On the Mechanisms of OH Radical Induced DNA-Base Damage: A Comparative Quantum Chemical and Car - Parrinello Molecular Dynamics Study

Understanding the basic chemistry of the interaction of radicals with DNA bases is imperative when trying to predict the potential effects of radiation on DNA. Experimental evidence points to guanine as having the highest affinity of all the DNA bases for undergoing damage. However, radiation-induced damage to other bases may also have important health effects, and therefore the reactions of other DNA bases are also of interest. To this end, numerous studies have been performed on thymine to elucidate its role in the initial phases of DNA damage. To date, the theoretical studies on this topic have only dealt with reaction energetics in the gas phase or within a continuum solvent model. We present a detailed Car - Parrinello molecular dynamics study of DNA bases in explicit water interacting with an OH radical. Our findings indicate that the specific mechanisms of the initial phase of DNA damage are different in thymine and guanine, which is consistent with experiment-based conjectures on this subject. We also compare the effects of different exchange and correlation functionals on the proposed reaction energetics as well as a comparison with traditional quantum chemistry methods. Our deduced mechanisms are consistent with the experimentally observed products.