Effect of proton transfer on the anionic and cationic pathways of pyrimidine photodimer cleavage.: A computational study

Proton exchange between pyrimidine photodimers and their environment may have a profound impact on DNA photorepair. On the basis of B3LYP/6-31G* and AM1 calculations, we present the first computational study of the influence of protonation and deprotonation on the splitting reactions of pyrimidine dimer ion radicals. While proton transfer from a complementary adenine to a Pyr >$($) over bar Pyr anion is calculated to be endothermic and, therefore, is unlikely in DNA, protonation of the dimer anion is feasible in polar solution. Cleavage of both nonprotonated and protonated dimer anions is a two-step reaction where C5-C5' bond splitting is followed by cleavage of the C6-C6' bond. However, the calculated activation barriers for the splitting of the protonated species are considerably higher than those for the corresponding nonprotonated anion. Proton transfer from a pyrimidine dimer cation to adenine is found to be energetically favorable. The opening of the cyclobutane ring in the dimer cation and its deprotonated state proceeds in reverse order: the C6-C6' bond is broken first, followed by splitting of the C5-C5' bond. Although the splitting of the dimer cation is activationless, rather high activation barriers are predicted for the cleavage of its deprotonated form in the gas phase. However, this barrier decreases substantially in a polar medium and, therefore, deprotonation of the dimer cation does not prevent its splitting in DNA nor in polar solution.