Radical-induced damage in 3′dTMP -: Insights into a mechanism for DNA strand cleavage

DNA strand scission and base release in 3'dTMP, induced by H and OH radical addition to thymine, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular the mechanism of H atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. Bulk solvation is found to lower the barrier by up to 5 kcal mol(-1) and the reaction energy by up to 12 kcal mol(-1) for the hydroxyl radical adducts. The strengths of the N1-C1'(N1-glycosidic bond) and C3'-O(P) bonds are calculated, showing that homolytic bond breaking processes are largely favored in both cases. The barrier for C3'-O(P) bond rupture is approximately 18.2 kcal mol(-1), and its breakage is preferred by 10-15 kcal mol(-1) over that of N1-glycosidic bond cleavage in both the gas phase and solvents, which is consistent with the changes in C3'-O(P) and N1-C1' bond lengths during the H transfer reactions. Mulliken spin densities, NPA charges, and vertical electron affinities are calculated to clarify the reactive properties of the intramolecular H-transfer radicals.