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