| Bao Shanshan,Hu Guang,Hu Huasi.A simulation study on the yields of proton irradiation-induced groove damage in B-DNA[J].Chinese Journal of Radiological Medicine and Protection,2026,46(8):740-748 |
| A simulation study on the yields of proton irradiation-induced groove damage in B-DNA |
| Received:March 17, 2026 |
| DOI：10.3760/cma.j.cn112271-20260317-00103 |
| KeyWords:Proton|DNA major groove|DNA minor groove|Geant4-DNA|PDB4DNA |
| FundProject:国家自然科学基金(11975182) |
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| Abstract:: |
| Objective To conduct a nanoscale simulation study on the correlations of proton irradiation-induced damage to the major and minor grooves in B-DNA (also referred to as MBD and mBD, respectively) with DNA structural parameters, including the dinucleotide step, major and minor groove widths (denoted by MW and mW, respectively), and sugar-phosphate groups (also referred to as the S-P groups). Methods The spatial conformation of the crystal structure of a tetranucleosome (PDB ID: 1ZBB) was analyzed using bioinformatics tools, with partial B-DNA segments in the structure selected as target sequences. Proton irradiation-induced B-DNA damage was then simulated using the Geant4-DNA toolkit, and data on groove damage were acquired. Baseed on the atomic composition of major and minor grooves in Watson-Crick base pairs, the yields of MBD and mBD (denoted by YMBD and YmBD, respectively) were quantified, thus achieving the precise atomic-scale characterization of groove damage. Results After B-DNA was exposed to proton irradiation with a linear energy transfer (LET) of 55.04 keV/μm, both YMBDand YmBD in B-DNA increased as the number of dinucleotide steps increased, with the average YMBD (3.27 Gy-1·Gbp-1) higher than the average YmBD (1.65 Gy-1·Gbp-1). The correlations between groove damage and the S-P groups were investigated by exposing B-DNA to proton irradiation with LET ranging from 2.59 to 62.93 keV/μm. The result indicated that with increasing LET, the YMBD in B-DNA increased at a rate of 10.40%, the probability of MBD (PMBD) declined at a rate of 9.66%, and YmBD and the probability of mBD (PmBD) increased at rates of 48.76% and 23.64%, respectively. In addition, the energy deposition of the minor groove (EmBD) and YmBD were lower than the energy deposition of the major groove (EMBD) and YMBD, respectively. Conclusions There are positive correlations between the yields of groove damage in B-DNA and the number of dinucleotide steps, while there is a lack of significant correlations between them and the groove widths. The S-P groups play a significant role in protecting the minor groove against proton irradiation; however, such protection weakens with increasing the LET of proton irradiation. |
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