Two perspectives on the twist of DNA
Two perspectives on the twist of DNA
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DOI：
10.1063/1.3273453
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发表时间：
2009-12-28
影响因子：
4.4
通讯作者：
Tobias, Irwin
中科院分区：
文献类型：
--
作者：
Britton, Lauren A.;Olson, Wilma K.;Tobias, Irwin
由于DNA的双螺旋结构，两条互补的核苷酸链相互缠绕在一起，一个共价封闭的DNA分子在任何一条链上都没有中断，可以被看作是两条互锁的单链环。数学家们早就知道，两条封闭空间曲线表现出一种被称为连接数的性质，这是一种拓扑不变的整数，可以用另外两个量的和来表示，一个是一条曲线绕另一条曲线的扭曲，另一个是扭动数，或扭动数，是两条封闭曲线之一的平面性引起的手性扭曲的度量。我们在此推导出超螺旋DNA的扭曲和封闭分子的扭曲的表达式，这些表达式与现代DNA作为碱基对步骤序列的观点一致。结构生物学家通常用六个刚体参数来描述每一步的空间分布，巧合的是，其中一个也被称为扭转。令人感兴趣的是，这种阶跃参数扭转与给定碱基对步长相关的超卷曲扭转之间的数学性质的差异。例如，事实证明，与前者不同，后者对分子的某些平移剪切扭曲很敏感，这些扭曲本质上是手性的。因此，通过比较蛋白质-DNA复合体的高分辨率结构的每一步的两个扭曲的值，我们可能能够确定各种蛋白质的结合如何有助于DNA的手性结构变化。
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked single-stranded rings. Two closed space curves have long been known by mathematicians to exhibit a property called the linking number, a topologically invariant integer, expressible as the sum of two other quantities, the twist of one of the curves about the other, and the writhing number, or writhe, a measure of the chiral distortion from planarity of one of the two closed curves. We here derive expressions for the twist of supercoiled DNA and the writhe of a closed molecule consistent with the modern view of DNA as a sequence of base-pair steps. Structural biologists commonly characterize the spatial disposition of each step in terms of six rigid-body parameters, one of which, coincidentally, is also called the twist. Of interest is the difference in the mathematical properties between this step-parameter twist and the twist of supercoiling associated with a given base-pair step. For example, it turns out that the latter twist, unlike the former, is sensitive to certain translational shearing distortions of the molecule that are chiral in nature. Thus, by comparing the values for the two twists for each step of a high-resolution structure of a protein-DNA complex, we may be able to determine how the binding of various proteins contributes to chiral structural changes of the DNA.