Multiscale QM/MM Molecular Dynamics Study on the First Steps of Guanine Damage by Free Hydroxyl Radicals in Solution

Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to understanding the indirect effect of ionizing radiation. Previous studies address the problem with truncated DNA bases as ab initio quantum simulations required to study such electronic...

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Bibliographic Details
Published in:The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory Molecules, spectroscopy, kinetics, environment, & general theory, 2012-04, Vol.116 (15), p.3940-3945
Main Authors: Abolfath, Ramin M, Biswas, P. K, Rajnarayanam, R, Brabec, Thomas, Kodym, Reinhard, Papiez, Lech
Format: Article
Language:English
Subjects:
Anisotropy
Computer simulation
Damage
Deoxyribonucleic acid
DNA - chemistry
Guanine - chemistry
Guanines
Hydroxyl Radical - chemistry
Hydroxyl radicals
Molecular dynamics
Molecular Dynamics Simulation
Radicals
Solutions
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Summary:Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to understanding the indirect effect of ionizing radiation. Previous studies address the problem with truncated DNA bases as ab initio quantum simulations required to study such electronic-spin-dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid quantum mechanical–molecular mechanical simulation to study the interaction of OH radicals with a guanine-deoxyribose-phosphate DNA molecular unit in the presence of water, where all of the water molecules and the deoxyribose-phosphate fragment are treated with the simplistic classical molecular mechanical scheme. Our result illustrates that the presence of water strongly alters the hydrogen-abstraction reaction as the hydrogen bonding of OH radicals with water restricts the relative orientation of the OH radicals with respect to the DNA base (here, guanine). This results in an angular anisotropy in the chemical pathway and a lower efficiency in the hydrogen-abstraction mechanisms than previously anticipated for identical systems in vacuum. The method can easily be extended to single- and double-stranded DNA without any appreciable computational cost as these molecular units can be treated in the classical subsystem, as has been demonstrated here.
ISSN:1089-5639
1520-5215
DOI:10.1021/jp300258n