Acta Phys. -Chim. Sin. ›› 2010, Vol. 26 ›› Issue (02): 478-486.doi: 10.3866/PKU.WHXB20100219

• BIOPHYSICAL CHEMISTRY • Previous Articles     Next Articles

Mobility of Na+ in a G-Quadruplex

GUO Ci, LIU Cui, YANG Zhong-Zhi   

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China
  • Received:2009-09-11 Revised:2009-11-20 Published:2010-01-26
  • Contact: YANG Zhong-Zhi E-mail:zzyang@lnnu.edu.cn

Abstract:

The Na+-G-quadruplex complex is a polarized system and the mobility of Na+ during its formation or decomposition is still unclear. The atombond electronegativity equalization method at the σπ level fused into molecular mechanics (ABEEMσπ/MM) model clearly defines the lone-pair electron, σ bond and π bond sites in addition to the atomic sites. The partial charge fluctuation is calculated in accordance with a change in the molecular environment and so this method should account well for the polarization effect. In this paper, we discuss some properties for the Na+-G-tetrad complex including its geometry, charge distribution, and binding energy according to the ABEEMσπ/MM method. We also investigate these properties for the Na+-G-tetrad complex using the ab initio method at the MP2/6-31G(d,p) level. The ABEEMσπ/MM results are in good agreement with the ab initio results. The presence of Na+ changes the hydrogen bonds in the G-tetrad. By comparing the binding energy of the systemfor every Na+ mobile path, we predict that the most probable path is that three Na+ ions move away individually from the G-quadruplex along the α orientation. This study lays a solid foundation for the dynamic simulation of ion exchange channels in a G-quadruplex using the ABEEMσπ/MM model.

Key words: G-quadruplex, Na+-G-tetrad, ABEEMσπ/MM method, Ab initio, Mobile path

MSC2000: 

  • O641