Yeh In-Chul, Hummer Gerhard
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Biophys J. 2004 Feb;86(2):681-9. doi: 10.1016/S0006-3495(04)74147-8.
Hydrodynamic properties of small single-stranded RNA homopolymers with three and six nucleotides in free solution are determined from molecular dynamics simulations in explicit solvent. We find that the electrophoretic mobility increases with increasing RNA length, consistent with experiment. Diffusion coefficients of RNA, corrected for finite-size effects and solvent viscosity, agree well with those estimated from experiments and hydrodynamic calculations. The diffusion coefficients and electrophoretic mobilities satisfy a Nernst-Einstein relation in which the effective charge of RNA is reduced by the charge of transiently bound counterions. Fluctuations in the counterion atmosphere are shown to enhance the diffusive spread of RNA molecules drifting along the direction of the external electric field. As a consequence, apparent diffusion coefficients measured by capillary zone electrophoresis can be significantly larger than the actual values at certain experimental conditions.
通过在显式溶剂中的分子动力学模拟，确定了在自由溶液中具有三个和六个核苷酸的小单链RNA同聚物的流体动力学性质。我们发现，电泳迁移率随RNA长度的增加而增加，这与实验结果一致。经有限尺寸效应和溶剂粘度校正后的RNA扩散系数，与根据实验和流体动力学计算估计的值吻合良好。扩散系数和电泳迁移率满足能斯特 - 爱因斯坦关系，其中RNA的有效电荷因瞬时结合抗衡离子的电荷而降低。结果表明，抗衡离子气氛中的涨落增强了沿外部电场方向漂移的RNA分子的扩散传播。因此，在某些实验条件下，毛细管区带电泳测量的表观扩散系数可能明显大于实际值。
