DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical

Eisuke Shimizu, Ryota Hoshino, Kazuya Nomura, Victor I. Danilov, Noriyuki Kurita

Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan.
Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine.

DOI: 10.4236/jmp.2013.43A062                

Abstract

In order to elucidate the indirect effect by radiation on DNA base pairs, we investigate the mechanism for the attacking reaction of a hydroxyl radical (^·OH-radical) to the G-C and A-T base pairs, by the density functional theory (DFT) calculations. The effect of solvation on the mechanism is also revealed by performing the same DFT calculations under the continuum solvation approximation. We find the stable structures for the dehydrogenated G-C and A-T base pairs, in which the hydrogen atom of NH₂ group of G or A base is abstracted by the ^·OH-radical. The solvation around the base pairs stabilizes the dehydrogenated structures significantly, indicating the acceleration of the attacking reaction by ^·OH-radical to the base pairs in water. Therefore, we conclude that the hydrogen atom of the NH₂ group of G or A base in the G-C and A-T base pairs is the most preferably abstracted by the ^·OH-radical in living cells.

Keywords

Density Functional Theory; DNA; Hydroxyl Radical; Base Pair; Reaction Mechanism; Dehydrogenation

Conflicts of Interest

The authors declare no conflicts of interest.

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