Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996-2200, USA.
J Phys Chem B. 2010 Feb 11;114(5):2015-22. doi: 10.1021/jp909564d.
We have carried out Brownian Dynamics calculations to investigate the mechanism of current blockade by double-stranded DNA (dsDNA) in a nanopore. We find that the blockade current crosses over from negative to positive as the ionic concentration decreases, similar to experiment. In addition to the volume exclusion and the counterion condensation, we find that the electric double layer overlap is a significant factor in the current blockade. The electric double layer overlap causes the ionic concentration beyond the immediate neighborhood of dsDNA and the wall to be lower in a dsDNA-blocked nanopore than the plateau ionic concentration away from the wall in an open nanopore, thus contributing importantly to the blockade current. On the basis of the calculated ion distribution function in the nanopore, we examined the counterion condensation to the dsDNA. We find the excess counterion condensation to be about 60% of the charge on the dsDNA, which is within the range of percentages obtained from experiments. We performed equilibrium and nonequilibrium (under an applied electric field) Brownian dynamics simulations to calculate the average mobility of the ions in nanopores. The calculated ion mobility is found to be reduced in DNA-blocked nanopores.
我们进行了布朗动力学计算，以研究双链 DNA（dsDNA）在纳米孔中电流阻断的机制。我们发现，随着离子浓度的降低，阻断电流从负变为正，这与实验结果相似。除了体积排除和抗衡离子凝聚之外，我们还发现双电层重叠是电流阻断的一个重要因素。双电层重叠导致 dsDNA 阻断的纳米孔中远离壁的 dsDNA 及其附近的离子浓度低于开放纳米孔中远离壁的平台离子浓度，从而对阻断电流有重要贡献。基于在纳米孔中计算出的离子分布函数，我们研究了抗衡离子对 dsDNA 的凝聚。我们发现过量的抗衡离子凝聚约占 dsDNA 电荷的 60%，这在实验得到的百分比范围内。我们进行了平衡和非平衡（在施加电场下）布朗动力学模拟，以计算离子在纳米孔中的平均迁移率。发现 DNA 阻断的纳米孔中的离子迁移率降低。
