STABLE CRUCIFORM FORMATION AT INVERTED REPEAT SEQUENCES IN SUPERCOILED DNA
STABLE CRUCIFORM FORMATION AT INVERTED REPEAT SEQUENCES IN SUPERCOILED DNA
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DOI：
10.1002/bip.360210314
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发表时间：
1982-01-01
期刊：
影响因子：
2.9
通讯作者：
BENHAM, CJ
中科院分区：
文献类型：
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作者：
BENHAM, CJ
在含有反向重复序列的 DNA 拓扑结构域中分析平衡超螺旋十字形的形成。当分子充分负超螺旋时，十字形构象是稳定的，但当分子是正超螺旋时则不稳定。对于包含单个反向重复序列的特定序列，稳定性的开始发生在一定程度的负超螺旋性上，该程度主要取决于分隔重复副本的碱基对的数量。与稳定十字形状态相关的自由能是恒定的，与超螺旋程度无关，直到完全反向重复参与十字形为止。相反，另一种未挤压状态的自由能随着超螺旋变形近似呈二次方增长。因此，会出现一定程度的负超螺旋，此时十字形状态在能量上变得有利。这种十字形挤出转变的平衡特性随片段长度、所涉及的反向重复序列的位置和大小、环境条件和施加的超螺旋程度而变化。在包含 1 个或多个序列的多个串联和反向重复的片段中，形成的十字形图案以复杂的方式依赖于超螺旋性。特定的十字形可能仅在超螺旋性的狭窄范围内处于平衡状态，它们的重吸收与其他十字形的挤出耦合。
Equilibrium superhelical cruciform formation is analyzed in a topological domain of DNA containing inverted repeat sequences. The cruciform conformation is stable when the molecule is sufficiently negatively supercoiled, but not when it is positively supercoiled. For a particular sequence containing a single inverted repeat, onset of stability occurs at a degree of negative superhelicity that depends critically on the number of base pairs separating the repeat copies. The free energy associated with the stable cruiform state is constant, independent of the degree of superhelicity, up to the point where the complete inverted repeat participates in the cruciform. In contrast, the free energy of the alternative, unextruded state grows approximately quadratically with the superhelical deformation. Therefore, a degree of negative supercoiling occurs at which the cruciform state becomes energetically favored. The equilibrium properties of this cruciform extrusion transition vary with segment length, the positions and sizes of the inverted repeats involved, environmental conditions and the degree of superhelicity imposed. In a segment containing multiple repeats, both tandem and inverted, of 1 or more sequences, the pattern of cruciforms that form is dependent on superhelicity in a complex way. Specific cruciforms may occur at equilibrium only in narrow ranges of superhelicity, their reabsorption being coupled to the extrusion of others.