Acta Phys. -Chim. Sin. ›› 2015, Vol. 31 ›› Issue (7): 1309-1314.doi: 10.3866/PKU.WHXB201505111


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
  • 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).


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