Dwyer J D, Bloomfield V A
Department of Chemistry, College of St. Catherine, St. Paul, MN 55105, USA.
Biophys Chem. 1995 Dec;57(1):55-64. doi: 10.1016/0301-4622(95)00045-y.
We have used Brownian dynamics simulation to study probe diffusion in solutions of short chain DNA using our previously developed simulation algorithm. We have examined the effect of probe size, charge, and DNA concentration on the probe diffusion coefficient, with the aim of gaining insight into the diffusion of proteins in a concentrated DNA environment. In these simulations, DNA was modeled as a worm-like chain of hydrodynamically equivalent spherical frictional elements while probe particles were modeled as spheres of given charge and hydrodynamic radius. The simulations allowed for both short range Lennard-Jones interactions and long ranged electrostatic interactions between charged particles. For uncharged systems, we find that the effects of probe size and DNA concentration on the probe diffusion coefficient are consistent with excluded volume models and we interpret our results in terms of both empirical scaling laws and the predictions of scaled particle theory. For charged systems, we observe that the effects of probe size and charge are most pronounced for the smallest probes and interpret the results in terms of the probe charge density. For an ionic strength of 0.1 M we find that, below a critical probe surface charge density, the probe diffusion coefficient is largely independent of probe charge and only weakly dependent on the DNA charge. These effects are discussed in terms of the interactions between the probe and the DNA matrix and are interpreted in terms of both the underlying physics of transport in concentrated solutions and the assumptions of the simulation model.
我们使用布朗动力学模拟，利用我们之前开发的模拟算法来研究短链DNA溶液中的探针扩散。我们研究了探针大小、电荷和DNA浓度对探针扩散系数的影响，目的是深入了解蛋白质在浓缩DNA环境中的扩散情况。在这些模拟中，DNA被建模为具有流体动力学等效球形摩擦元件的蠕虫状链，而探针颗粒被建模为具有给定电荷和流体动力学半径的球体。模拟考虑了带电粒子之间的短程 Lennard-Jones 相互作用和长程静电相互作用。对于不带电的系统，我们发现探针大小和DNA浓度对探针扩散系数的影响与排阻体积模型一致，并且我们根据经验标度律和标度粒子理论的预测来解释我们的结果。对于带电系统，我们观察到探针大小和电荷的影响对于最小的探针最为显著，并根据探针电荷密度来解释结果。对于0.1 M的离子强度，我们发现，在临界探针表面电荷密度以下，探针扩散系数在很大程度上与探针电荷无关，仅微弱地依赖于DNA电荷。我们根据探针与DNA基质之间的相互作用来讨论这些影响，并根据浓缩溶液中传输的基础物理原理和模拟模型的假设来解释这些影响。
