Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases
Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases
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DOI：
10.1093/nar/gkm532
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发表时间：
2007-08-01
影响因子：
14.9
通讯作者：
Stasiak, Andrzej
中科院分区：
文献类型：
--
作者：
Burnier, Yannis;Weber, Cedric;Stasiak, Andrzej
我们对DNA链进行了数值模拟，以了解结DNA分子中并列片段的局部几何形状如何引导II型DNA拓扑异构酶非常有效地放松DNA结。我们研究了在II型DNA拓扑异构酶介导的节段间传代反应中，定义节段间并置的几何形状的各种参数如何影响这些反应的拓扑结果。我们证实了这样的假设，即通过识别结DNA分子中并置DNA片段的特定几何形状，II型DNA拓扑异构酶可以维持低于拓扑平衡的稳态结水平。此外，我们揭示了对特定几何形状的并置片段作为链传递反应位点的偏好，使II型DNA拓扑异构酶能够选择最有效的途径来放松复杂的DNA结。对复杂结有效松弛的最佳选择准则进行了分析，结果表明，给定结类型的随机构型中的局部结构在统计上表现为相应结类型的理想几何构型中的类似局部结构。
We performed numerical simulations of DNA chains to understand how local geometry of juxtaposed segments in knotted DNA molecules can guide type II DNA topoisomerases to perform very efficient relaxation of DNA knots. We investigated how the various parameters defining the geometry of intersegmental juxtapositions at sites of inter-segmental passage reactions mediated by type II DNA topoisomerases can affect the topological consequences of these reactions. We confirmed the hypothesis that by recognizing specific geometry of juxtaposed DNA segments in knotted DNA molecules, type II DNA topoisomerases can maintain the steady-state knotting level below the topological equilibrium. In addition, we revealed that a preference for a particular geometry of juxtaposed segments as sites of strand-passage reaction enables type II DNA topoisomerases to select the most efficient pathway of relaxation of complex DNA knots. The analysis of the best selection criteria for efficient relaxation of complex knots revealed that local structures in random configurations of a given knot type statistically behave as analogous local structures in ideal geometric configurations of the corresponding knot type.