Mills P A, Rashid A, James T L
Department of Chemistry, Hunter College, New York, New York 10021.
Biopolymers. 1992 Nov;32(11):1491-501. doi: 10.1002/bip.360321108.
We calculated the uni-univalent ion distributions around the oligonucleotide d(AT)5.d(AT)5 in the A, B and wrinkled D conformation using the Metropolis Monte Carlo method. All atoms were included in the oligonucleotide model with partial charges and hard sphere radii assigned to each atom. The univalent counter- and coions were modeled as hard spheres with radius 0.3 nm. The solvent was assigned a dielectric constant of 80, corresponding to a temperature of 298K. The counterion distribution surrounding each of the conformers and the distribution surrounding an impenetrable cylinder, were calculated for four salt concentrations. We found significant counterion density in the major groove of the A DNA while fewer counterions occupied the grooves of B DNA. In the wrinkled D DNA, where groove occupancy is sterically hindered, the ion distributions were identical to the distributions surrounding the impenetrable, cylindrical model. This suggests that excluded volume effects significantly influence the details of the ion distributions near the oligomer, while the detailed charge distributions of the oligomer affects the ion distributions only minimally. Although substantial variation in counterion density was observed near the oligomers of differing conformations, the total number of counterions located within a cylinder surrounding the oligomer bounded radially by 2.4 nm was independent of the conformation of the oligomer. Therefore, for this model system, the local univalent counterion distributions are extremely sensitive to the geometry of the oligonucleotide whereas the extent of neutralization of the oligoanion is insensitive to the conformation of the oligomer.
我们使用 metropolis 蒙特卡罗方法计算了处于 A、B 和皱缩 D 构象的寡核苷酸 d(AT)5.d(AT)5 周围的单价离子分布。寡核苷酸模型中包含了所有原子，并为每个原子分配了部分电荷和硬球半径。单价抗衡离子和共离子被建模为半径为 0.3 nm 的硬球。溶剂的介电常数设定为 80，对应温度为 298K。针对四种盐浓度，计算了每种构象周围的抗衡离子分布以及围绕一个不可穿透圆柱体的分布。我们发现 A 型 DNA 的大沟中有显著的抗衡离子密度，而 B 型 DNA 的沟中占据的抗衡离子较少。在皱缩 D 型 DNA 中，由于沟的占据在空间上受到阻碍，其离子分布与围绕不可穿透圆柱体模型的分布相同。这表明排除体积效应显著影响寡聚物附近离子分布的细节，而寡聚物的详细电荷分布对离子分布的影响极小。尽管在不同构象的寡聚物附近观察到抗衡离子密度有很大变化，但在以 2.4 nm 为半径围绕寡聚物的圆柱体内的抗衡离子总数与寡聚物的构象无关。因此，对于这个模型系统，局部单价抗衡离子分布对寡核苷酸的几何形状极为敏感，而寡阴离子的中和程度对寡聚物的构象不敏感。
