Electronic Excited States Responsible for Dimer Formation upon UV Absorption Directly by Thymine Strands: Joint Experimental and Theoretical Study.
ABSTRACT The study addresses interconnected issues related to two major types of cycloadditions between adjacent thymines in DNA leading to cyclobutane dimers (T<>Ts) and (6-4) adducts. Experimental results are obtained for the single strand (dT)(20) by steady-state and time-resolved optical spectroscopy, as well as by HPLC coupled to mass spectrometry. Calculations are carried out for the dinucleoside monophosphate in water using the TD-M052X method and including the polarizable continuum model; the reliability of TD-M052X is checked against CASPT2 calculations regarding the behavior of two stacked thymines in the gas phase. It is shown that irradiation at the main absorption band leads to cyclobutane dimers (T<>Ts) and (6-4) adducts via different electronic excited states. T<>Ts are formed via (1)ππ* excitons; [2 + 2] dimerization proceeds along a barrierless path, in line with the constant quantum yield (0.05) with the irradiation wavelength, the contribution of the (3)ππ* state to this reaction being less than 10%. The formation of oxetane, the reaction intermediate leading to (6-4) adducts, occurs via charge transfer excited states involving two stacked thymines, whose fingerprint is detected in the fluorescence spectra; it involves an energy barrier explaining the important decrease in the quantum yield of (6-4) adducts with the irradiation wavelength.
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ABSTRACT: The photochemical reactions of eleven synthetic DNA hairpins possessing a single TT step either in a base-paired stem or in a hexanucleotide linker have been investigated. The major reaction products have been identified as the cis-syn (2 + 2) adduct and the (6 - 4) adduct on the basis of their spectroscopic properties including 1D and 2D NMR spectra, UV spectra and stability or instability to photochemical cleavage. Product quantum yields and ratios determined by HPLC analysis allow the behaviour of the eleven hairpins to be placed into three groups: Group I in which the (2 + 2) adduct is the major product, as is usually the case for DNA, Group II in which comparable amounts of (2 + 2) and (6 - 4) adducts are formed, and Group III in which the major product is the (6 - 4) adduct. The latter behaviour is without precedent in natural or synthetic DNA and appears to be related to the highly fluxional structures of the hairpin reactants. Molecular dynamics simulation of ground state conformations provides quantum yields and product ratios calculated using a single parameter model that are in reasonable agreement with most of the experimental results. Factors which may influence the observed product ratios are discussed.Photochemical and Photobiological Sciences 11/2013; · 2.92 Impact Factor
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ABSTRACT: Induction of DNA damage is one of the major consequences of exposure to solar UV radiation in living organisms. UV-induced DNA photoproducts are mostly pyrimidine dimers, including cyclobutane pyrimidine dimers, pyrimidine (6-4) pyrimidone photoproducts and Dewar valence isomers. In the last few decades, a large number of methods have been developed for the quantification of these pyrimidine dimers. The present review emphasizes the contribution of chromatographic techniques to our better understanding of the basic DNA photochemistry and the better description of damage in cells.Photochemical and Photobiological Sciences 04/2013; · 2.92 Impact Factor
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ABSTRACT: The nature of electronically excited states in DNA is analyzed in detail using a combination of quantum mechanical (QM) semiempirical calculations and molecular dynamics (MD). For this purpose, we consider homogeneous π stacks extracted from the MD trajectory of a poly(A)·poly(T) oligomer. The environment is accounted for within the QM/MM scheme. The effects of structural fluctuations on exciton delocalization and photoinduced charge separation are explored using the quantitative analysis of the electron density in the excited states. We distinguish the effects generated by the vibronic interactions within nucleobases and by the environment of the π stack. While in ideal B-DNA stacks (A-T)(n) singlet excited states are spread over all intrastrand nucleobases, the average exciton length is ∼0.75n, thermal fluctuations decrease considerably the extent of delocalization. The QM/MD model predicts that the excitons in (A-T)(n) stacks are spread over 3 bases (for n = 4 and 6, the average exciton length is found to be 2.6 ± 0.3 and 2.8 ± 0.3, respectively). We show that the main factor reducing the exciton length is the vibronic interactions within nucleobases whereas fluctuations of the π stack environment play a relatively minor role. The oscillator strength of electronic transitions from the ground state to charge-separated states A(k)(+)A(k±1)(-) and T(k)(+)T(k±1)(-) is found to be strong enough to populate directly these states by UV absorption at E = 5.0-5.3 eV. In contrast, the direct formation of interstrand charge transfer states A(i)(+)T(j)(-) is predicted to be unlikely.Photochemical and Photobiological Sciences 01/2013; · 2.92 Impact Factor