We calculated solvent accessibility of DNA backbone hydrogen sites, H1’-H5’ by using molecular dynamics simulation of DNA. The result of accessibility is well correlated with the site-dependent reactivity with OH radicals experimentally reported, indicating that the different DNA-radical reactivity is mainly caused by the difference in the solvent accessibility of each hydrogen site. Compared with the previous calculation with solvent-accessible surface area, the present MD-based counting of molecular access provided a slightly improved result, which suggests importance of more realistic molecular components such as electrostatic interactions and DNA conformational fluctuation.

我们通过使用分子的DNA分子动力学模拟来计算DNA骨架氢位点H1'-H5'的溶剂可及性。可达性的结果与实验报道的与OH自由基的位点依赖性反应性密切相关，这表明不同的DNA自由基反应性主要是由于每个氢位点的溶剂可达性不同所致。与先前使用溶剂可及表面积的计算相比，当前基于MD的分子可及性计数提供了稍微改善的结果，这表明更现实的分子成分（如静电相互作用和DNA构象波动）的重要性。