Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment:: Comparison of atomic point-charge, extra-point, and polarizable force fields
Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment:: Comparison of atomic point-charge, extra-point, and polarizable force fields
复制标题
DOI：
10.1063/1.1788631
复制
发表时间：
2004-10-08
影响因子：
4.4
通讯作者：
Sagui, C
中科院分区：
文献类型：
--
作者：
Baucom, J;Transue, T;Sagui, C
对DNA双链d(CCAACGTTGG)(2)进行分子动力学模拟，以研究晶体环境中DNA序列与结构之间的关系。使用了三种不同的力场：基于原子点电荷的传统描述、可极化力场和“额外点”力场（在核外位点有额外电荷）。发现所有力场都能较好地重现实验结构的序列依赖性特征。然而，可极化力场对晶体结构以及实验中观察到的序列依赖性效应提供了最准确的描述。这些结果表明，为了准确描述DNA，需要考虑极化作用。（C）2004美国物理学会。
Molecular dynamics simulations of the DNA duplex d(CCAACGTTGG)(2) were used to study the relationship between DNA sequence and structure in a crystal environment. Three different force fields were used: a traditional description based on atomic point charges, a polarizable force field, and an "extra-point" force field (with additional charges on extranuclear sites). It is found that all the force fields reproduce fairly well the sequence-dependent features of the experimental structure. The polarizable force field, however, provides the most accurate representation of the crystal structure and the sequence-dependent effects observed in the experiment. These results point out to the need of the inclusion of polarization for accurate descriptions of DNA. (C) 2004 American Institute of Physics.