离子溶液中三链DNA介电响应的模拟研究
Dielectric response of triplex DNA in ionic solution from simulations.
作者信息
Yang L, Weerasinghe S, Smith P E, Pettitt B M
机构信息
Department of Chemistry, University of Houston, Texas 77204-5641, USA.
出版信息
Biophys J. 1995 Oct;69(4):1519-27. doi: 10.1016/S0006-3495(95)80022-6.
Abstract
We have analyzed a 1.2-ns molecular dynamics simulation of 51 mM d(CG.G)7 with 21 Na+ counter-ions and 1 M NaCl in water. Via the dipole fluctuations, the dielectric constant for the DNA is found to be around 16, whereas that for the bases and sugars combined is only 3. The dielectric constant for water in this system is 41, which is much smaller than 71 for pure SPC/E water, because of the strong restriction imposed on the motion of water molecules by the DNA and the ions. Also addressed in the present work are several technical issues related to the calculation of the dipole moment of an ionic solution from molecular dynamics simulations using periodic boundary conditions.
摘要
我们分析了在水中含有21个Na⁺抗衡离子和1 M NaCl的51 mM d(CG.G)7的1.2纳秒分子动力学模拟。通过偶极涨落，发现DNA的介电常数约为16，而碱基和糖组合的介电常数仅为3。该系统中水的介电常数为41，由于DNA和离子对水分子运动施加的强烈限制，远小于纯SPC/E水的71。本工作还讨论了与使用周期性边界条件从分子动力学模拟计算离子溶液偶极矩相关的几个技术问题。
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