B-DNA TWISTING CORRELATES WITH BASE-PAIR MORPHOLOGY
B-DNA TWISTING CORRELATES WITH BASE-PAIR MORPHOLOGY
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DOI：
10.1006/jmbi.1994.0120
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发表时间：
1995-03-17
影响因子：
5.6
通讯作者：
OLSON, WK
中科院分区：
文献类型：
--
作者：
GORIN, AA;ZHURKIN, VB;OLSON, WK
在 38 个 B-DNA 晶体结构中观察到的平均扭转角的序列依赖性可以根据组成碱基对的简单几何特征来理解。低扭曲的结构似乎会解开，以响应主凹槽和小凹槽中大外环基团（例如 NH2-NH2）的严重空间碰撞，而高扭曲的结构则受到较少的接触（H-O 和 H-H）。我们提供了一个简单的碰撞函数，该函数取决于碱基对形态（即碱基对的化学组成），并令人满意地解释了十种常见 Watson-Crick 的扭曲角 二聚体在固态和溶液中都有步骤。当扩展到修改的碱基时，我们在这里发现的扭曲冲突相关性仍然成立。除了Calladine的嘌呤-嘌呤冲突之外，我们还添加了凹槽中碱基之间的其他紧密接触，并考虑了糖-磷酸骨架的几何构象限制（即，我们强调DNA保存虚拟骨架长度的趋势）。这一发现的意义有三重：（1）序列依赖性DNA扭曲直接参与蛋白质-DNA相互作用； (2) Twist 和 Roll 之间的强相关性有助于阐明双螺旋的弯曲作为碱基序列的函数； (3)可以预测化学改性对扭曲和弯曲的影响。其他结构参数与扭曲的相互关联使得该角度成为 DNA 构象异质性的主要决定因素。
The observed sequence dependence of the mean twist angles in 38 B-DNA crystal structures can be understood in terms of simple geometrical features of the constituent base-pairs. Structures with low twist appear to unwind in response to severe steric clashes of large exocyclic groups (such as NH2-NH2) in the major and minor grooves, while those with high twist are subjected to lesser contacts (H-O and H-H).We offer a simple clash function that depends on base-pair morphology (i.e. the chemical constitution of base-pairs) and satisfactorily accounts for the twist angles of the ten common Watson-Crick dimer steps both in the solid state and in solution. The twist-clash correlation that we find here still holds when extended to modified bases. In addition to Calladine's purine-purine clashes, we add other close contacts between bases in the grooves, and consider the conformational restrictions on the geometry of the sugar-phosphate backbone (namely, we emphasize the tendency of DNA to conserve virtual backbone length).The significance of this finding is threefold: (1) sequence-dependent DNA twisting is directly involved in protein-DNA interactions; (2) strong correlation between Twist and Roll helps to elucidate the bending of the double helix as a function of base sequence; (3) it is possible to anticipate the effects of chemical modifications on twisting and bending. The mutual correlations of other structural parameters with the twist make this angle a primary determinant of DNA conformational heterogeneity.