Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996-2200, USA.
J Phys Chem B. 2011 Sep 15;115(36):10699-706. doi: 10.1021/jp111111u. Epub 2011 Aug 18.
We have carried out Brownian dynamics calculations to investigate the effect of DNA-ion interaction on ion transport in a nanopore. We calculated the self-diffusion coefficient of monovalent ions in the presence of DNA in a nanopore and compared the result with that through an open pore, that is, without the presence of DNA. We find that the self-diffusion coefficient of the co-ions is essentially unaffected by the DNA. The self-diffusion coefficient of the counterions, on the other hand, is significantly reduced depending on the ion concentration. At high ion concentration, around 1 M, the effect of DNA on counterion diffusion is relatively small, causing a slight reduction in counterion diffusion coefficient. At low concentrations of a few millimolar, the effect is much larger, resulting in a reduction in counterion diffusion coefficient by a factor of about 2.5. The variation in the self-diffusion of the counterion is well described by accounting for the contributions from two components: the adsorbed counterions and the free counterions. Detailed dynamics of the DNA-counterion interaction is characterized by the varying length of the transient adsorption time of the counterions to the DNA charge sites and the exchange rate with the environment. This variation in counterion adsorption time is attributed to the ionic electric screening effect, which is in turn determined by the ion concentration.
我们进行了布朗动力学计算，以研究 DNA-离子相互作用对纳米孔中离子传输的影响。我们计算了纳米孔中存在 DNA 时单价离子的自扩散系数，并将结果与没有 DNA 时通过开放孔（即无 DNA 存在时）的结果进行了比较。我们发现，同离子的自扩散系数基本不受 DNA 的影响。另一方面，由于离子浓度的不同，反离子的自扩散系数显著降低。在高离子浓度（约 1 M）下，DNA 对反离子扩散的影响相对较小，导致反离子扩散系数略有降低。在几毫摩尔的低浓度下，影响要大得多，导致反离子扩散系数降低约 2.5 倍。通过考虑两个组成部分的贡献，可以很好地描述反离子的自扩散变化：吸附的反离子和游离的反离子。通过 DNA-反离子相互作用的详细动力学，反离子的瞬态吸附时间和与环境的交换率发生变化。这种反离子吸附时间的变化归因于离子的电屏蔽效应，而电屏蔽效应反过来又由离子浓度决定。
