Dynamics of Photoinduced Charge Separation and Charge Recombination in Synthetic DNA Hairpins with Stilbenedicarboxamide Linkers

Abstract

The dynamics of photoinduced charge separation and charge recombination in synthetic DNA hairpins have been investigated by means of femtosecond and nanosecond transient spectroscopy. The hairpins consist of a stilbene linker connecting two complementary 6-mer or 7-mer oligonucleotide strands. Base pairing between these strands results in formation of hairpins in which the stilbene is approximately parallel to the adjacent base pair. The singlet stilbene is selectively quenched by guanine, but not by the other nucleobases, via an electron-transfer mechanism in which the stilbene singlet state is the electron acceptor and guanine is the electron donor. In a hairpin containing only A:T base pairs, no quenching occurs and the restricted geometry results in a long stilbene lifetime and high fluorescence quantum yield. In families of hairpins which contain a single G:C base pair at varying locations in the hairpin stem, the stilbene fluorescence lifetime and quantum yield decrease as the stilbene-guanine distance decreases. Transient absorption spectroscopy is used to monitor the disappearance of the stilbene singlet and the formation and decay of the stilbene anion radical. Analysis of these data provides the rate constants for charge separation and charge recombination. Both processes show an exponential decrease in rate constant with increasing stilbene-guanine distance. Thus, electron transfer is concluded to occur via a single-step superexchange mechanism with a distance dependence β ) 0.7 Å -1 for charge separation and 0.9 Å -1 for charge recombination. The rate constants for charge separation and charge recombination via polyA vs polyT strands are remarkably similar, slightly larger values being observed for polyA strands. The dynamics of electron transfer in hairpins containing two adjacent G:C base pairs have also been investigated. When the guanines are in different strands, the second guanine has little effect on the efficiency or dynamics of electron transfer. However, when the guanines are in the same strand, somewhat faster charge separation and slower charge recombination are observed than in the case of hairpins with a single G:C base pair. Thus, the GG step functions as a shallow hole trap. The relationship of these results to other theoretical and experimental studies of electron transfer in DNA is discussed.

Fluorescence-Quenching Phenomenon by Photoinduced Electron Transfer between a Fluorescent Dye and a Nucleotide Base

“…Some fluorophores conjugated DNA were reported to quench its fluorescence upon hybridization by photoinduced electron transfer accompanying DNA damage, such as irreversible electron transfer with guanine and/or DNA cleavage. 13,[25][26][27][40][41][42][43][44] These matters are greatly related to recent topics of DNA electron transfer, 45 but are too complicated to understood. Some researchers examined both forward and reverse electron transfer in the photoinduced electron transfer process, e.g.…”

Distance Dependence of Electron Transfer in DNA: The Role of the Reorganization Energy and Free Energy

“…Numerous experimental studies have been performed, resulting in reports of widely varying distance dependences of the electron transfer. [1][2][3][4][5][6][7][8][9][10][11][12][13][14] Some of the experimental systems studied appear to undergo almost distance-independent electron transfer. [4][5][6][7][8][9][10] Theories to explain this work include pair wise hopping mechanisms, 15 wavelike electron transfer through a delocalized bridge system, 16 and thermally activated pair wise transfer via base pairs.…”

“…17 Some experimental work shows a distance dependence typical of superexchange or electron tunneling (Marcuslike) observed for inter-and intramolecular electron transfer in a wide variety of environments, including proteins, liquids, and micelles. [1][2][3][11][12][13][14] It has recently been suggested that electron transfer in DNA may occur by different mechanisms depending on the energetics of a specific system. 15 The focus of this paper is to examine the role played by the distance dependence of the reorganization energy and the free energy associated with electron transfer on the overall distance dependence of single-step electron transfer (Marcus-like transfer) in the heterogeneous DNA environment.…”

“…Model calculations are presented to illustrate the nature of the effects, and the model is applied to examples of data reported in the literature. 1,2 Previously, data have been analyzed primarily using a simple exponential distance-dependent rate, k e (r), [1][2][3]11 where r e is the edge-to-edge distance between the donor and acceptor molecules, A is a preexponential factor, and e characterizes the exponential distance dependence of the transfer. Equation 1 can be useful to characterize the distance dependence approximately.…”

Effects of strand and directional asymmetry on base–base coupling and charge transfer in double-helical DNA

“…A wealth of experimental evidence has established, undeniably, that DNA can act as a conduit for rapid and long-range charge transfer (CT), not only in DNA assemblies designed in the laboratory (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24), but also in biologically significant environments (25,26). DNA, remarkable for its role in the molecular basis of life, may also play a role as a mediator of CT in diverse areas of chemistry and biology.…”