Changes in molecular conformation and electronic structure of DNA under C ions based on first-principles calculations

Sekikawa, Takuya; Matsuya, Yusuke; Hwang, B.*; Ishizaka, Masato*; Kawai, Hiroyuki*; Ono, Yoshiaki*; Sato, Tatsuhiko; Kai, Takeshi

Nuclear Instruments and Methods in Physics Research B, 548, p.165231_1 - 165231_6, 2024/03

https://doi.org/10.1016/j.nimb.2023.165231

One of the main causes of radiation effects on the human body is thought to be damage to DNA, which carries genetic information. However, it is not fully understood what kind of molecular structural changes DNA undergoes upon radiation damage. Since it has been reported that various types of DNA damage are formed when DNA is irradiated, our group has investigated the relationship between DNA damage and various patterns of radiation-induced ionization induced by radiation. Although we have so far analyzed DNA damage in a simple system using a rigid body model of DNA, more detailed calculations are required to analyze the molecular structural changes in DNA, which are considered to be important in considering the effects on the human body. In this study, we attempted to clarify the molecular conformational changes of DNA using OpenMX, a first-principles calculation software that can discuss electronic states based on molecular structures. Specifically, we calculated the most stable structure, band dispersion, and wave function of DNA under the assumption that one and two electrons are ionized by various radiation. In the presentation, we will discuss the relationship between the energy dependence of each incident radiation type and the molecular conformational change of DNA. In addition, the radiation-induced changes in the basic physical properties of DNA (corresponding to the initial stage of DNA damage) will be discussed from the viewpoints of both radiation physics and solid state physics.

Programmable synthesis of silver wheels

Kwon, H.*; Pietrasiak, E.*; Ohara, Takashi; Nakao, Akiko*; Chae, B.*; Hwang, C.-C.*; Jung, D.*; Hwang, I.-C.*; Ko, Y. H.*; Kim, K.*; et al.

Inorganic Chemistry, 60(9), p.6403 - 6409, 2021/05

https://doi.org/10.1021/acs.inorgchem.1c00106

Studies of high density baryon matter with high intensity heavy-ion beams at J-PARC

Sako, Hiroyuki; Harada, Hiroyuki; Sakaguchi, Takao*; Chujo, Tatsuya*; Esumi, Shinichi*; Gunji, Taku*; Hasegawa, Shoichi; Hwang, S.; Ichikawa, Yudai; Imai, Kenichi; et al.

Nuclear Physics A, 956, p.850 - 853, 2016/12

https://doi.org/10.1016/j.nuclphysa.2016.03.030

Development of a GEM-TPC for H-dibaryon search experiment at J-PARC

Sako, Hiroyuki; Ahn, J. K.*; Baek, K. H.*; Bassalleck, B.*; Fujioka, H.*; Guo, L.*; Hasegawa, Shoichi; Hicks, K.*; Honda, R.*; Hwang, S. H.*; et al.

Journal of Instrumentation (Internet), 9(4), p.C04009_1 - C04009_10, 2014/04

https://doi.org/10.1088/1748-0221/9/04/C04009

A TPC has been developed for J-PARC E42 experiment to search for H-dibaryon in (, ) reaction. An event with 2 and 2 protons decaying from H-dibaryon is searched for inside the TPC. The TPC has octagonal prism shape drift volume with about 50 cm diameter with 55 cm drift length filled with Ar-CH (90:10) gas. At the end of the drift volume, 3-layer GEMs are equipped. In order to analyze momenta of produced particles, the TPC is applied with 1 T dipole magnetic field parallel to the drift electric field with a superconducting Helmholz magnet. In order to maximize the acceptance of H-dibaryon events, a diamond target is installed inside the TPC drift volume, in a cylindrical hole opened from the top to the middle of the drift volume. Since extremely high-rate beam is directly injected into the TPC drift volume to the target, a gating grid and GEMs are adopted to suppress positive-ion feedback.

First-principles calculations of molecular structure and electronic state changes in DNA induced by radiation-induced holes

Sekikawa, Takuya; Hwang, B.*; Ishizaka, Masato*; Matsuya, Yusuke*; Kawai, Hiroyuki*; Ono, Yoshiaki*; Sato, Tatsuhiko; Kai, Takeshi

no journal, , 

Deoxyribonucleic acid (DNA) carries the genetic information of living organisms through various combinations of guanine, cytosine, adenine, and thymine, and radiation biological effects are mainly caused by damage to DNA. In this study, in order to theoretically investigate the transient molecular conformational changes that occur before DNA damage takes hold, we analyzed the behavior of the sites responsible for the conformational changes and chemical reactions by targeting the DNA that produced the holes using the first-principles calculation software OpenMX. As a result, it was confirmed that the holes reproduce the event of trapping in the guanine molecule of DNA, which reproduces the experimental results, and it was also newly found that the DNA sugar chain shows intense molecular fluctuation. The results of this study are expected to contribute to the elucidation of the first-phase process of radiation biological effects.

Computer simulation of the first stage of radiation biological effects; Effects of radiation damage on the electronic state of DNA

Sekikawa, Takuya; Matsuya, Yusuke; Hwang, B.*; Ishizaka, Masato*; Kawai, Hiroyuki*; Ono, Yoshiaki*; Sato, Tatsuhiko; Kai, Takeshi

no journal, , 

Deoxyribonucleic acid (DNA) carries the genetic information of living organisms through various combinations of guanine, cytosine, adenine, and thymine, and biological effects of radiation are mainly caused by damage to this DNA. In this study, in order to theoretically investigate the transient changes in molecular structure until DNA damage is established, the number of holes produced by radiation-induced carbon beams was calculated using the Particle and Heavy Ion Transport code System (PHITS), and the number of holes produced by the first The first principle calculation software OpenMX was used to calculate the sites responsible for conformational changes and chemical reactions by targeting the DNA that produced the holes. As a result, the experimental result that a small number of holes are trapped in the guanine molecule of DNA is reproduced, while a large number of holes are trapped in the hybrid orbital of the sugar chain and guanine molecule of DNA. The results of this study are expected to contribute to the elucidation of the initial processes of radiation biological effects.