First principles electrochemical study of redox events in DNA bases and chemical repair in aqueous solution

Abstract

Primary and secondary radiation-induced damage to DNA, and chemical repair of the lesions on the nucleobases in solution involve a cascade of proton transfer (PT), electron transfer (ET), and proton-coupled electron transfer (PT-ET) reactions. The rate constants of these reactions depend on the standard Gibbs energy changes that can be derived from experiment. We here apply a first principles approach to calculate standard Gibbs energy changes of proton, electron, and proton-coupled electron transfer reactions in solution, wherein electrons and protons participate as independent ions; data that is fully compatible with that experimentally derived. Hence, the thermodynamic feasibility of ET and PT-ET pathways for these reactions depending on the effective concentration of hydrogen ions can be directly rationalized from first principles. The focus of this study is the primary and secondary ionization events in nucleobases in the presence of hydrogen atoms, solvated electrons and protons in aqueous solution, leading to the formation of nucleobase radical anions B˙−, radical cations B˙+ and their major deprotonated radical forms B(–H)˙. We also examine the chemical repair reaction by thiols, B(–H)˙(aq) + RSH(aq) = B(aq) + RS˙(aq), where B = A,G,C,T. Our results for the chemical repair of B(–H)˙ suggest that a PT-ET pathway should be favored for A and C at any pH, whereas for G and T, a PT-ET pathway is preferred at acidic and near neutral pH, but in the pH range 9-11, the ET pathway would dominate.