Reactive Molecular Dynamics Study on the First Steps of DNA Damage by Free Hydroxyl Radicals

Abstract

We employ a large scale molecular simulation based on bond-order ReaxFF to simulate the chemical reaction and study the damage to a large fragment of DNA-molecule in the solution by ionizing radiation. We illustrate that the randomly distributed clusters of diatomic OH-radicals that are primary products of megavoltage ionizing radiation in water-based systems are the main source of hydrogen-abstraction as well as formation of carbonyl-and hydroxyl-groups in the sugar-moiety that create holes in the sugar-rings. These holes grow up slowly between DNA-bases and DNA-backbone and the damage collectively propagate to DNA single and double strand break.PACS numbers: 87.64.Aa It is known that megavoltage radiation (X/γ-rays, α-particles, and heavy ions) ionizes the water molecule and creates neutral free-radicals and aqueous electrons 1-9 . In particular OH-radicals with a very short life-time that is reported to be within nano-seconds 10 , are major contributors to the single/double strand breaking of the DNA molecules and the nucleotide-base damage, as 2/3 of environment surrounding DNA molecules in the cell-nucleus is composed of water molecules 4 . Various effects of the ionizing radiation on biological systems that ranges from the development of genetic aberrations, carcinogenesis to aging, have attributed to the role of free radicals.Computational modeling is a valuable tool in understanding the basic mechanisms that underlie DNA damage. Great effort has been devoted to the statistical modeling of the damage sites based on Monte-Carlo (MC) sampling, using empirical reaction rates and radiation scattering cross-sections 4-9 . These models are limited to MC sampling on a static structure of DNA or dynamical models based on molecular-mechanics (MM) and empirical force-fields (FF), e.g. AMBER/CHARMM FF, that are developed for simulation of the non-reactive aspects of bio-molecules.The reactive aspects and the time evolution of the multi-site DNA damages driven by cascade of chemical reactions, that are beyond MM methods and empirical FF, require the calculation of the potential energies onthe-fly using first-principle quantum mechanical (QM) models. Recently ab-initio simulations of the hydrogen abstraction were developed 11-15 . However realistic modeling of DNA molecule with its environment requires extensive computer resources and is a major draw-back of QM methods. The DFT calculation for hydrogen abstraction in vacuum is limited to the initial damage of a single base [11][12][13] or single sugar-moiety 15 . Despite recent advances in QM/MM methods that allows simulation of larger molecules 14 and inclusion of solvation 15 , the real time simulation of DNA-damage remains still elusive.To address the above considerations regarding to the large scale modeling of DNA-damage, we have studied the evolution of randomly distributed hydroxyl-radicals in small pockets surrounding the DNA-molecule at room temperature using molecular dynamics simulations where the atomic interactions are described by the reactive force f...

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