TITLE:
DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical
AUTHORS:
Eisuke Shimizu, Ryota Hoshino, Kazuya Nomura, Victor I. Danilov, Noriyuki Kurita
KEYWORDS:
Density Functional Theory; DNA; Hydroxyl Radical; Base Pair; Reaction Mechanism; Dehydrogenation
JOURNAL NAME:
Journal of Modern Physics,
Vol.4 No.3A,
March
29,
2013
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.