Molecular dynamics study on DNA damage by tritium disintegration
Japanese Journal of Applied Physics 59, SAAE01 (2020)
Hiroaki Nakamura1, Hisanori Miyanishi2, Takuo Yasunaga3, Susumu Fujiwara4 ,
Tomoko Mizuguchi4 , Ayako Nakata5 , Tsuyoshi Miyazaki5 , Takao Otsuka6 , Takahiro Kenmotsu7 ,Yuji Hatano8
1 Department of Helical Plasma Research, National Institute for Fusion Science, Toki, Gifu, JAPAN
2 Department of Energy Engineering and Sciences, Nagoya University, Nagoya, Aichi, JAPAN
3 Kyushu Institute of Technology, IIzuka, Fukuoka, JAPAN
4 Kyoto Institute of Technology, Kyoto, JAPAN
5 National Institute for Materials Science, Tsukuba, Ibaraki, JAPAN
6 RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, JAPAN
7 Doshisha University, Kyotanabe, Kyoto, JAPAN
8 University of Toyama, Toyama, Toyama, JAPAN
9 Institute for Molecular Science, Okazaki, JAPAN
Abstract
Using molecular dynamics, we simulate the structural change of a telomeric DNA by β-decay of substituted tritium to helium-3. The configuration of the telomeric DNA is obtained by removing TRF2 protein from the TRF2-Dbd-DNA complex (PDBID: 3SJM). We assume that hydrogens of guanines in the DNA are replaced to helium-3. The charge distribution in the MD simulation for the modified guanine is obtained by DFT simulation. We adopt, as the MD simulation, Nanoscale Molecular Dynamics code with CHARMM36 force field and Langevin thermostat algorithm. Changing both the number of replaced guanine N and the temperature T, we calculate the root mean square deviation to quantify the durability of DNA. It is found that as N or T becomes larger, the RMSD of the DNA becomes also larger. Namely, as the intensity of the β-decays becomes larger or as the temperature is increased, the DNA structure becomes more fragile.
Accepted :19 September 2019