Reactive Molecular Dynamics study on the first steps of DNA-damage by free hydroxyl radicals

TL;DR

This study uses reactive molecular dynamics simulations to investigate how hydroxyl radicals from ionizing radiation cause chemical damage to DNA, leading to strand breaks through hydrogen abstraction and hole formation.

Contribution

It introduces large-scale ReaxFF molecular simulations to model the initial chemical reactions of hydroxyl radicals with DNA in aqueous environments.

Findings

Hydroxyl radicals primarily cause hydrogen abstraction in DNA.

Damage propagates to DNA strand breaks over time.

Holes in sugar rings contribute to DNA backbone damage.

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.