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错配核苷酸对诱变环状 1,N-丙炔基鸟嘌呤的掺入:计算研究。

On the misincorporation of nucleotides opposite mutagenic cyclic 1,N-propanoguanine: A computational investigation.

机构信息

Department of Chemistry and Biochemistry, National Chung-Cheng University, Chia-Yi, 621, Taiwan; Division of Chemistry, Department of Sciences and Humanities, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur, 522 213, Andhra Pradesh, India.

Department of Chemistry and Biochemistry, National Chung-Cheng University, Chia-Yi, 621, Taiwan.

出版信息

J Mol Graph Model. 2018 Oct;85:270-280. doi: 10.1016/j.jmgm.2018.08.016. Epub 2018 Sep 13.

DOI:10.1016/j.jmgm.2018.08.016
PMID:30253282
Abstract

The misincorporation properties of exocyclic DNA adduct, cyclic 1,N-propanoguanine with nucleobases have been investigated using DFT and DFT-D methods. Number of possible and stable mispairing conformations of cyclic 1,N-propanoguanine with A,T,G and C have been considered for our investigation. The single point energy calculations have been carried out at the M06/6-311++G**, ωB97XD/6-311++G** and MP2/6-311++G** levels on corresponding optimized geometries. The reaction enthalpy values were employed at the M06/6-31 + G* and ωB97XD/6-31 + G* levels. The energies have been compared among the cyclic 1,N-propanoguanine adduct with nucleobases to find the most stable conformer. The CPCM model was utilized on account of solvent phase and overall polarizability. The computed binding energies follow the order as CPr-Gua-G(2)(-23.2 kcal/mol) > CPr-Gua-C(1) (-16.1 kcal/mol) > CPr-Gua-A(2)(-10.6 kcal/mol) > CPr-Gua-T(2)(-9.6 kcal/mol) in the gas phase at M06 level, which indicates the guanine and cytosine are favorable for mispairing with the cyclic 1,N-propanoguanine adduct. The obtained results using computational tools are in good agreement with the experimental observation.

摘要

我们使用 DFT 和 DFT-D 方法研究了环外 DNA 加合物,即环 1,N-丙基鸟嘌呤与碱基的错配性质。我们考虑了环 1,N-丙基鸟嘌呤与 A、T、G 和 C 形成可能的和稳定的错配构象。单点能计算是在相应优化几何形状的 M06/6-311++G**、ωB97XD/6-311++G和 MP2/6-311++G水平上进行的。反应焓值是在 M06/6-31+G和 ωB97XD/6-31+G水平上使用的。我们比较了环 1,N-丙基鸟嘌呤加合物与碱基的能量,以找到最稳定的构象。CPCM 模型被用于考虑溶剂相和整体极化率。计算的结合能顺序为 CPr-Gua-G(2)(-23.2 kcal/mol) > CPr-Gua-C(1)(-16.1 kcal/mol) > CPr-Gua-A(2)(-10.6 kcal/mol) > CPr-Gua-T(2)(-9.6 kcal/mol),这表明在 M06 水平的气相中,鸟嘌呤和胞嘧啶有利于与环 1,N-丙基鸟嘌呤加合物错配。使用计算工具获得的结果与实验观察结果非常吻合。

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