Effects of electron attachment on C5′O5′ and C1′N1 bond cleavages of pyrimidine nucleotides: A theoretical study

Abstract

Sugar-base C(1')-N(1) and phosphate-sugar C(5')-O(5') bond breakings of 2'-deoxycytidine-5'-monophosphates (dCMP) and 2'-deoxythymidine-5'- monophosphates (dTMP) and their radical anions have been explored theoretically at the B3LYP/DZP++ level of theory. Calculations show that the low-energy electrons attachment to the pyrimidine nucleotides results in remarkable structural and chemical bonding changes. Predicted Gibbs free energies of reaction DeltaG for the C(5')-O(5') bond dissociation process of the radical anions are -14.6 and -11.5 kcal mol(-1), respectively, and such dissociation processes may be intrinsically spontaneous in the gas phase. Furthermore, the C(5')-O(5') bond cleavage processes of the anionic dCMP and dTMP were predicted to have activation energies of 6.9 and 8.0 kcal mol(-1) in the gas phase, respectively, much lower than the barriers for the C(1')-N(1) bond breaking process, showing that the C-O bond dissociation in DNA single strand breaks is a dominant process as observed experimentally.