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

https://mdr.nims.go.jp/datasets/97de151c-95e5-4997-8288-f77d0c82bf1f

## Files

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## Id

97de151c-95e5-4997-8288-f77d0c82bf1f

## Local identifier



## Visibility

open_to_public

## State

published

## Created at

2024-12-20T08:21:26.717897Z

## Updated at

2025-12-09T23:30:41.279284Z

## Published at

2025-12-09T23:23:50.627606Z

## Doi

https://doi.org/10.48505/nims.5255

## First published url

https://doi.org/10.35848/1347-4065/ad8b54

## Date published

2024-12-02

## Recorded date published

2024-12-2

## Resource type

journal_article

## Manuscript type

accepted_manuscript

## Collection



## Title

- title: Reactive molecular dynamics simulation on DNA double-strand breaks induced
    by hydrogen elimination
  title_type: original
  lang: en

## Description

- description: 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.
  description_type: abstract
  lang: und

## Creator

- name: Hiroaki Nakamura
  role: author
  orcid: https://orcid.org/0000-0002-0593-8810
- name: Kento Ishiguro
  role: author
- name: Ayako Nakata
  role: author
  orcid: https://orcid.org/0000-0002-3311-6283
  organization: National Institute for Materials Science
  ror: https://ror.org/026v1ze26
- name: Shunsuke Usami
  role: author
- name: Seiki Saito
  role: author
  orcid: https://orcid.org/0000-0002-0332-8189
- name: Susumu Fujiwara
  role: author

## Contact agent



## Publisher

organization: IOP Publishing

## Managing organization



## Keyword

- subject: strand breaks
  schema: not_defined
- subject: telomeric DNA
  schema: not_defined
- subject: β-decay
  schema: not_defined
- subject: Molecular dynamics simulations
  schema: not_defined
- subject: reactive force field
  schema: not_defined

## Rights

- description: "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\r\nany version derived from it. The Version of Record is available online at
    https://doi.org/10.35848/1347-4065/ad8b54."
  identifier: https://creativecommons.org/licenses/by-nc-nd/4.0/

## Other identifier(s)



## Data origin

- data_origin_type: other

## Embargo

start_date: 2024-12-10
end_date: 2025-12-10

## Journal

- title: Japanese Journal of Applied Physics
  issn: '00214922'
  volume: '63'
  issue: '12'
  article_number: 12SP09

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## Fileset

- id: 68c8c140-92e4-4c4a-b70d-c9515643d38c
  filename: isplasma2024nakamura-fin.pdf
  content_type: application/pdf
  size: 13855478
  md5: 7aa28dcff26b3a3815233ecd1a3ec125

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filename: isplasma2024nakamura-fin.pdf