Acta Chimica Sinica ›› 2010, Vol. 68 ›› Issue (08): 739-746. Previous Articles     Next Articles

Full Papers

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

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