Conformational and thermodynamic properties of supercoiled DNA.
Conformational and thermodynamic properties of supercoiled DNA.
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DOI：
10.1146/annurev.bb.23.060194.003141
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发表时间：
1994
期刊：
影响因子：
--
通讯作者：
A. Vologodskii;N. Cozzarelli
中科院分区：
文献类型：
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作者：
A. Vologodskii;N. Cozzarelli
20世纪90年代的工作大大增加了我们对超螺旋构象和能量学的理解。我们现在知道了超螺旋DNA的许多基本性质，这是实验和理论分析协同作用的结果。最后，我们总结了结果。1.所有可用的数据表明超螺旋DNA的plectonemic结构。首先，三种类型的EM（常规，冷冻和扫描力）显示plectonemic形式。第二，由Int重组酶从超螺旋DNA产生的索烃和结的拓扑结构要求底物超螺旋是plectonemic的，2型拓扑异构酶的结的拓扑结构也是如此。第三，所有的理论和计算机分析表明，超螺旋线具有缠绕的形式。2.超螺旋构象往往是分支，如使用EM和Monte Carlo模拟观察到的。此外，需要分支来解释由Int或拓扑异构酶产生的结和索烃的分布以及S和Rg对西格玛的依赖性。分支频率对西格玛、DNA长度、离子条件、DNA弯曲和温度非常敏感。尽管定性的协议，实验和计算数据之间的定量差异指出，需要进一步研究的分支。3.蒙特卡罗模拟、理论分析和冷冻电镜的结果表明，超螺旋DNA的构象和热力学性质强烈依赖于离子条件。这种依赖性的原因是显而易见的。抗衡离子屏蔽DNA负电荷，降低DNA片段在紧密缠绕结构中的排斥作用。当盐浓度从1.00 M降低到0.01 M时，有效双螺旋直径从3 nm增加到15 nm。超螺旋DNA性质对离子条件的依赖性的实验研究才刚刚开始。以下结论涉及中等至高单价或二价离子浓度的条件（分别为>或= 0.1 M [Na+]或>或= 0.01 M [Mg 2 +]）。1. Wr约占Δ Lk的3/4，对于长度≥ 2.5kb的DNA，Wr/Δ Tw与σ无关。一个恒定的比率是隐含的CD数据，和Wr/Δ Tw已确定与传统的EM，cryo-EM，的Int拓扑方法，和蒙特卡洛模拟。2.超螺旋的平均数为（0.8至0.9）× Δ Lk，与DNA长度无关。这些结果是用EM，Int拓扑方法和计算机模拟得到的。（400字处删节）
Work in the 1990s has substantially increased our understanding of supercoiling conformations and energetics. We now know many of the basic properties of supercoiled DNA as a result of the synergy between experimental and theoretical analyses. We conclude by summarizing the results. 1. All available data indicate a plectonemic structure for supercoiled DNA. First, three types of EM (conventional, cryo, and scanning force) show the plectonemic form. Second, the topology of the catenanes and knots generated from supercoiled DNA by the Int recombinase demands that the substrate supercoils are plectonemic, as does the topology of knotting by type-2 topoisomerases. Third, all the theoretical and computer analyses indicate that the superhelix has the interwound form. 2. The superhelix conformations are often branched, as observed using EM and Monte Carlo simulation. Moreover, branching is required to explain the distribution of knots and catenanes produced by Int or topoisomerases as well as the dependence of s and Rg on sigma. Branching frequency is very sensitive to sigma, DNA length, ionic conditions, DNA bends, and temperature. Despite the qualitative agreement, the quantitative differences between experimental and computational data point out the need for further studies of branching. 3. The results of Monte Carlo simulations, theoretical analyses, and cryo-EM show that the conformational and thermodynamic properties of supercoiled DNA depend strongly on ionic conditions. The reason for such a dependence is clear. Counterions shield DNA negative charges and decrease the repulsion of DNA segments in the tight interwound structure. The effective double-helix diameter increases from 3 to 15 nm as the salt concentration is reduced from 1.00 to 0.01 M. Experimental investigations of the dependence on ionic conditions of supercoiled DNA properties are just beginning. The following conclusions refer to conditions of moderate to high monovalent or divalent ion concentrations (> or = 0.1 M [Na+] or > or = 0.01 M [Mg2+], respectively). 1. Wr takes up about 3/4 of the delta Lk, and Wr/delta Tw is independent of sigma for DNA > or = 2.5 kb in length. A constant ratio is implied by the CD data, and Wr/delta Tw has been determined with conventional EM, cryo-EM, the Int topological method, and Monte Carlo simulation. 2. The average number of supercoils is (0.8 to 0.9) x delta Lk and is independent of DNA length. These results were obtained with EM, the Int topological method, and computer simulation.(ABSTRACT TRUNCATED AT 400 WORDS)