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化学学报
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化学学报 ›› 2011, Vol. 69 ›› Issue (23): 2787-2795.DOI: 10.6023/A1106172 上一篇    下一篇

研究论文

O6-鸟嘌呤和O4-胸腺嘧啶甲基化与DNA碱基异常氢键作用的理论研究

林雪飞,孙成科,杨思娅*, 余仕问, 姚立峰, 陈益山   

  1. (曲靖师范学院化学化工学院 曲靖 655000)
  • 投稿日期:2011-06-17 修回日期:2011-10-20 发布日期:2011-11-01
  • 通讯作者: 杨思娅 E-mail:yangsiyall@163.com
  • 基金资助:

    国家自然科学基金资助项目

Theoretical Studies of the Abnormal Hydrogen-bond Interactions between O6-Methylguanine and O4-Methylthymine and DNA Bases

LIN Xue-Fei, SUN Cheng-Ke, YANG Si-Ya, YU Shi-Wen, YAO Li-Feng, CHEN Yi-Shan   

  1. (School of Chemistry & Chemical Engineering, Qujing Normal University, Yunnan 655000)
  • Received:2011-06-17 Revised:2011-10-20 Published:2011-11-01

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用密度泛函B3LYP方法在6-311＋G**基组水平上对顺(cis-)、反式(anti-)O6-甲基鸟嘌呤(O6-MeG)和O4-甲基胸腺嘧啶(O4-MeT)与DNA碱基(腺嘌呤A、鸟嘌呤G)的非Watson-Crick氢键二聚体进行了优化. 在MP2/cc-pVXZ (X＝D,T)//B3LYP/6-311＋G**水平上, 采用完全基组外推方法校正了氢键二聚体的相互作用能, 并用完全均衡校正法(CP)校正了基组重叠误差(BSSE). 此外, 在B3LYP/6-311＋G**水平上计算了各氢键碱基对的全电子波函数, 并用分子中的原子理论(AIM)和电子密度拓扑方法分析了碱基间的弱相互作用. 计算结果显示, 甲基化使碱基对间的氢键作用模式发生了明显的扭转和不同程度的位移, 碱基间的电子密度分布和氢键作用能明显减小, 甲基化对O6-MeG和O4-MeT与DNA碱基间的氢键作用是去稳定化的, 这种影响主要来自于大体积的甲基的空间效应和给电子效应, 且对顺式的影响明显大于反式. 计算结果与文献给出的实验结论基本一致.

关键词: 甲基化, DNA碱基, 氢键, AIM, 拓扑分析

The geometries of abnormal Watson-Crick hydrogen-bond dimers between cis/trans- O6-methylguanine and cis/trans-O4-methylthymine and DNA bases (adenine, thymine, cytosine and guanine) have been optimized at the B3LYP/6-311＋G** level. The complete basis-set extrapolation method was employed at the MP2/cc-pVXZ (X＝D, T)//B3LYP/6-311＋G** levels in order to obtain more accurate interaction energies. Counterpoise correction (CP) scheme was also used to take into account of basis set superposition error (BSSE). The all-electron wave functions of these dimers were calculated at the B3LYP/ 6-311＋G** level, and the weak interactions were analyzed by atoms in molecules (AIM) theory. The calculation results show that the methylation of O6-guanine and O4-thymine can lead to changes of hydrogen-bond interactions between DNA base-pairs, which results in propeller torsions and various displacements between base pairs. The obvious decreases in interaction energies and electron densities between base-pairs is attributed to the methylation on O6-guanine and O4-thymine. Furthermore, the methylation of O6-guanine and O4-thymine destabilize the hydrogen-bond interactions of DNA base-pairs, and compared with anti conformations, the destabilization effect of the methylation on cis DNA base-pairs is more evident. Our calculation results are basically in agreement with the experiments.

Key words: methylation, DNA base, hydrogen-bond, AIM, topology analysis