Free energy calculations for DNA base stacking by replica-exchange umbrella sampling
Free energy calculations for DNA base stacking by replica-exchange umbrella sampling
复制标题
DOI：
10.1016/j.cplett.2003.10.159
复制
发表时间：
2004-02-02
影响因子：
2.8
通讯作者：
Okamoto, Y
中科院分区：
文献类型：
--
作者：
Murata, K;Sugita, Y;Okamoto, Y
我们用基于复制交换伞采样的分子动力学模拟方法研究了DNA二聚体堆积过程中的自由能变化。这种方法交换了具有不同伞势的复制品对，使得模拟可以采样更宽的构象空间，从而比传统的伞形采样得到更准确的自由能分布。从自由能谱中，我们观察到所有DNA二聚体都具有良好的堆积能力和依赖于序列的堆积稳定性。这种堆积自由能的顺序依赖关系与实验结果是一致的。(C)2003爱思唯尔B.V.保留所有权利。
We have investigated the free energy change of the stacking process of DNA dimers using molecular dynamics simulations based on replica-exchange umbrella sampling. Pairs of replicas with different umbrella potentials are exchanged in this method, which allows the simulation to sample much wider conformational space and, therefore, to yield more accurate free energy profiles than by the conventional umbrella sampling. From the free energy profiles, we observed good stacking for all DNA dimers and sequence-dependent stacking stability. This sequence dependence of the stacking free energy is in accord with the experimental results. (C) 2003 Elsevier B.V. All rights reserved.