Efficient and Substantial DNA Lesions From Near 0 eV Electron-Induced Decay of the O4-Hydrogenated Thymine Nucleotides: A DFT Study.

Possible electron-induced ruptures of C3'-O3', C5'-O5', and N1-C1' bonds in O4-hydrogenated 2'-deoxythymidine-3'-monophosphate (3'-dT(O4H)MPH) and 2'-deoxythymidine-5'-monophosphate (5'-dT(O4H)MPH) are investigated using density functional theory calculations, and efficient pathways are proposed. Electron attachment causes remarkable structural relaxation in the thymine C6 site. A concerted process of intramolecular proton transfer (IPT) from the C2' site of 2'-deoxyribose to the C6 site and the C3'-O3' bond rupture is observed in [3'-dT(O4H)MPH](-). A low activation barrier (9.32 kcal/mol) indicates that this pathway is the most efficient one as compared to other known pathways leading to backbone breaks of a single strand DNA at the non-3'-end thymine, which prevents the N1-C1' bond cleavage in [3'-dT(O4H)MPH](-). However, essentially spontaneous N1-C1' bond cleavage following similar IPT is predicted in [5'-dT(O4H)MPH](-). A moderate activation barrier (13.02 kcal/mol) for the rate-controlling IPT step suggests that base release from the N1-C1' cleavage arises readily at the 3'-end of single strand DNA with the strand ended by a thymine. The C5'-O5' bond has only an insignificant change in the IPT process. Solvent effects are found to increase slightly the energy requirements for either bond ruptures (11.23 kcal/mol (C3'-O3') vs 16.18 kcal/mol (N1-C1')), but not change their relative efficiencies.