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

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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.

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