UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA.
Nucleic Acids Res. 2024 Jan 11;52(1):22-48. doi: 10.1093/nar/gkad1092.
Closing each strand of a DNA duplex upon itself fixes its linking number L. This topological condition couples together the secondary and tertiary structures of the resulting ccDNA topoisomer, a constraint that is not present in otherwise identical nicked or linear DNAs. Fixing L has a range of structural, energetic and functional consequences. Here we consider how L having different integer values (that is, different superhelicities) affects ccDNA molecules. The approaches used are primarily theoretical, and are developed from a historical perspective. In brief, processes that either relax or increase superhelicity, or repartition what is there, may either release or require free energy. The energies involved can be substantial, sufficient to influence many events, directly or indirectly. Here two examples are developed. The changes of unconstrained superhelicity that occur during nucleosome attachment and release are examined. And a simple theoretical model of superhelically driven DNA structural transitions is described that calculates equilibrium distributions for populations of identical topoisomers. This model is used to examine how these distributions change with superhelicity and other factors, and applied to analyze several situations of biological interest.
双链 DNA 自身的每条链的闭合都会固定其连接数 L。这种拓扑条件将产生的 ccDNA 拓扑异构体的二级和三级结构耦合在一起，这在其他相同的切口或线性 DNA 中是不存在的。固定 L 具有一系列结构、能量和功能后果。在这里，我们考虑不同整数（即不同超螺旋度）值的 L 如何影响 ccDNA 分子。所使用的方法主要是理论上的，并且是从历史角度发展而来的。简而言之，无论是松弛还是增加超螺旋度，还是重新分配超螺旋度的过程，都可能释放或需要自由能。所涉及的能量可能很大，足以直接或间接地影响许多事件。这里介绍了两个例子。检查了核小体附着和释放过程中超螺旋度的变化。并描述了一个简单的超螺旋驱动 DNA 结构转变的理论模型，该模型计算了相同拓扑异构体的种群的平衡分布。该模型用于检查这些分布如何随超螺旋度和其他因素而变化，并应用于分析几种具有生物学意义的情况。
