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化学学报
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化学学报 ›› 2010, Vol. 68 ›› Issue (08): 739-746. 上一篇    下一篇

研究论文

DNA甲基化-非甲基化碱基间堆积作用的理论研究

陈益山，余仕问，杨思娅   

  1. (曲靖师范学院化学与化工学院 曲靖 655000)
  • 投稿日期:2009-08-24 修回日期:2009-11-27 发布日期:2009-12-23
  • 通讯作者: 陈益山 E-mail:chenyishan916@163.com
  • 基金资助:

    国家自然科学基金资助(批准号：No. 20763007)项目；云南省教育厅重点资助(批准号：No.07z11574)项目

Theoretical Studies on the Stacking Interactions between Methylated and Unmethylated DNA Bases

CHEN Yi-Shan, TU Shi-Wen, YANG Sai-Ya   

  1. (School of Chemistry & Chemical Engineering, Qujing Normal University, Yunnan 655000)
  • Received:2009-08-24 Revised:2009-11-27 Published:2009-12-23

PDF

1336

被引次数

9 | 2

运用二级M?ller-Plesset(MP2)理论方法和cc-pVDZ基组优化了6-甲基鸟嘌呤(O6-MethylG), 4-甲基胸腺嘧啶(O4-MethylT)以及5-甲基胞嘧啶(C5-MethylC)与DNA碱基鸟嘌呤(G), 腺嘌呤(A), 胞嘧啶(C), 胸腺嘧啶(T)之间的堆积构型. 在MP2/aug-cc-pVXZ//MP2/cc-pVDZ (X＝D, T)水平上, 采用完全基组外推方法校正了堆积碱基对间的相互作用能, 并用完全均衡校正法(CP)校正了基组重叠误差(BSSE). MP2计算结果表明, DNA碱基甲基化使得嘧啶-嘧啶、嘧啶-嘌呤堆积碱基间的平行旋转角发生明显改变, 并使堆积碱基间的相互作用能增大. 在MP2/cc-pVDZ计算级别上得到了各堆积碱基对的全电子波函数, 并用分子中的原子理论(AIM)分析了堆积碱基对间的弱相互作用. AIM分析结果显示, 甲基化增强了堆积碱基间的(-(作用, 且甲基氢与相邻碱基间形成H2CH…X (X＝O, N, CH3, NH2)等类型的氢键. 甲基化损伤使碱基间重叠程度增大、(-(作用增强以及堆积碱基间形成多个氢键, 是堆积作用能增加的主要原因.

关键词: DNA, 甲基化, 碱基对, 堆积, 相互作用能

The stacking geometries of normal DNA bases (adenine, thymine, guanine and cytosine) and methylated bases (O6-methylguanine, O4-methylthymine and C5-methylcytosine) have been optimized at the MP2/cc-pVDZ level. Counterpoise correction (CP) scheme of Boys-Bernardi has been used to take into account of basis set superposition error (BSSE), and aug-cc-pVXZ (X＝D, T) basis sets were used to extrapolate the complete basis set limit in order to obtain more accurate binding energies. Moreover, the interactions between stacking base-pairs were also analyzed by atoms in molecules (AIM) method. Our calculation results show that the methylation of DNA bases can lead to obvious changes of parallel twist angles between the stacking pyridine-pyridine and pyridine-purine base-pairs, and the increases of interaction energies between the stacking base-pairs can also be attributed to the methylation of DNA bases. Furthermore, AIM analysis reveals that the methylation of bases can enhance the (-( interactions between the stacking base-pairs, and the formation of a variety of hydrogen-bonds, H2CH…X (X＝O, N, (, CH3, NH2), was also confirmed by AIM analysis.

Key words: DNA, methylation, base-pairs, stacking, interaction energies