Changes in molecular conformation and electronic structure of DNA under 12C ions based on first-principles calculations

Abstract

Fundamental studies on the interaction between ionizing radiation and deoxyribonucleic acid (DNA) can contribute to understanding the biological effects of radiation protection and radiotherapy. The transitional process from ionized and excited DNA to DNA lesions, such as strand breaks and base lesions, remains uncertain. In this study, we focused in particular on the direct effects of radiation on DNA and calculated the number of ionizations induced within 10 base pairs of DNA using the Particle and Heavy Ion Transport code System, a general-purpose Monte Carlo code for radiation transport. The electronic structure of the ionized DNA is subsequently calculated using the first-principles calculation software OpenMX. Through these calculations, we successfully identified the redox site of DNA and quantitatively evaluated the amount of molecular bond cleavage. The scientific findings of this study will elucidate the cleavage mechanism of DNA in the high-density radiation field realized by ion beam irradiation by determining the redox sites.