nm excitation for 3 and 4 are shown in Figure 3 (333 nm
excitation data for 1 and 2 are not shown). In all cases, there is
an ultrafast rise (<1 ps) of the 575 nm band attributed to Sa*
and Sd* transient absorption and a negative band at 380 nm
attributed to Sa* stimulated emission (Sd-AT is nonfluorescent).
In the cases of 2-4, this rise is followed by a fast decay of the
380 and 575 nm bands (ca. 1 ps) attributed to relaxation of the
singlet excited states. Spectra for 2-4 in the 0.2-1.9 ns time
range are shown in Figure S3. Kinetic analysis of the femto-
second pump-probe data for 1-4 is presented below and
summarized in Table 2, with assignments provided in the
footnotes. Negative amplitudes are reported for components with
increasing optical density, and positive amplitudes are reported
for components with decreasing optical density. The kinetic data
extracted from the transient spectra obtained with 333 nm
excitation of 1 and 2 (data not shown) are similar to those for
355 nm excitation.
conjugate
380 nm t, psb
575 nm
τ
, psc
525 nm
τ
, psd
525/575, pse
Sa-AT
23 (-19)
470 (-5)
18 (25)f
930 (17)g
30
790 (32)g
>2 ns (8.4)g
0.6f
>2 ns (3.8)g
Sd-ATh
1
32g
35g
2.2 (-3.5)
1.5 (6.0)f
9.3 (5.8)g
490 (1.9)g
24 (3.4)f
>1 ns (7.6)g
33 (1.1)f
>1 ns (1.3)g
∼1.0 (-3.8)f
1.7
9.9 (9.8)g
360 (4.2)g
31 (-5.1)f
>1 ns (11)g
41 (1.5)i
2
3
25 (-3.4)
36
53 (-0.57)
290
440 (-1.0)f
>1 ns (1.8)g
43 (2.7)i
4
77 (-1.1)
56 (2.4)f
∼1 ns
>1 ns (2.7)g
>1 ns (1.7)g
a Rise and decay times (preexponentials in parentheses are negative for
components with increasing optical density and positive for components
with decreasing optical density). b Decay times for the stimulated emission
of Sa*. c Decay times for the transient absorption of Sa* or Sd* (shortest
decay times) and Sa-• (longer decay times). d Rise and decay times for the
transient absorption of Sd+• and/or Sa-• e Rise time for the 525/575 nm
.
band intensity ratio attributed to hole injection for Sa-AT and hole arrival
for 1-4. f Component attributed to hole injection or hole arrival. g Com-
ponent attributed to charge recombination. h Data from ref 25. i Component
attributed to charge recombination of Sd+•/T-•
.
(ca. 1 ps) of the 575 and 380 nm transients assigned to the Sa*
singlet state. In the case of Sa-An, the 380 band and the long-
wavelength tail of the 575 nm band decay within a few
picoseconds accompanied by the rise in the 525 nm shoulder
(Figure 2a). The 525/575 nm band intensity ratio also reaches
a maximum value of ca. 1:3 within a few picoseconds, and both
bands decay with a decay time of ca. 20 ps. These changes
have been attributed to charge separation with formation of the
Sa-•An+• radical ion pair followed by charge recombination.3
Because the An+• radical cation does not have an absorption
band in this spectral region, both the 575 nm band and the 525
nm shoulder are attributed to Sa-•. Thus, the growth of the 525/
575 nm band intensity ratio provides a direct measurement of
the charge separation time constant.
In the case of 1, the decay of the 380 nm band and the initial
decay of the 575 nm band occur with time constants of ca. 2
ps, attributed to charge separation (see Discussion). There is
also a fast rising component of the 525 nm transient that is not
well resolved from the subsequent fast decay. The rise of the
525/575 nm band ratio (Figure 4) has a time constant of 1.7 ps
and is thought to provide the most accurate measure of the time
required for charge separation (hole arrival on Sd). This ratio
attains a maximum value of ca. 2.2:1, substantially larger than
the value of ca. 0.3:1 observed for Sa-TA. A ratio of 2:1 would
be expected for overlapping Sa-• (1:3) and Sd+• (525 nm only)
transients, assuming that both radical ions have similar molar
absorbance. The 525 and 575 nm bands decay with time
constants of ca. 9 ps and 0.4 ns, tentatively attributed to charge
recombination of the charge separated state prior to and
following solvent and nuclear relaxation, respectively.
The spectral changes observed for Sa-AT (Figure 2b) are
similar to those observed for Sa-An; however, they occur on a
much longer time scale. Decay of the negative 380 nm and
positive 575 nm bands has fast and slow picosecond compo-
nents, which are reported in Table 2. The growth of the 525
nm shoulder occurs during the initial phase of the 380 and 575
nm decay. The 525 and 575 nm bands attain a constant band
intensity ratio of ca. 1:3 with a rise time of 30 ps and decay
together with both a 0.8-0.9 ns component (similar to the slow
component of 380 nm decay) and a component that is longer
than the experimental 1.9 ns time window. The 380 nm band is
outside the spectral window employed in previous studies of
Sa-AT, and the growth of the 525 nm shoulder was not observed
previously.3 The femtosecond transient spectra of Sd-AT have
been reported, and the results have subsequently been con-
firmed.25 The 575 nm band assigned to Sd* decays with a time
constant of <0.5 ps concomitant with the growth of the 525
nm band assigned to Sd+•. The 525 nm band has a decay time
of 32 ps assigned to charge recombination. Transient decay data
for Sa-AT and Sd-AT are summarized in Table 2.
The spectral changes observed for 2 are similar; however,
the time constants are slower. Following the fast relaxation
processes that occur within a few picoseconds, the decay of
the 380 nm band, the initial decay of the 575 nm band, the rise
of the 525 nm band, and the rise of the 525/575 nm band
intensity ratio (Figure 4) occur with time constants of 24-36
ps. The decay of the 525 and 575 nm bands is incomplete after
1.9 ns (Figure S3), the longest pump-probe delay time,
indicative of slow charge recombination.
Changes in the pump-probe spectra of 3 and 4 (Figure 3)
occur more slowly than is the case for 1 or 2. Following the
fast relaxation processes that occur within 1-2 ps, the 380 and
575 nm bands have decay times of 33-77 ps assigned to hole
injection, by analogy to the behavior of Sa-AT. The 525 nm
bands of 3 and 4 have decay times of 41 and 43 ps, attributed
to charge recombination of the Sd+•/T-• contact radical ion pair
by analogy to the behavior of Sd-AT (Table 2).25 The 41 ps
decay for 3 is followed by a slow rise with time constant of
Femtosecond Pump-Probe Experiments: Donor-Accep-
tor Hairpins. Pump-probe spectra for 1-4 were obtained using
333 nm excitation, the excitation wavelength used for the
9
J. AM. CHEM. SOC. VOL. 128, NO. 3, 2006 795

A R T I C L E S
Lewis et al.
Figure 3. Temporal evolution of the pump-probe spectra of hairpins 1-4 in the time range of -0.1 ps to 150 ps after excitation at 355 nm (1 and 2) or
333 nm (3 and 4). Early spectra are shown in blue/green, and late spectra are shown in orange/red colors.
Figure 5. Nanosecond time-resolved spectra of 6. The 525 nm band is
assigned to overlapping absorption of Sd+• and Sa-•, and the 575 nm band
Figure 4. Time dependence of the 525/575 nm band intensity ratios for 1
(inset), 2 (∆), and 3 (0).
is assigned to absorption of Sa-•
.
0.44 ns. Similarly, the 525/575 nm band intensity ratios display
an initial decrease (due to the fast decay of the 525 nm band
created by direct excitation of Sd) followed by a rise with a
time constant of 0.29 ns for 3 (Figure 4) and ca. 1 ns for 4
(Figure S3), attributed to hole arrival. Decay of the 525 and
575 nm bands of 3 and 4 is incomplete after 1.9 ns (Figure
S3), indicative of slow charge recombination.
Nanosecond Transient Absorption. The transient absorption
spectra of 3-7 were obtained using 355 nm excitation provided
by nanosecond Nd:YAG laser pulses and a pulsed xenon arc
lamp for detection with an instrument response time of ca. 30
ns.14 Satisfactory signal/noise ratios were observed after a single
laser pulse for argon-purged solutions and are independent of
the number of laser pulses, even though sample degradation
occurs with repeated pulsing. Sample degradation occurs rapidly
in the presence of oxygen. The time-resolved spectra for
conjugate 6 are shown in Figure 5. As is the case for the
femtosecond transient spectra, the absorption band at 525 nm
is assigned to overlapping absorption of Sd+• and Sa-• and the
band at 575 nm is assigned to Sa-•. Similar spectra were
obtained for the other donor-acceptor hairpins. The rise times
for these spectra were not resolved and thus are assumed to be
comparable to or faster than the instrument response time. Decay
traces obtained at 525 and 575 nm are best fitted by single-
exponential functions, which are assigned to charge recombina-
tion (Table 3). Similar decay times were obtained at both
9
796 J. AM. CHEM. SOC. VOL. 128, NO. 3, 2006

Crossover from Superexchange to Hopping
A R T I C L E S
Table 3. Nanosecond Laser Flash Photolysis Transient Decaysa
The lower oxidation potential of Sd (Eox ) 0.92 V vs SCE)
versus G results in more exergonic photoinduced electron
transfer (∆Get ) -0.52 eV) than the value estimated with G as
the electron donor. The well-resolved transient absorption
spectra of the Sa-•/Sd+• charge-separated state provide definitive
evidence for the occurrence of charge separation and charge
recombination via a DNA bridge. The values of â for charge
separation and charge recombination in these systems are similar
to those for the Sa/G hairpin systems.15 However, in the
published transient data neither the Sa/G nor the Sa/Sd system
serves to distinguish between a single-step superexchange
process (Scheme 1a) and a multistep hopping process, in which
the distance-dependent time constant for charge separation
would, in effect, become the hole arrival time on guanine
(Scheme 1b).
conjugate
575 nm,
µ
s
525 nm, µs
2
3
4
5
6
7
0.0084b
0.22
8.5
30
160
590
0.23
8.4
30
140
830
a Single-exponential fits to the transient decays. b Data from ref 15.
Chart 2. Singlet Energies and Reduction Potentials of Several
Arenedicarboxamides26
In view of the continuing uncertainty about the mechanism
and dynamics of charge separation and charge migration
processes in DNA, we have undertaken a comprehensive study
of the Sa/Sd capped hairpin systems 1-7 shown in Chart 1.
These capped hairpins have simpler structures than the capped
hairpins studied previously, which possess 5′-nucleotides.15,29
The present studies provide (a) a wider spectral range for
femtosecond pump-probe measurements, (b) improved time
resolution for fluorescence decay measurements, and (c) nano-
second transient absorption measurements for capped hairpins
with longer base pair domains.
wavelengths, except in the case of 7, which has the weakest
transient signals. In the case of Sa-AT, a weak 575 nm transient
signal with a decay time of 290 ns was observed, whereas no
long-lived transient could be observed for Sd-AT.
Linkers and Hairpins. The photochemical behavior of the
stilbene linkers Sa and Sd has been well characterized.3,25 The
singlet states of both stilbenes display strong fluorescence and
transient absorption (Figure S2) with decay times of 280-380
ps (Table 1). Extension of the transient spectral measurements
to include the 350-450 nm spectral region permits observation
of the stilbene stimulated emission, which has the same decay
time as the fluorescence and transient absorption.
Discussion
Our approach to the study of the distance and driving force
dependence of DNA electron-transfer dynamics has employed
synthetic DNA hairpins in which an organic chromophore serves
both as the hairpin linker and as a singlet state electron
acceptor.26 The distance-dependent dynamics of DNA electron
transfer were initially investigated in hairpins possessing the
Sa linker (e.g., Sa-AT, Chart 1) and a single G:C base pair
separated by a variable number of A:T base pairs.2,3 The free
energy for electron transfer from G to Sa* was estimated to be
As in our previous studies, the covalently linked donor-
acceptor Sa-An serves as a model for conversion of the Sa*
singlet state to the anion radical Sa-•.3 Its pump-probe spectra
in methanol (Figure 2a) display growth of the Sa* 575 nm
transient absorption and 380 nm stimulated emission within the
first picoseconds, followed by rapid decay of the 380 nm band
and of the red-edge of the 575 nm band, as well as growth of
the 525 nm shoulder, with time constants of ca. 1.0 ps. The
resultant spectrum is assigned to Sa-•. It has a 525/575 nm band
intensity ratio of ca. 1:3 and a decay time of ca. 20 ps. The rise
and decay times are faster than those previously determined in
tetrahydrofuran solvent,3 in accord with the known effect of
solvent polarity on the dynamics of charge separation and charge
recombination in donor-acceptor systems with flexible tethers.30
In our previous studies of Sa-AT, the high fluorescence
quantum yield, long fluorescence decay time, and absence of
pronounced changes in the transient absorption band shape were
taken as evidence for the absence of photoinduced charge
separation.3 The femtosecond pump-probe spectra of Sa-AT
(Figure 2b) reveal both a fast decay of the stimulated emission
of Sa* and a rise of the 525/575 nm band intensity ratio, similar
to the changes observed for Sa-An (Figure 2a). These processes
have time constants of 20-30 ps. Reinvestigation of the
ca. -0.20 eV, using Weller’s equation (∆Get ) -ES - Erdn
+
Eox), the measured singlet energy and oxidation potential of Sa
(Chart 2), and the reported oxidation potential of G (1.24 V vs
SCE in acetonitrile).27,28 Rate constants for charge separation
and charge recombination in Sa/G systems were obtained from
analysis of the femtosecond transients assigned to the decay of
Sa* and Sa-•. The formation and decay of G+• is not directly
observed due to the absence of measurable transient absorption.
Analysis of the kinetic data for Sa/G hairpins using a super-
exchange model provided a distance dependence of â ) 0.65
Å-1 for charge separation and â ) 0.95 Å-1 for charge
recombination.2
Donor-acceptor capped hairpin systems related to 2-7 were
introduced several years ago for the study of DNA electron-
transfer dynamics and exciton-coupled circular dichroism.15,29
(26) (a) Lewis, F. D.; Letsinger, R. L.; Wasielewski, M. R. Acc. Chem. Res.
2001, 34, 159-170. (b) Lewis, F. D.; Wu, Y. J. Photochem. Photobiol.,
C: ReV. 2001, 2, 1-16. (c) Lewis, F. D.; Wasielewski, M. R. In Charge
Transfer in DNA; Wagenknecht, H. A., Ed.; Wiley-VCH: Weinheim, 2005;
pp 93-116.
(27) Weller, A. Z. Phys. Chem. Neue. Folg. 1982, 133, 93-98.
(28) Seidel, C. A. M.; Schulz, A.; Sauer, M. H. M. J. Phys. Chem. 1996, 100,
5541-5553.
(29) Lewis, F. D.; Wu, Y.; Hayes, R. T.; Wasielewski, M. R. Angew. Chem.,
Int. Ed. 2002, 41, 3485-3487.
(30) (a) Mataga, N.; Nishikawa, S.; Asahi, T.; Okada, T. J. Phys. Chem. 1990,
94, 1443-1447. (b) Okada, T.; Migita, M.; Mataga, N.; Sakata, Y.; Misumi,
S. J. Am. Chem. Soc. 1981, 103, 4715-4720.
9
J. AM. CHEM. SOC. VOL. 128, NO. 3, 2006 797

A R T I C L E S
Lewis et al.
Table 4. Summary of Kinetic Data for Hole Arrival, Hole Injection,
and Charge Recombination
hole injection
hole arrival
charge recombination
1 a
1 b
1 c
conjugate
10-10 ki, s-
10-10 ka, s-
10-8 kr, s-
Sa-AT
3.3b
1
2
3
4
5
6
7
58
24
1.2
2.6 (4.0)
1.5 (1.9)
2.5 (1.3)
1.2
1.1
2.3
2.7
0.34
0.1
4.4 × 10-2
1.2 × 10-3
3.3 × 10-4
6.7 × 10-5
1.4 × 10-5
a Estimated from the fast component of fluorescence decay (Table 1) or
from the decay of the 380 nm stimulated emission (Table 2, data in
parentheses). b Estimated from the rise in the 525/575 nm band intensity
ratio (Table 2). c Estimated from the average of the 525 and 575 nm transient
decays (Tables 2 and 3).
fluorescence properties of Sa-AT with picosecond time resolu-
tion reveals a major fluorescence decay component having a
decay time of 45 ps, near the time resolution of the picosecond
fluorescence instrument (Table 1). Both the decay of the
fluorescence and the 575 nm femtosecond transient absorption
of Sa-AT display longer lived components with decay times of
0.5-2.0 ns (Tables 1 and 2).
Figure 6. Distance dependence of the rate constants for hole injection,
hole arrival, and charge recombination.
independent of the charge separation mechanism. Rate constants
for hole arrival, ka, for 1-4 obtained from femtosecond pump-
probe data (Figures 3 and 4) are summarized in Table 4 and in
Figure 6. Hole arrival rates for 5-7 are too slow for study with
our femtosecond apparatus and too fast for our nanosecond
apparatus. Based on the time resolution of these experiments,
values of 5 × 108 s-1 > ka > 5 × 107 s-1 can be estimated for
5-7. The plot of ka versus RDA shown in Figure 6 displays
curvature, indicative of a possible change in mechanism.
However, the slope obtained from a linear fit to the data for
1-4 provides a value of â ) 0.67 Å-1, essentially the same as
that reported previously for charge separation in Sa/G hairpin
systems (â ) 0.65 Å-1).2
On the basis of these observations, the fast decay of Sa* and
formation of Sa-• in Sa-AT are attributed to hole injection to
the poly(A:T) base pair domain, which occurs with a rate
constant of ki ≈ 3 × 1010 s-1 (Table 4), significantly slower
than the rate constant of 1 × 1012 s-1 previously reported for
oxidation of a neighboring guanine by Sa*.31 The longer lived
0.86 and 2.2 ns fluorescence decay components (Table 1) and
similar transient decays (Table 2) for Sa-AT are attributed to
charge recombination processes for charge separated states with
one or more A:T base pairs separating the radical ions. Charge
recombination to regenerate the fluorescence singlet state is
commonly observed for singlet contact radical ion pairs and
donor-bridge-acceptor charge separated states.32 Alternatively,
the longer lived fluorescence decays might be attributed to
multiple hairpin conformations with different lifetimes, as has
been suggested for aminopurine fluorescence decay in DNA
duplex structures.5,33 However, molecular dynamics simulations
for Sa-capped hairpins indicate that they are conformationally
homogeneous.22 Furthermore, the similarity of the fluorescence
and 575 nm transient decay times for Sa-AT suggests that the
decay of Sa* and of Sa-• are related processes, in accord with
the occurrence of reversible hole injection.
The Sa* decay times for 1-4 can be obtained from the decay
of the 380 nm stimulated emission (Table 2), and the decay
times for 2-7 can be obtained from the fluorescence decays
(Table 1). In the case of 1, the decay time of the 380 nm
stimulated emission is similar to the rise of the 525/575 nm
band ratio, both of which are significantly faster than the hole
injection time for Sa-AT. These data are consistent with a single-
step superexchange mechanism for charge separation. The
assignment of transients and the kinetic behavior of 1 are
summarized in Scheme 2a. It is possible that the behavior of 1
is influenced by nondegenerate exciton coupling between the
two stilbenes. A 5 nm red-shift in the absorption maximum is
observed for a capped hairpin possessing two Sa chromophores
separated by a single base pair, in agreement with a calculated
Charge Separation in Donor-Acceptor Hairpins. The
observation of reversible hole injection for Sa-AT suggests that
charge separation in the donor-acceptor hairpins 1-7 might
occur via either a hopping mechanism or the previously
proposed superexchange mechanism. As discussed in the
Results, the rise time of the 525/575 nm band intensity ratio
provides the time required for arrival of a hole on Sd, which is
exciton splitting of 560 cm-1 22
. However, there is no detectable
shift in the absorption or fluorescence spectra of 1 when
compared to 2-7.
In the case of both 3 and 4, the fast components of the
fluorescence decays (Table 1) and the 380 nm transient decays
(Table 2) are distinctly faster than their hole arrival times (Table
4). The assignment of transients and the kinetic behavior of 3
are summarized in Scheme 2b. Values of ki for 3-7 estimated
from the fluorescence and 380 nm transient decays are reported
in Table 4. Hole arrival times are not available for 5-7;
however, they presumably are slower than the hole injection
rates provided by the fast component of fluorescence decay.
(31) Lewis, F. D.; Kalgutkar, R. S.; Wu, Y.; Liu, X.; Liu, J.; Hayes, R. T.;
Wasielewski, M. R. J. Am. Chem. Soc. 2000, 122, 12346-12351.
(32) (a) Gould, I. R.; Farid, S. Acc. Chem. Res. 1996, 29, 522-528. (b) Overing,
H.; Paddon-Row, M. N.; Heppener, M.; Oliver, A. M.; Cotsaris, E.;
Verhoeven, J. W.; Hush, N. S. J. Am. Chem. Soc. 1987, 109, 3258-3269.
(c) Gould, I. R.; Young, R. H.; Mueller, A.; Albrecht, A. C.; Farid, S. J.
Am. Chem. Soc. 1994, 116, 8188-8199. (d) Lor, M.; Thielemans, J.; Viaene,
L.; Cotlet, M.; Hofkens, J.; Weil, T.; Hampel, C.; Muellen, K.; Verhoeven,
J. W.; Van der Auweraer, M.; De Schryver, F. C. J. Am. Chem. Soc. 2002,
124, 9918-9925.
(33) Rachofsky, E. L.; Osman, R.; Ross, J. B. A. Biochemistry 2001, 40, 946-
956.
9
798 J. AM. CHEM. SOC. VOL. 128, NO. 3, 2006

Crossover from Superexchange to Hopping
A R T I C L E S
Scheme 2. Dynamics of Charge Separation and Charge Recombination in (a) Hairpin 1 and (b) Hairpin 3 (Hole on Bridge Shown As Being
Localized on the Middle A)a
a Dashed arrows indicate transient assignments.
Thus, we conclude that charge separation in conjugates 3-7
occurs via a multistep mechanism consisting of photoinduced
hole injection (ki), followed by hole transport (A-hopping) and
hole trapping by Sd (kt, Scheme 2b).
In principle, the dynamics of the individual steps in the
reversible hole injection and hole migration processes might
be determined from the decay times and preexponentials for
the decay of Sa* and/or from the hole arrival times. However,
because the fast fluorescence decay components are near the
time resolution of our instrumentation, fluorescence data with
improved time resolution as well as hole arrival times from
nanosecond pump-probe experiments for hairpins 2-7 would
be required for complete kinetic analysis of the reversible hole
injection and hole migration processes. Takada et al. have
estimated a value of 2 × 1010 s-1 for the rate constant for
A-hopping from an analysis of the distance dependence of the
quantum yields for charge separation in systems having a
naphthaldiimide acceptor and phenothiazine donor, assuming a
random walk mechanism.36,37
The kinetic behavior of 2 is intermediate between that of 1
and 3. As is the case for 1, the decay of Sa* (Table 1) and the
rise of the 525/575 nm band ratio (Table 2) have similar time
constants. The hole arrival rate for 2 is similar to the hole
injection rate for Sa-AT, 3, and 4. These data are consistent
with either a superexchange mechanism or a hopping mecha-
nism, in which hole injection is slower than hole trapping and
thus rate determining. If we assume a value of â ≈ 1.0 Å-1 for
superexchange, similar to that for charge recombination (see
below), the rate constant for hole arrival in 2 would be ca. 3 ×
109 s-1. This value is smaller than either the value of ka
determined from the rise of the 525/575 nm absorption band
ratio or the value of ki estimated from either the fluorescence
decay or the decay of the 380 nm transient (Table 2). Thus, we
tentatively conclude that charge separation in 2 occurs via a
hopping mechanism.
The efficiency of charge separation for 2-7 has not been
determined directly. However, the modest decrease in the
pump-probe spectral intensity for 3 and 4 at long delay times
(Figure S3) and the observation of the charge separated state
with a single nanosecond laser pulse (Figure 5) are indicative
of efficient charge separation. The fluorescence quantum yields
of Φf ≈ 0.3 for 4-6 (Table 1) place an upper bound of Φcs for
the charge separation efficiencies (Φcs e 1 - Φf).
Hole Injection and Hole Transport. The observation of both
short-lived and long-lived components for the decay of the Sa*
fluorescence and stimulated emission in Sa-AT indicates that
the hole injection process is reversible. As such, these decay
components cannot be assigned to individual kinetic processes
by means of simple first-order analysis. The fast 40-90 ps
fluorescence decay components presumably represent the re-
versible formation of a Sa-•/A+• contact radical ion pair,
whereas the longer lived components may arise from the charge
recombination of Sa-•/A+• radical ion pairs separated by one
or more A:T base pairs. The short-lived fluorescence decay times
are independent of the length of the A-tract in 2-7 and are
significantly slower than the 1 ps hole injection time for the
Sa*/G system. Based on our studies of the driving force
dependence of hole injection to an adjacent nucleobase in DNA
hairpins, a Sa* decay time of ca. 50 ps is indicative of a value
of ∆Gi ≈ 0 eV.31 Comparison to the value of ∆Gi ) -0.2 eV
for photooxidation of G suggests that the difference in oxidation
potentials for G versus A is ca. 0.2 eV, smaller than earlier
estimates based on nonaqueous oxidation potentials.28 However,
this value is entirely consistent with estimates from time-
resolved charge-transfer dynamics in bimolecular nucleotide
complexes and with studies of hole transport dynamics and
equilibria.34,35
Charge Recombination. The observation of similar first-
order rate constants for decay of both the Sd+• and the Sa-•
transient absorption bands (Figures 3 and 5) provides definitive
evidence for decay of the charge separated state via charge
recombination. Rate constants for charge recombination are
summarized in Table 4, and their distance dependence is shown
in Figure 6. The longer time constant for charge recombination
versus charge separation in 1 (Scheme 2a) is consistent with
the large energy gap for charge recombination, which is
responsible for Marcus inverted kinetics.31 The values for kcr
decrease from 1.0 × 1011 s-1 for 1 to 1.4 × 103 s-1 for 7, a
dynamic range of nearly 108! The values of kr for 1-4 provide
a value of â ) 0.97 Å-1, similar to that reported for Sa/G
systems.3 The values of kr for 5-7 display a weaker distance
dependence with a value of â ) 0.42 Å-1
.
The values of â ≈ 1.0 Å-1 for charge recombination in 1-4
and Sa/G systems are similar to that for charge separation in
donor-bridge-acceptor systems with protein â-strand bridges,
which undergo electron transfer via a single-step superexchange
(36) Takada, T.; Kawai, K.; Cai, X.; Sugimoto, A.; Fujitsuka, M.; Majima, T.
J. Am. Chem. Soc. 2004, 126, 1125-1129.
(37) Kawai, K.; Takada, T.; Tojo, S.; Fujitsuka, M.; Majima, T. J. Am. Chem.
Soc. 2003, 125, 6842-6843.
(34) Lewis, F. D.; Wasielewski, M. R. Top. Curr. Chem. 2004, 236, 45-65.
(35) Fiebig, T.; Wan, C.; Zewail, A. H. ChemPhysChem 2002, 3, 781-788.
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A R T I C L E S
Lewis et al.
mechanism.38 The value of â ≈ 0.4 Å-1 for charge recombina-
tion in 5-7 is similar to the values reported by Shafirovich et
al.39 for hole transport from aminopurine cation radical to
guanine and by Takada et al. for naphthaldiimide/phenothiazine
systems separated by 4-8 A:T base pairs.36 The smaller slope
may reflect an increasing contribution of multistep hole hopping
to the charge recombination dynamics at longer distances.40 If
so, the onset of crossover occurs at much larger value of RDA
(five intervening base pairs or ca. 20 Å) than is the case for
charge separation. Abdel Malak et al. have recently reported a
crossover in mechanism for electron transfer across helical poly-
(proline) bridges from superexchange (â ) 1.4 Å-1) to hopping
(â ) 0.18 Å-1) that occurs at a donor-acceptor edge-to-edge
distance of ca. 20 Å.8
The occurrence of crossover from superexchange to hole
hopping at a longer distance for charge recombination than for
charge separation is a consequence of donor-bridge acceptor
energetics. Whereas reversible hole injection is approximately
isoergonic, hole trapping by Sd is estimated to be exergonic by
ca. 0.5 eV (Scheme 2a). Paulson et al. have recently reported
that rate constants for superexchange are only weekly dependent
upon the free energy for electron transfer, whereas rate constants
for hopping are strongly dependent upon the free energy
change.9 Thus, superexchange will dominate at short distances
when ∆Get is large, as it is for charge recombination in 2-4.
Å-1, consistent with a superexchange mechanism, as previously
proposed. The singlet acridinium acceptor Acr* studied by
Fukui and by Michel-Beyerle reportedly does not oxidize
neighboring A.4 Oxidation of G or Z by Acr* is strongly
distance dependent (â ≈ 1.4 Å-1), consistent with a super-
exchange mechanism. Values of â > 1 Å-1 have also been
reported for DNA-mediated photoinduced charge separation
between both intercalated and end-tethered donor-acceptor
pairs, which are not capable of hole injection.42
Hole injection for the stronger acceptor diphenylacetylene
dicarboxamide Dpa (Chart 2) is estimated to be exergonic by
∼0.1 eV. Rate constants for conversion of Dpa to Dpa-• are
independent of the presence of guanine, consistent with a
hopping mechanism for Dpa/G systems with 1-5 intervening
A:T base pairs.43 Reanalysis of the published results for these
systems indicates that hole trapping by guanine does occur
following hole injection and hole transport. Photoinduced charge
separation in systems having an intercalated ethidium acceptor
and deazaguanine donor is also reported to occur via hole
injection followed by irreversible hole trapping.5
The behavior of the Pa/Z and Dpa/G systems provides
examples of superexchange and hopping mechanisms, respec-
tively, whereas the Sa/Sd system exhibits crossover between
these two limiting mechanisms. Another likely example of
crossover is provided by the results of Wan et al. for photo-
induced electron transfer in systems possessing an aminopurine
(Ap) acceptor and guanine donor separated by several A:T base
pairs.6 An increase in Ap* lifetime with increasing Ap/G
separation is attributed to competing superexchange quenching
by G and A, but also could result from reversible hole injection
followed by distance-dependent charge trapping by G.
In summary, the coordinated application of several transient
spectroscopic methods has succeeded in disentangling for the
first time the complex kinetics of photoinduced charge separa-
tion and charge recombination in DNA. Charge separation is
found to occur via a single-step superexchange mechanism only
at short donor-acceptor distances. At longer distances, charge
separation occurs via a multistep mechanism: hole injection,
hole migration, and hole trapping. The superexchange, hole
migration, and charge recombination processes are all distance
dependent, whereas the hole injection process is independent
of donor-acceptor distance, but dependent upon its energetics.
The dynamics and mechanism of hole migration in A-tracts and
other base sequences are the subjects of continuing investigation.
Concluding Remarks
The observation of charge separation via a multistep hole
hopping mechanism for Sa/Sd hairpin systems possessing two
or more A:T base pairs necessitates reexamination of the
literature relating to the mechanism and dynamics of photo-
induced charge separation in donor-bridge-acceptor systems
with DNA bridges. The results of collaborative studies in our
laboratories indicate that charge separation in Sa/G systems with
two or more intervening A:T base pairs also occurs via hole
hopping rather than superexchange. A hole hopping mechanism
can also readily explain the observation of similar rate constants
for charge separation in Sa-linked hairpins possessing Sd, G,
GG, GGG, and Z hole traps.41 Increasing the depth of the hole
trap should have little effect on the dynamics of charge
separation in these systems. Rate constants reported in our
previous study of reversible hole transport between primary and
secondary hole traps are not dependent upon the assumed
mechanism for hole injection and thus should not require
revision.34
Acknowledgment. This research is supported by the Office
of Basic Energy Sciences, U.S. Department of Energy under
Contract DE-FG02-96ER14604 (F.D.L.), Boston College (T.F.),
and the National Institutes of Health, Grant 5 R01 ES11589,
and the Kresge Foundation (V.S.).
The use of different singlet acceptors can affect the competi-
tion between superexchange versus hole hopping. Hole injection
for the weaker phenanthrenedicarboxamide acceptor Pa (Chart
2) is estimated to be endergonic by ∼0.25 eV.39 The distance
dependence of singlet quenching of Pa* by deazaguanine
separated by 1-3 A:T base pairs provides a value of â ) 1.1
Supporting Information Available: Fluorescence decay
traces for 3, transient absorption spectra for Sa and Sd, and
transient absorption spectra for 2-4 at delay times of 0.2-1.9
ns. This material is available free of charge via the Internet at
http://pubs.acs.org.
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