Reactive molecular dynamics simulation on DNA double-strand breaks induced by hydrogen elimination

Hiroaki Nakamura; Kento Ishiguro; Ayako Nakata; Shunsuke Usami; Seiki Saito; Susumu Fujiwara

doi:10.35848/1347-4065/ad8b54

論文 Reactive molecular dynamics simulation on DNA double-strand breaks induced by hydrogen elimination

Hiroaki Nakamura ; Kento Ishiguro ; Ayako Nakata (National Institute for Materials Science) ; Shunsuke Usami ; Seiki Saito ; Susumu Fujiwara

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Hiroaki Nakamura, Kento Ishiguro, Ayako Nakata, Shunsuke Usami, Seiki Saito, Susumu Fujiwara. Reactive molecular dynamics simulation on DNA double-strand breaks induced by hydrogen elimination. Japanese Journal of Applied Physics. 2024, 63 (12), 12SP09. https://doi.org/10.35848/1347-4065/ad8b54

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(abstract)

We propose a scar model to reproduce how double-strand breaks occur in the telomeric DNA damaged by the effect of the beta-decay of tritium to helium. In this scar model, the two hydrogens bonded to the 5' carbon connecting the pentasaccharides and phosphate are removed. Molecular dynamics simulations using the reactive force field are carried out for 10 cases for the telomeric DNA consisting of 16 base pairs (32 nucleotides). It results in double-strand breaks (DSBs) being observed for structures with more than 24 scars. For 16 scars cases, only single-strand breaks (SSB) are observed. Moreover, in the case of {16,0} and {0,16}, where only one of the strands had scars, SSB occurs only in the scarred strand. Secondly, in the {16,8} and {8, 16} cases, DSBs occurs. Therefore, we conclude that the following conditions are necessary for DSBs：(i) Scars must occur on both the L and R strands. (ii) A large number of scars (24 or more) must occur in close proximity to each other.

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Creative Commons BY-NC-ND Attribution-NonCommercial-NoDerivs 4.0 International
This is an author-created, un-copyedited version of an article accepted for publication/published in Japanese Journal of Applied Physics. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at https://doi.org/10.35848/1347-4065/ad8b54.