Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003, USA.
Phys Chem Chem Phys. 2009 Dec 7;11(45):10543-52. doi: 10.1039/b910812b. Epub 2009 Oct 23.
DNA catenanes are important objects in biology, foremost as they appear during replication of circular DNA molecules. In this review we analyze how conformational properties of DNA catenanes can be studied by computer simulation. We consider classification of catenanes, their topological invariants and the methods of calculation of these invariants. We briefly analyze the DNA model and the simulation procedure used to sample the equilibrium conformational ensemble of catenanes with a particular topology. We consider how to avoid direct simulation of many DNA molecules when we need to account for the linking-unlinking process. The simulation methods and their comparisons with experiments are illustrated by some examples. We also describe an approach that allows simulating the steady state fraction of DNA catenanes created by type II topoisomerases.
DNA 连环体是生物学中的重要对象，主要是因为它们出现在环状 DNA 分子的复制过程中。在这篇综述中，我们分析了如何通过计算机模拟研究 DNA 连环体的构象性质。我们考虑了连环体的分类、它们的拓扑不变量以及这些不变量的计算方法。我们简要分析了 DNA 模型和模拟程序，用于采样具有特定拓扑的连环体的平衡构象集合。我们考虑了在需要考虑连接-解链过程时如何避免直接模拟许多 DNA 分子。我们通过一些例子说明了模拟方法及其与实验的比较。我们还描述了一种方法，该方法允许模拟由 II 型拓扑异构酶创建的 DNA 连环体的稳定状态分数。
