Vologodskii A V, Cozzarelli N R
Department of Molecular and Cell Biology, University of California, Berkeley 94720.
Annu Rev Biophys Biomol Struct. 1994;23:609-43. doi: 10.1146/annurev.bb.23.060194.003141.
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)
20世纪90年代的研究极大地增进了我们对超螺旋构象和能量学的理解。由于实验分析与理论分析的协同作用，我们现在已经了解了超螺旋DNA的许多基本特性。我们通过总结结果来得出结论。1. 所有现有数据都表明超螺旋DNA具有麻花状结构。首先，三种类型的电子显微镜（传统电子显微镜、冷冻电子显微镜和扫描力显微镜）都显示出麻花状形态。其次，由Int重组酶从超螺旋DNA产生的连环体和纽结的拓扑结构要求底物超螺旋是麻花状的，2型拓扑异构酶的纽结拓扑结构也是如此。第三，所有的理论和计算机分析都表明超螺旋具有相互缠绕的形式。2. 超螺旋构象通常是分支的，这在电子显微镜和蒙特卡洛模拟中都有观察到。此外，需要分支来解释由Int或拓扑异构酶产生的纽结和连环体的分布，以及s和Rg对sigma的依赖性。分支频率对sigma、DNA长度、离子条件、DNA弯曲和温度非常敏感。尽管有定性的一致性，但实验数据和计算数据之间的定量差异表明需要对分支进行进一步研究。3. 蒙特卡洛模拟、理论分析和冷冻电子显微镜的结果表明，超螺旋DNA的构象和热力学性质强烈依赖于离子条件。这种依赖性的原因很明显。抗衡离子屏蔽了DNA的负电荷，减少了紧密相互缠绕结构中DNA片段的排斥力。随着盐浓度从1.00 M降低到0.01 M，有效双螺旋直径从3 nm增加到15 nm。对超螺旋DNA性质对离子条件依赖性的实验研究才刚刚开始。以下结论适用于中等至高单价或二价离子浓度的条件（分别为≥0.1 M [Na+]或≥0.01 M [Mg2+]）。1. Wr约占ΔLk的3/4，对于长度≥2.5 kb的DNA，Wr/ΔTw与sigma无关。圆二色性数据暗示了一个恒定的比例，并且Wr/ΔTw已经通过传统电子显微镜、冷冻电子显微镜、Int拓扑方法和蒙特卡洛模拟确定。2. 超螺旋的平均数量为(0.8至0.9)×ΔLk，并且与DNA长度无关。这些结果是通过电子显微镜、Int拓扑方法和计算机模拟获得的。（摘要截断于400字）
