DNA bending: The prevalence of kinkiness and the virtues of normality
DNA bending: The prevalence of kinkiness and the virtues of normality
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DOI：
10.1093/nar/26.8.1906
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发表时间：
1998-04-15
影响因子：
14.9
通讯作者：
Dickerson, RE
中科院分区：
文献类型：
--
作者：
Dickerson, RE
用法矢量图、螺旋中所有碱基对之间的法矢夹角矩阵和一位数的滚动/滑动/扭转表研究了86个序列特异蛋白质复合体的DNA弯曲。FREEHELIX是一个专门为分析严重弯曲和扭曲的复式结构而设计的新程序，它可以生成前述量加上局部滚动、倾斜、扭转、滑动、移位和上升参数，完全不需要任何关于整体螺旋轴的假设。在几乎所有的情况下，弯曲都是由嘧啶-嘌呤碱基对的正滚动引起的：C-A(=T-G)，T-A，或者不太频繁的C-G，在压缩主要凹槽的方向上。在86个例子中，法矢量图显示了三种明确的弯曲类型：(I)在一个或两个离散碱基对台阶上的正滚动产生的局部扭结，(Ii)在一系列相邻碱基对台阶上的正滚动产生的三维扭曲，或(Iii)每5个BP的正负滚动交替产生的连续曲率，中间位置为侧到侧之字形滚动。在任何情况下，倾斜都不是弯曲过程中的重要组成部分。在具有两个局域扭结的序列中，如CAP和IHF，由三个螺旋片段形成的二面角是扭结之间碱基对步数的线性函数：二面角=36度x扭结间隔。86个例子中的28个可以被描述为主要的弯曲，以及蛋白质识别给定碱基序列的重要元件。但即使是微小的弯曲也在微调蛋白质/DNA相互作用方面发挥了作用。序列依赖的螺旋变形性是蛋白质/DNA识别的重要组成部分，同时也是公认的氢键模式。FREEHELIX、法向量图、全向量角矩阵和一位数滚动/滑动/扭转表的组合为DNA弯曲的评估提供了一种快速而方便的方法。
DNA bending in 86 complexes with sequence-specific proteins has been examined using normal vector plots, matrices of normal vector angles between all base pairs in the helix, and one-digit roll/slide/twist tables. FREEHELIX, a new program especially designed to analyze severely bent and kinked duplexes, generates the foregoing quantities plus local roll, tilt, twist, slide, shift and rise parameters that are completely free of any assumptions about an overall helix axis. In nearly every case, bending results from positive roll at pyrimidine-purine base pair steps: C-A (= T-G), T-A, or less frequently C-G, in a direction that compresses the major groove. Normal vector plots reveal three well-defined types of bending among the 86 examples: (i) localized kinks produced by positive roll at one or two discrete base pairs steps, (ii) three-dimensional writhe resulting from positive roll at a series of adjacent base pairs steps, or (iii) continuous curvature produced by alternations of positive and negative roll every 5 bp, with side-to-side zig-zag roll at intermediate position. In no case is tilt a significant component of the bending process. In sequences with two localized kinks, such as CAP and IHF, the dihedral angle formed by the three helix segments is a linear function of the number of base pair steps between kinks: dihedral angle = 36 degrees x kink separation. Twenty-eight of the 86 examples can be described as major bends, and significant elements in the recognition of a given base sequence by protein. But even the minor bends play a role in fine-tuning protein/DNA interactions. Sequence dependent helix deformability is an important component of protein/DNA recognition, alongside the more generally recognized patterns of hydrogen bonding. The combination of FREEHELIX, normal vector plots, full vector angle matrices, and one-digit roll/ slide/twist tables affords a rapid and convenient method for assessing bending in DNA.