Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA.
Phys Rev E. 2017 Feb;95(2-1):022501. doi: 10.1103/PhysRevE.95.022501. Epub 2017 Feb 15.
Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well-defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths.
许多实验都利用 DNA 作为模型系统来检验针对受限聚合物的理论。在分析这些数据时，一个默认的假设是存在一个明确的耗尽长度，用于描述 DNA-壁相互作用，使得实验系统（带电荷壁的通道中的聚电解质）可以映射到理论模型（带硬壁的中性聚合物）。我们使用修剪富集罗森布鲁斯方法（PERM）模拟了受限在管中的类似 DNA 的半柔性聚合物，来检验这个假设。聚合物-壁相互作用通过在硬壁相互作用上增加一个指数衰减的排斥性软势来建模。在存在软壁势的情况下获得的自由能、平均跨度和平均跨度的方差与不存在软壁势的等效模拟进行了比较，以确定耗尽长度。我们发现，对于我们测试的所有软势，平均跨度和平均跨度的方差都具有相同的耗尽长度。相比之下，对于自由能的耗尽长度，只有当耗尽长度不再取决于通道尺寸时，它才接近平均跨度的耗尽长度。这些结果对低离子强度下 DNA 限制实验的解释具有重要意义。
