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DNA base damage: A Car-Parrinello molecular dynamics study of guanine and thymine with an OH radical

Christopher J. Mundy, Yudong Wu, Michael E. Colvin, Roberto Car, and Andrew A. Quong
Lawrence Livermore National Labs, US

Keywords: DFT, DNA-bases, chemical reactions, Base-damage

Abstract:
Understanding the basic chemistry of radicals and DNA bases is an important step in characterizing the potential damage to DNA. The chemical level understanding of such damage has far reaching implications for radiation therapy, health effects of radiation exposure, and aging. Although there are numerous experimental studies on the initial phases of DNA base oxidation, there are still open questions as to the precise mechanisms of the initial stages of the oxidative process. Our theoretical study focuses on using dynamical methods to try to elucidate possible reaction mechanisms for the initial stages of oxidation in guanine and thymine. In this study both traditional static quantum chemical methods and Car-Parrinello molecular dynamics (CPMD) are used to investigate and identify transition states and reaction mechanisms for an isolated guanine and thymine interacting with an OH radical in both gas-phase and solvent conditions.

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