Norberg J, Nilsson L
Department of Bioscience at NOVUM, Karolinska Institute, Huddinge, Sweden.
Biophys J. 1998 Jan;74(1):394-402. doi: 10.1016/S0006-3495(98)77796-3.
In this paper we present a detailed analysis of the base-stacking phenomenon in different solvents, using nanosecond molecular dynamics simulations. The investigation focuses on deoxyribo- and ribodinucleoside monophosphates in aqueous and organic solutions. Organic solvents with a low dielectric constant, such as chloroform, and solvents with intermediate dielectric constants, such as dimethyl sulfoxide and methanol, were analyzed. This was also done for water, which is highly polar and has a high dielectric constant. Structural parameters such as the sugar puckering and the base-versus-base orientations, as well as the energetics of the solute-solvent interactions, were examined in the different solvents. The obtained data demonstrate that base stacking is favored in the high dielectric aqueous solution, followed by methanol and dimethyl sulfoxide with intermediate dielectric constants, and chloroform, with a low dielectric constant.
在本文中，我们使用纳秒分子动力学模拟对不同溶剂中的碱基堆积现象进行了详细分析。研究重点是脱氧核糖核苷单磷酸和核糖核苷单磷酸在水溶液和有机溶液中的情况。分析了低介电常数的有机溶剂，如氯仿，以及介电常数适中的溶剂，如二甲基亚砜和甲醇。对高极性且介电常数高的水也进行了分析。在不同溶剂中研究了诸如糖环构象和碱基与碱基的取向等结构参数，以及溶质 - 溶剂相互作用的能量学。获得的数据表明，碱基堆积在高介电常数的水溶液中最为有利，其次是介电常数适中的甲醇和二甲基亚砜，而介电常数低的氯仿中最不利。
