物理化学学报 >> 2015, Vol. 31 >> Issue (7): 1309-1314.doi: 10.3866/PKU.WHXB201505111

理论与计算化学 上一篇    下一篇

非共价作用对气相中B-DNA双螺旋结构稳定性的贡献:基于GEBF方法的密度泛函理论计算

花书贵1, 金浩1, 欧阳永中2   

  1. 1 江苏第二师范学院生命科学与化学化工学院, 江苏省生物功能分子重点建设实验室, 南京210013;
    2 东华理工大学软件学院, 南昌市气相分子科学重点实验室, 南昌330013
  • 收稿日期:2015-03-16 修回日期:2015-05-11 发布日期:2015-07-08
  • 通讯作者: 花书贵 E-mail:shugui.hua@gmail.com
  • 基金资助:

    江苏省自然科学基金(BK20130748), 江苏省高校自然科学研究项目(13KJB150012), 江西省自然科学基金(20142BAB213010)和国家自然科学基金(21405013)资助项目

Contribution of Non-Covalent Interactions to the Gas-Phase Stability of the Double-Helix of B-DNA: A Density Functional Theory Study with GEBF Approach

HUA Shu-Gui1, JIN Hao1, OUYANG Yong-Zhong2   

  1. 1 College of Life Science and Chemistry, Jiangsu Key Laboratory of Biological Functional Molecules, Jiangsu Second Normal University, Nanjing 210013, P. R. China;
    2 Software College, Nanchang Key Laboratory for Gas Phase Molecular Science, East China Institute of Technology, Nanchang 330013, P. R. China
  • Received:2015-03-16 Revised:2015-05-11 Published:2015-07-08
  • Contact: HUA Shu-Gu E-mail:shugui.hua@gmail.com
  • Supported by:

    The project was supported by the Natural Science Foundation in Jiangsu Province of China (BK20130748), Natural Science Fund for Colleges and Universities in Jiangsu Province of China (13KJB150012), Jiangxi Provincial Natural Science Foundation of China (20142BAB213010), and National Natural Science Foundation of China (21405013).

摘要:

采用密度泛函理论, 将基于能量的分子片方法(GEBF)应用于气相中优化B型脱氧核糖核酸(碱基对数目N=2, 5, 10)双螺旋构型的结构. 通过比较M06-2X泛函和其他方法(B3LYP、B3LYP-vdW和TPSS泛函)的结果, 发现不考虑碱基之间的π-π堆积作用将会导致碱基之间的纵向距离拉长. 随着体系双螺旋链长的增加, 没有考虑碱基堆积作用而导致的相邻碱基纵向距离拉长的程度快速衰减. 计算表明, 气相中B-DNA双螺旋结构的稳定性来源于其作用力(主要是氢键和π-π堆积作用)的协同性, 对不多于10组碱基对的体系而言, 其氢键的贡献明显大于碱基堆积作用.

关键词: 碱基对, 氢键, 基于能量的分子片方法, π-π堆积作用

Abstract:

We employed the generalized energy-based fragmentation (GEBF) approach to investigate the gas-phase structures of B-DNA double-helices up to 10 base pairs at several theoretical levels. By comparing the results obtained using the M06-2X functional and other methods (including the B3LYP, B3LYP-vdW, and TPSS functionals), we found that the absence of stacking interactions could lead to the enlargement of the vertical distance between adjacent bases. The magnitude of this enlargement of the vertical distance quickly decreases as the length of the double-helix increases. The gas-phase stabilization of the double-helical structure of B-DNA is a cooperative effect, in which hydrogen bonding plays a more important role than stacking interaction does up to 10 base pairs.

Key words: Base pair, Hydrogen bond, Generalized energy-based fragmentation approach, π-π stacking interaction

MSC2000: 

  • O641