Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
J Phys Chem B. 2012 Nov 1;116(43):12946-54. doi: 10.1021/jp306598y. Epub 2012 Oct 19.
The concept of "ion atmosphere" is prevalent in both theoretical and experimental studies of nucleic acid systems, yet the spatial arrangement and the composition of ions in the ion atmosphere remain elusive, in particular when several ionic species (e.g., Na(+), K(+), and Mg(2+)) compete to neutralize the charge of a nucleic acid polyanion. Complementing the experimental study of Bai and co-workers (J. Am. Chem. Soc.2007, 129, 14981), here we characterize ion atmosphere around double-stranded DNA through all-atom molecular dynamics simulations. We demonstrate that our improved parametrization of the all-atom model can quantitatively reproduce the experimental ion-count data. Our simulations determine the size of the ion atmosphere, the concentration profiles of ionic species competing to neutralize the DNA charge, and the sites of the cations' preferential binding at the surface of double-stranded DNA. We find that the effective size of the ion atmosphere depends on both the bulk concentration and valence of ions: increasing either reduces the size of the atmosphere. Near DNA, the concentration of Mg(2+) is strongly enhanced compared to monovalent cations. Within the DNA grooves, the relative concentrations of cations depend on their bulk values. Nevertheless, the total charge of competing cations buried in the DNA grooves is constant and compensates for about ~30% of the total DNA charge.
“离子气氛”的概念在核酸体系的理论和实验研究中都很常见，但离子气氛中离子的空间排列和组成仍然难以捉摸，特别是当几种离子物种（例如 Na(+)、K(+) 和 Mg(2+)）竞争中和核酸多阴离子的电荷时。补充 Bai 及其同事的实验研究（J. Am. Chem. Soc.2007, 129, 14981），我们在这里通过全原子分子动力学模拟来描述双链 DNA 周围的离子气氛。我们证明，我们对全原子模型的改进参数化可以定量再现实验的离子计数数据。我们的模拟确定了离子气氛的大小、竞争中和 DNA 电荷的离子物种的浓度分布，以及阳离子在双链 DNA 表面优先结合的位置。我们发现，离子气氛的有效大小取决于离子的体相浓度和价态：增加任何一个都会减小气氛的大小。在 DNA 附近，与单价阳离子相比，Mg(2+)的浓度大大增强。在 DNA 沟槽内，阳离子的相对浓度取决于它们的体相值。然而，埋藏在 DNA 沟槽内的竞争阳离子的总电荷是恒定的，大约补偿了总 DNA 电荷的 30%左右。
