Laskar Baharul Islam, Shukla Pradeep Kumar
Department of Physics, Assam University, 788 011, Silchar, Assam, India.
J Mol Model. 2025 Jun 23;31(7):196. doi: 10.1007/s00894-025-06419-3.
Graphene is considered to be a wonder material with widespread applications. However, its potential for recovering methylated DNA bases has not yet been explored. DNA methylation is implicated in the development of several health issues such as mutation, ageing, cancer and neurodegenerative diseases. The cytotoxic N7-methylated guanine (N7mG) is the most abundantly occurring methylated DNA lesion. Therefore, we have theoretically investigated the reactions of pristine, heteroatom-doped and functionalized graphene with N7mG cation with an intention to understand the efficacy of graphene in repairing this lesion. The epoxide- and thioepoxide-functionalized graphene can effectively restore guanine from the N7mG cation in both gas and aqueous phases. Pristine and BN-codoped graphene are, however, found to be unsuitable for this work. Thus, the present study offers valuable insights into how graphene may help in repairing N7mG and other modified DNA bases.
The calculations related to energetics, structural optimizations, natural bond orbitals (NBOs) and DOS were performed using two functionals (M06-2X and wB97X-D) of density functional theory (DFT) in association with 6-31G* and 6-31+G** basis sets, as available in the Gaussian 09 quantum chemistry code. The IEF-PCM was used for the aqueous phase calculations. The CHelpG charges were used for charge transfer analysis.
石墨烯被认为是一种具有广泛应用的神奇材料。然而，其在修复甲基化DNA碱基方面的潜力尚未得到探索。DNA甲基化与多种健康问题的发展有关，如突变、衰老、癌症和神经退行性疾病。细胞毒性的N7-甲基鸟嘌呤（N7mG）是最常见的甲基化DNA损伤。因此，我们从理论上研究了原始的、杂原子掺杂的和功能化的石墨烯与N7mG阳离子的反应，旨在了解石墨烯修复这种损伤的效果。环氧基和硫代环氧基功能化的石墨烯在气相和水相中都能有效地从N7mG阳离子中还原鸟嘌呤。然而，发现原始的和BN共掺杂的石墨烯不适合这项工作。因此，本研究为石墨烯如何帮助修复N7mG和其他修饰的DNA碱基提供了有价值的见解。
使用密度泛函理论（DFT）的两种泛函（M06-2X和wB97X-D）结合高斯09量子化学代码中可用的6-31G*和6-31+G**基组，进行了与能量学、结构优化、自然键轨道（NBO）和态密度（DOS）相关的计算。IEF-PCM用于水相计算。CHelpG电荷用于电荷转移分析。
