Yan J, Magnasco M O, Marko J F
Department of Physics, The University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Mar;63(3 Pt 1):031909. doi: 10.1103/PhysRevE.63.031909. Epub 2001 Feb 27.
The enzymes that pass DNA through DNA so as to remove entanglements, adenosine-triphosphate-hydrolyzing type-II topoisomerases, are able to suppress the probability of self-entanglements (knots) and mutual entanglements (links) between approximately 10 kb plasmids, well below the levels expected, given the assumption that the topoisomerases pass DNA segments at random by thermal motion. This implies that a 10-nm type-II topoisomerase can somehow sense the topology of a large DNA. We previously introduced a "kinetic proofreading" model which supposes the enzyme to require two successive collisions in order to allow exchange of DNA segments, and we showed how it could quantitatively explain the reduction in knotting and linking complexity. Here we show how the same model quantitatively explains the reduced variance of the double-helix linking number (supercoiling) distribution observed experimentally.
能够通过DNA传递DNA以消除缠结的酶，即水解三磷酸腺苷的II型拓扑异构酶，能够抑制大约10 kb质粒之间的自我缠结（纽结）和相互缠结（连环）的概率，远低于在拓扑异构酶通过热运动随机传递DNA片段这一假设下预期的水平。这意味着10纳米的II型拓扑异构酶能够以某种方式感知大型DNA的拓扑结构。我们之前引入了一个“动力学校对”模型，该模型假设酶需要两次连续碰撞才能允许DNA片段交换，并且我们展示了它如何能够定量解释纽结和连环复杂性的降低。在这里，我们展示了相同的模型如何定量解释实验观察到的双螺旋连环数（超螺旋）分布方差的降低。
