Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2.
Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2.
复制标题
DNA寡核苷酸静态和动态螺旋变形的持久性分析：应用于d(CGCGAATTCGCG)2的晶体结构和分子动力学模拟。
DOI：
10.1002/bip.360330303
复制
发表时间：
1993
期刊：
影响因子：
2.9
通讯作者：
Beveridge,DL
中科院分区：
文献类型：
--
作者：
Prevost,C;Louise-May,S;Ravishanker,G;Lavery,R;Beveridge,DL
本文提出了一种分析寡核苷酸螺旋结构和变形的理论和图解方法。本文在寡核苷酸水平上对无限长聚合物构型统计中定义的参数“持久性”和“柔性”进行了重新表述，并对J. A. Schellman方法[（1974）Biopolymers，Vol.17，pp. 217-226]，并用作结构中所有可能的双螺旋的螺旋变形特性的系统“持久性分析”的基础。分析的基础是一组参考单个碱基对的连接向量，并且限于仅表现出扰动的杆状行为的序列，即，低于超螺旋的临界值该方法的应用涉及弯曲角分量的物理模型，因此连杆矢量被定义为通过R. Lavery和H. Sklenar [（1988）J. Biomol.结构动力学，Vol. 6，pp. 63-91;（1989）J. Biomol.结构动力学，Vol. 6，pp. 655-667]。讨论了碱基对的整体弯曲和相对取向之间的关系。我们的方法是通过分析一些模型寡核苷酸结构与内在扭结，晶体结构的十二聚体d（CGCGAATTCGCG）2，和两个分子动力学模拟的结果，这十二聚体使用两个变化的GROMOS力场。结果表明，基本上可以确定短寡核苷酸中曲率的所有方面，例如每个弯曲的位置和方向、锐度或平滑度以及双折射的位置和线性。在分子动力学模拟的情况下，在玻尔兹曼系综的结构进行分析，变形（灵活性）的空间范围也被认为是。John Wiley & Sons，Inc.
A theory and graphical presentation for the analysis of helix structure and deformations in oligonucleotides is presented. The parameters “persistence” and “flexibility” as defined in the configurational statistics of polymers of infinite length are reformulated at the oligonucleotide level in an extension of J. A. Schellman's method [(1974)Biopolymers, Vol. 17, pp. 217–226], and used as a basis for a systematic “Persistence Analysis” of the helix deformation properties for all possible subsequences in the structure. The basis for the analysis is a set of link vectors referenced to individual base pairs, and is limited to sequences exhibiting only perturbed rod‐like behavior, i.e., below the threshold for supercoiling. The present application of the method is concerned with a physical model for the angular component of bending, so the link vectors are defined as the unit components of a global helix axis obtained by the procedure “Curves” of R. Lavery and H. Sklenar [(1988)J. Biomol. Struct. Dynam., Vol. 6, pp. 63–91; (1989)J. Biomol. Struct. Dynam., Vol. 6, pp. 655–667]. A discussion, of the relationship between global bending and relative orientation of base pairs is provided. Our approach is illustrated by analysis of some model oligonucleotide structures with intrinsic kinks, the crystal structure of the dodecamer d (CGCGAATTCGCG)2, and the results of two molecular dynamics simulations on this dodecamer using two variations of the GROMOS force field. The results indicate that essentially all aspects of curvature in short oligonucleotides can be determined, such as the position and orientation of each bend, the sharpness or smoothness, and the location and linearity of subsequences. In the case of molecular dynamics simulations, where a Boltzmann ensemble of structures is analyzed, the spatial extent of the deformations (flexibility) is also considered. © 1993 John Wiley & Sons, Inc.