Dickerson R E, Chiu T K
Oxford University Laboratory of Molecular Biophysics, UK.
Biopolymers. 1997;44(4):361-403. doi: 10.1002/(SICI)1097-0282(1997)44:4<361::AID-BIP4>3.0.CO;2-X.
Normal vectors perpendicular to individual base pairs are a powerful tool for studying the bending behavior of B-DNA, both in the form of normal vector plots and in matrices that list angles between vectors for all possible base pair combinations. A new analysis program, FREEHELIX, has been written for this purpose, and applied to 86 examples of sequence-specific protein/DNA complexes whose coordinates are on deposit in the Nucleic Acid Data Base. Bends in this sample of 86 structures almost invariably follow from roll angles between adjacent base pairs; tilt makes no net contribution. Roll in a direction compressing the broad major groove is much more common than that which compresses the minor groove. Three distinct types of B-DNA bending are observed, each with a different molecular origin: (1) Localized kinking is produced by large roll at single steps or at two steps separated by one turn of helix. (2) Smooth, planar curvature is produced by positive and negative roll angles spaced a half-turn apart, with random side-to-side zigzag roll at intermediate points, rather than a tilt contribution that might have been expected theoretically. (3) Three-dimensional writhe results from significant roll angles at a continuous series of steps. Writhe need not change the overall direction of helix axis, if it is continued indefinitely or for an integral number of helical turns. A-DNA itself can be formally considered as possessing uniform, continuous writhe that yields no net helix bending. Smooth curvature is the most intricate deformation of the three, and is least common. Writhe is the simplest deformation and is most common; indeed, a low level of continuous writhe is the normal condition of an otherwise unbent B-DNA helix of general sequence. With one exception, every example of major kinking in this sample of 86 structures involves a pyrimidine-purine step: C-A/T-G, T-A, or C-G. Purine-purine steps, especially A-A, show the least tendency toward roll deformations.
垂直于单个碱基对的法向量是研究B-DNA弯曲行为的有力工具，既可以用于法向量图形式，也可以用于列出所有可能碱基对组合的向量间角度的矩阵形式。为此编写了一个新的分析程序FREEHELIX，并将其应用于86个序列特异性蛋白质/DNA复合物实例，这些复合物的坐标存于核酸数据库中。在这86个结构样本中，弯曲几乎总是由相邻碱基对之间的滚动角引起；倾斜没有净贡献。向压缩宽的大沟方向的滚动比压缩小沟方向的滚动更为常见。观察到三种不同类型的B-DNA弯曲，每种弯曲都有不同的分子起源：（1）局部扭结是由单步或相隔一圈螺旋的两步处的大滚动产生的。（2）平滑的平面曲率是由相隔半圈的正负滚动角产生的，中间点有随机的左右曲折滚动，而不是理论上可能预期的倾斜贡献。（3）三维缠绕是由一系列连续步骤中的显著滚动角产生的。如果缠绕无限延续或为整数个螺旋圈数，则缠绕不必改变螺旋轴的总体方向。A-DNA本身可以形式上被认为具有均匀、连续的缠绕，不会产生净螺旋弯曲。平滑曲率是这三种变形中最复杂的，也是最不常见的。缠绕是最简单的变形，也是最常见的；实际上，低水平的连续缠绕是一般序列的未弯曲B-DNA螺旋的正常状态。在这86个结构样本中，除了一个例外，每一个主要扭结的例子都涉及嘧啶-嘌呤步骤：C-A/T-G、T-A或C-G。嘌呤-嘌呤步骤，尤其是A-A，显示出最小的滚动变形倾向。
