Computer Analysis of DNA Unknotting by Topoisomerase (pilot)

II型拓扑异构酶是所有生物体共同的必需酶。它们的细胞功能包括 维持染色体致密化的水平并确保细胞分裂时的适当分离。在 此外，它们通常用作抗微生物剂和抗癌药物的靶。了解 拓扑异构酶II（topo II）简化其DMA底物的拓扑复杂性的过程如下： 关键的重要性。通过剪切和粘贴机制，这是很好地理解在分子水平上，拓扑异构酶II是 能够通过另一个DMA段传递DMA段。topo II如何识别两个DMA段仍然是 不清楚已知Topo II可解开DMA并使DMA解链至低于随机试验预期的水平。 海滨通道这些和其他实验观察表明，手性驱动的非随机 Topo II的作用机制。许多实验和理论研究已经解决了这些问题 问题.然而，对拓扑异构酶II的机制仍然缺乏明确的了解。我们的长期目标是 为拓扑II的拓扑简化机理找到了一个精确的模型。我们在这里关注 DNA解结的过程我们的目标是验证topo II是否有能力解开DMA在 最小的可能数量的链通道，或者是否手性偏置结合其他局部 这些信息足以达到实验观察到的解结水平。我们提出了一个 涉及基于数学结的复杂理论框架的跨学科方法 理论和Monte Carlo计算机模拟，并随后进行实验验证。计算机 该实现是基于一种新颖思想， 解结的计算模型 与公共卫生的相关性：我们的方法将使我们能够有效地模拟野生型topo II DNA结的分布除了具有理论意义外，这种建模还与公众相关 健康解结分析用于抗癌药物的设计，以识别新的拓扑异构酶II抑制剂。 我们的工作将被应用于定量的解结能力的拓扑结构II的一个给定的有机体， 并且不存在抑制剂，从而建立抑制剂的精确测量。 有效性

Type II topoisomerases are essential enzymes common to all organisms. Their cellular functions include maintaining the levels of chromosome compaction and ensuring proper segregation at cell division. In addition they are often used as targets for antimicrobial agents and anticancer drugs. Understanding the process by which topoisomerase II (topo II) simplifies the topological complexity of its DMA substrate is of key importance. By a cut-and-paste mechanism, which is well understood at the molecular level, topo II is able to pass a DMA segment through another. How topo II recognizes the two DMA segments is still unclear. Topo II is known to unknot and decatenate DMA to levels below those expected by random strand-passage. These and other experimental observations suggest a chirality-driven non-random mechanism of topo II action. Numerous experimental and theoretical studies have addressed these questions. However a clear picture of the mechanism of topo II is still lacking. Our long-term goal is to find an accurate model for the mechanism of topology simplification by topo II. We here focus on the process of DNA unknotting. Our objective is to verify whether topo II has the ability to unknot DMA in the smallest possible number of strand-passages, or whether a chirality bias combined with other local information are sufficient to reach the experimentally observed unknotting levels. We propose an interdisciplinary approach involving a sophisticated theoretical framework based on mathematical knot theory and Monte Carlo computer simulations, and followed by experimental validation. The computer implementation is based on a novel idea which will greatly reduce computation time as compared to other computational models of unknotting. Relevance to Public Health: Our method will give us the ability to efficiently simulate wild-type topo II on any distribution of DNA knots. Besides being of theoretical interest, such modeling is relevant to public health. Unknotting assays are used in the design of anti-cancer drugs to identify new topo II inhibitors. Our work will be applied to quantifying the unknotting capabilities of the topo II of a given organism with and without the presence of an inhibitor, thus establishing a precise measure of the inhibitor's effectiveness.