A FREE-ENERGY ANALYSIS OF NUCLEIC-ACID BASE STACKING IN AQUEOUS-SOLUTION

被引:211
作者
FRIEDMAN, RA [1 ]
HONIG, B [1 ]
机构
[1] COLUMBIA UNIV, DEPT BIOCHEM & MOLEC BIOPHYS, NEW YORK, NY 10032 USA
关键词
D O I
10.1016/S0006-3495(95)80023-8
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
This paper reports a theoretical study of the free energy contributions to nucleic acid base stacking in aqueous solution. Electrostatic interactions are treated by using the finite difference Poisson-Boltzmann method and nonpolar effects are treated with explicit calculation of van der Waals interactions and/or free energy-surface area relationships. Although for some pairs of bases there is a favorable Coulombic interaction in the stacked conformation, generally the net effect of electrostatic interactions is to oppose stacking. This result is caused by the loss of favorable base-solvent electrostatic interactions, that accompany the partial removal of polar atoms from water in the stacked conformation. Nonpolar interactions, involving the hydrophobic effect and enhancement of van der Waals interactions caused by close-packing, drive stacking. The calculations qualitatively reproduce the experimental dependence of stacking free energy on purine-pyrimidine composition.
引用
收藏
页码:1528 / 1535
页数:8
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