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DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical
Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
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
Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
- 1 Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
- 2 Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
- 3 Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
- 4 Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- 5 Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
Journal of Modern Physics·Volume 04 (2013)·Pages 442–451·Published 29 March 2013·DOI10.4236/jmp.2013.43A062
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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 NH 2 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 NH 2 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.
KeywordsDensity Functional TheoryDNAHydroxyl RadicalBase PairReaction MechanismDehydrogenation
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