A FREE-ENERGY ANALYSIS OF NUCLEIC-ACID BASE STACKING IN AQUEOUS-SOLUTION
A FREE-ENERGY ANALYSIS OF NUCLEIC-ACID BASE STACKING IN AQUEOUS-SOLUTION
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DOI：
10.1016/s0006-3495(95)80023-8
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发表时间：
1995-10-01
影响因子：
3.4
通讯作者：
HONIG, B
中科院分区：
文献类型：
--
作者：
FRIEDMAN, RA;HONIG, B
本文从理论上研究了水溶液中核酸碱基堆积的自由能贡献。静电相互作用的处理，使用有限差分泊松-玻尔兹曼方法和非极性效应处理明确计算的货车德瓦尔斯相互作用和/或自由能表面积的关系。虽然对于一些碱基对，在堆叠构象中存在有利的库仑相互作用，但通常静电相互作用的净效应是反对堆叠。这一结果是由有利的碱-溶剂静电相互作用的损失引起的，所述静电相互作用伴随着在堆叠构象中极性原子从水中的部分去除。非极性相互作用，包括疏水效应和由紧密堆积引起的货车范德华相互作用的增强，驱动堆积。计算定性地再现了实验上的嘌呤-嘧啶组合物的堆积自由能的依赖性。
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.