Sequence-dependent DNA structure: A database of octamer structural parameters
Sequence-dependent DNA structure: A database of octamer structural parameters
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DOI：
10.1016/j.jmb.2003.08.006
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发表时间：
2003-10-03
影响因子：
5.6
通讯作者：
Willett, P
中科院分区：
文献类型：
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作者：
Gardiner, EJ;Hunter, CA;Willett, P
我们已经构建了双螺旋 DNA 中所有独特的四聚体、六聚体和八聚体的势能表面，作为中心步骤的两个主要自由度（滑动和移位）的函数。根据这些势能图，我们计算了每个序列的结构和灵活性特性的数据库。这些属性包括： 对于序列的每个步骤，六个步骤参数（扭转滚动、倾斜、上升、滑动和移位）中每一个的值；针对中心步骤的最小能量构象的每个属性值的减少和增加的灵活性措施；以及与假设的直八聚体路径的偏差。在对作为序列长度函数的结构变化的分析中，我们观察到几乎所有 DNA 都趋向于 B-DNA 并且变得不太灵活。对八聚体特性的更详细分析使我们能够确定特定序列元件的结构偏好。 GGC 和 GCC 序列倾向于赋予双稳定性、低稳定性和 A 型 DNA 的倾向，而 AA 步骤强烈偏爱 B-DNA 并抑制 A 型结构。柔韧性和固有曲率之间没有相关性，但弯曲的 DNA 不如直的 DNA 稳定。最困难的变形是扭转不足。就减少扭曲和增加滚动而言，TA 步骤脱颖而出，成为最灵活的序列元素。然而，与结构属性一样，这种行为高度依赖于上下文，并且一些 TA 步骤非常直接。 (C) 2003 Elsevier Ltd. 保留所有权利。
We have constructed the potential energy surfaces for all unique tetramers, hexamers, and octamers in double helical DNA, as a function of the two principal degrees of freedom, slide and shift at the central step. From these potential energy maps, we have calculated a database of structural and flexibility properties for each of these sequences. These properties include: the values of each of the six step parameters (twist roll, tilt, rise, slide and shift), for each step of the sequence; flexibility measures for both decrease and increase in each property value from the minimum energy conformation for the central step; and the deviation from the path of a hypothetical straight octamer. In an analysis of structural change as a function of sequence length, we observe that almost all DNA tends to B-DNA and becomes less flexible. A more detailed analysis of octamer properties has allowed us to determine the structural preferences of particular sequence elements. GGC and GCC sequences tend to confer bistability, low stability and a predisposition to A-form DNA, whereas AA steps strongly prefer B-DNA and inhibit A-structures. There is no correlation between flexibility and intrinsic curvature, but bent DNA is less stable than straight. The most difficult deformation is undertwisting. The TA step stands out as the most flexible sequence element with respect to decreasing twist and increasing roll. However, as with the structural properties, this behavior is highly context-dependent and some TA steps are very straight. (C) 2003 Elsevier Ltd. All rights reserved.