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Citation: GUO Ci, LIU Cui, YANG Zhong-Zhi. Mobility of Na⁺ in a G-Quadruplex[J]. Acta Physico-Chimica Sinica, ;2010, 26(02): 478-486. doi: 10.3866/PKU.WHXB20100219 shu

Mobility of Na⁺ in a G-Quadruplex

1.
School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China

Received Date: 11 September 2009
Available Online: 28 December 2009

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 od 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.
- G-quadruplex,
- Na+-G-tetrad,
- ABEEMσπ/MM method,
- Ab initio,
- Mobile path
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沈阳化工大学材料科学与工程学院沈阳 110142

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Mobility of Na⁺ in a G-Quadruplex