THE ASSESSMENT OF THE GEOMETRY OF DINUCLEOTIDE STEPS IN DOUBLE-HELICAL DNA - A NEW LOCAL CALCULATION SCHEME
THE ASSESSMENT OF THE GEOMETRY OF DINUCLEOTIDE STEPS IN DOUBLE-HELICAL DNA - A NEW LOCAL CALCULATION SCHEME
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DOI：
10.1006/jmbi.1995.0462
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发表时间：
1995-09-01
影响因子：
5.6
通讯作者：
CALLADINE, CR
中科院分区：
文献类型：
--
作者：
ELHASSAN, MA;CALLADINE, CR
在本文中，我们开发了一个新的本地欧拉角为基础的计划，以评估内部的运动学或几何的一般双螺旋DNA中的二核苷酸步骤。二核苷酸台阶的几何结构完全由以下参数定义：（1）描述标准沃森-克里克碱基对中一个碱基相对于另一个碱基的相对位置和方向的碱基对参数，以及（2）描述两个碱基对的相对位置和方向的台阶参数。我们的方案的主要特点是它利用了中间步骤参考系的概念，除了确保步骤参数的相同值获得与二核苷酸步骤的推算方向无关之外，（沿沿着任一链的5 '->3'方向），这中间的一步，三元组概念导致步骤参数的局部定义，使得它们独立于低聚物的整体整体构象，问题。除了提出我们自己的计算方案，我们还严格审查了最广泛使用的软件包计算的一些步骤和碱基对参数，即，NEWHELIX套件的程序由R。E.迪克森最后，从公共数据库（N.D.B at Rutgers）中任意选取了十二聚体、十聚体和八聚体，并用NEWHELIX和所提出的方案计算了它们的阶跃参数。结果的比较，从而表明，对于步骤参数：螺旋扭曲和滑动，和基对参数螺旋桨和扣，NEWHELIX和我们提出的计划给出相当相似的值。然而，在Rise的情况下，可以看到实质性的差异。NEWHELIX给出了两个可供选择的定义，用于计算滚动和滚动。虽然一个定义与我们提出的方案完全一致，但另一个定义却有很大的不同。(C)1995年学术出版社
In this paper, we develop a new local Euler-angle-based scheme for assessing the internal kinematics or geometry of a general dinucleotide step in double-helical DNA. The geometry of a dinucleotide step is completely defined by: (1) the base-pair parameters that describe the relative position and orientation of one base with respect to the other in a standard Watson-Crick base-pair, and (2) the step parameters that describe the relative position and orientation of the two base-pairs. The key feature of our scheme is that it makes use of the concept of a mid-step reference frame, In addition to ensuring that identical values of step parameters are obtained irrespective of the direction of reckoning of a dinucleotide step (in the 5'-->3' direction along either strand), this mid-step-triad concept leads to local definitions of the step parameters that render them independent of the overall global conformation of the oligomer in question.In addition to presenting our own calculation scheme we also examine critically the most widely used package for the calculation of some of the step and base-pair parameters, viz, the NEWHELIX suite of programmes by R. E. Dickerson. Finally, a dodecamer, a decamer and an octamer are arbitrarily selected from a public data-base (N.D.B at Rutgers), and their step parameters are calculated by using both NEWHELIX and the proposed scheme. A comparison of the results is given whereby it is shown that for the step parameters: Helical Twist and Slide, and the base-pair parameters Propeller and Buckle, NEWHELIX and our proposed scheme give rather similar values. Substantial differences are seen, however, in the case of Rise. Two alternative definitions are given by NEWHELIX for the calculation of Roll and Tilt. Whereas one definition agrees well with our proposed scheme, the other is substantially different. (C) 1995 Academic Press Limited