Ab initio study of DNA double-strand breaks by hydroxyl radical

Abstract

To investigate the detailed mechanism underlying double-stranded DNA (dsDNA) breaks caused by electron or photon impact, a physical model is proposed and ab initio quantum chemical calculation is employed. In our model, we neglect the backbone of DNA and focus on the interaction between a hydroxyl radical and a single-base pair. By Becke's three-parameter hybrid Lee-Yang-Parr (B3LYP) functionals method based on a density functional theory, we calculate the optimized structure of base pair-hydroxyl radical complex by the energy minimization. The results suggest that the hydroxyl radical can stably exist near the hydrogen bond between adenine and thymine, or between guanine and cytosine. Consequently, we have found that the hydroxyl radical weakens the hydrogen bonds and the corresponding bond length of the base pair in dsDNA increases.