DFT study of adenine‐uracil base pair damage by OH radical

Abstract

The hydrogen abstraction and addition reactions of OH radical with A·U base pair have been explored by using density functional theory (DFT) both in gas phase and in aqueous solution. Solvent effects were taken into consideration by using the polarized continuum model. All the reaction pathways are exothermic in energy, and the compounds in aqueous phase are more favorable than those in gas phase. The relative free energies of adducts in the addition reaction are lower than those obtained for products in hydrogen abstraction reaction. Among dehydrogenation reaction, the hydrogen abstractions from AC2·U and AN6·U sites are more favorable than those from AC8·U, A·UC5, and A·UC6 sites. In addition, hydroxylation at AC8·U, A·UC5, and A·UC6 sites are more probable than other investigated positions. The hydroxylation at AH8·U site is most favorable, and hydroxylation at A·UC5 site is more preference than that at A·UC6 site controlled by the kinetics factors. The data in both gas phase and water solution demonstrated that addition of OH radical to A·UC5 and A·UC6 sites are more thermodynamically and kinetically favorable than abstracting the hydrogen atom form A·UC5 and A·UC6 sites. The phenomena are in agreement with the experimental observations. Copyright © 2015 John Wiley & Sons, Ltd.