Computer Analysis of DNA Unknotting by Topoisomerase (pilot)

拓扑异构酶 DNA 解结的计算机分析（中试）

• 批准号: 7229137
• 负责人: Mariel Vazquez
• 金额: $ 7.5万
• 依托单位: SAN FRANCISCO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-01-01 至 2010-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7229137
• 关键词: Address; Anti-Bacterial Agents; Antineoplastic Agents; Arts; Bacterial Typing; Bacteriophages; Biological Assay; Capsid; Catenanes; Cell Death; Cell division; Cell physiology; Cells; Chromosomes; Circular DNA; Computer Analysis; Computer Simulation; Computers; Count; DNA; DNA Topoisomerase IV; Data; Effectiveness; Electron Microscopy; Ensure; Environment; Enzymes; Equilibrium; Eukaryotic DNA Topoisomerases II; Funding; Goals; Human; International; Lead; Length; Life; Mathematics; Measures; Mentors; Methods; Modeling; Molecular; Molecular Biology; Monte Carlo Method; Numbers; Organism; Paste substance; Pathway interactions; Personal Satisfaction; Physics; Polymers; Process; Public Health; Recording of previous events; Reporting; Research; Research Personnel; Resources; Role; Sampling; Scientist; Simulate; Solutions; Students; Techniques; Testing; Theoretical Studies; Time; Topoisomerase; Topoisomerase II; Topoisomerase-II Inhibitor; Two-Dimensional Gel Electrophoresis; Underrepresented Minority; Validation; Woman; Work; Yeasts; antimicrobial drug; base; catenane; design; inhibitor/antagonist; innovation; interdisciplinary approach; interest; novel; research study; segregation; simulation; success; theories

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.

II 型拓扑异构酶是所有生物体共有的必需酶。它们的细胞功能包括 维持染色体压缩水平并确保细胞分裂时适当分离。在 此外，它们还经常被用作抗菌剂和抗癌药物的靶标。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是 关键重要性。通过在分子水平上充分理解的剪切和粘贴机制，拓扑 II 是 能够将一个 DMA 段传递到另一个段。 topo II如何识别这两个DMA段仍然是 不清楚。已知 Topo II 可以将 DMA 解开并串联至低于随机预期的水平 链通道。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，对于拓扑异构酶II的机制仍然缺乏清晰的认识。我们的长期目标是 通过 topo II 找到拓扑简化机制的准确模型。我们这里重点关注的是 DNA解结过程。我们的目标是验证 topo II 是否有能力解开 DMA 尽可能少的链通道数，或者手性偏差是否与其他局部相结合 信息足以达到实验观察到的解结水平。我们提出一个 涉及基于数学结的复杂理论框架的跨学科方法 理论和蒙特卡罗计算机模拟，然后进行实验验证。电脑 实现基于一种新颖的想法，与其他方法相比，它将大大减少计算时间 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模拟野生型拓扑结构 II DNA 结的任意分布。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，以鉴定新的拓扑 II 抑制剂。 我们的工作将应用于量化给定生物体的拓扑 II 的解结能力 并且在不存在抑制剂的情况下，从而建立了抑制剂的精确测量 效力。