Superhelical DNA with local substructures. A generalization of the topological constraint in terms of the intersection number and the ladder-like correspondence surface.
Superhelical DNA with local substructures. A generalization of the topological constraint in terms of the intersection number and the ladder-like correspondence surface.
复制标题
具有局部亚结构的超螺旋 DNA。
DOI：
10.1016/0022-2836(87)90337-8
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发表时间：
1987
影响因子：
5.6
通讯作者：
Bauer,WR
中科院分区：
文献类型：
--
作者：
White,JH;Bauer,WR
超螺旋DNA中某些局部结构元素的存在，如十字形和变性环，使这些分子的拓扑和几何分析变得复杂。特别是，双工轴通常难以定义。因此，通常的保守条件，Lk=Tw+Wr，往往是不适用的，因为制定了关于双链体轴的DNA的任何一条链的缠绕。我们在这里提出了一个更一般的配方的拓扑守恒条件的模型，其中的两条DNA链被认为是相互扭曲，其中的两条链被认为是扭动。我们定义了一个梯形的对应面，它连接两条链，是独立的，是否有一个独特的双链轴是本地可用的。这些考虑导致超螺旋DNA的一个新的拓扑性质的定义，交叉数，在。这个数量描述了局部结构元件的复杂性;例如，在十字形的情况下，交叉数是通过十字形形成从DNA的主要片段去除的双链体转角的数量的度量。更一般地说，适用于闭合环状DNA的拓扑约束由LK（W，C）+In（S，C）=Tw（W，C）+Wr（C）给出，其中W和C代表DNA的两条链，S是连接两条链的梯形对应面。
The presence of certain local structural elements in superhelical DNA, such as cruciforms and denatured loops, complicates the topological and geometric analysis of these molecules. In particular, the duplex axis is often difficult to define. In consequence, the usual conservation condition,Lk=Tw+Wr, is often inapplicable as formulated in terms of the winding of either strand of the DNA about the duplex axis. We present here a more general formulation of the topological conservation condition in terms of a model in which the two strands of DNA are regarded as twisting about one another, and in which one of the two strands is considered to writhe. We define a ladder-like correspondence surface, which connects the two strands and is independent of whether or not a unique duplex axis is locally available. These considerations lead to the definition of a new topological property of superhelical DNA, the intersection number,In. This quantity describes the complexity of a local structural element; in the case of a cruciform, for example, the intersection number is a measure of the number of duplex turns removed from the major segment of the DNA by the cruciform formation. In more general terms, the topological constraint applicable to closed circular DNA is given byLK(W,C) +In(S,C) =Tw(W,C) +Wr(C), where W and C represent the two strands of the DNA and S is the ladder-like correspondence surface that connects the two strands.