Theoretical Aspects of DNA Supercoiling

DNA 超螺旋的理论方面

• 批准号: 7932644
• 负责人: Wilma K Olson
• 金额: $ 19.11万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7932644
• 关键词: Accounting; Address; Bacterial Chromosomes; Base Pairing; Base Sequence; Binding; Binding Proteins; Biochemical; Biological Models; Biological Process; Cell physiology; Cells; Chemicals; Chromatin; Chromatin Loop; Chromosomes; Complex; Computational Technique; Computer Simulation; Coupling; Cyclization; DNA; DNA Folding; DNA Sequence; Data; Development; Environment; Enzymes; Equation; Equilibrium; Gene Expression; Goals; HU Protein; Investigation; Knowledge; Learning; Length; Life; Ligand Binding; Link; Location; Measures; Mediating; Metabolism; Modeling; Modification; Molecular; Nature; Nucleosomes; Nucleotides; Pattern; Plasmids; Polymers; Positioning Attribute; Property; Protein Binding; Proteins; Publishing; Qualifying; Research; Resolution; Role; Series; Shapes; Site; Stress; Structure; Sugar Phosphates; Superhelical DNA; System; Techniques; Test Result; Testing; Therapeutic; Time; Transcriptional Regulation; Vertebral column; Viral Genome; Work; base; design; ds-DNA; endodeoxyribonuclease EcoRV; enzyme activity; human disease; in vivo; insight; knowledge base; molecular assembly/self assembly; novel; physical property; retinal rods; simulation; theories; three dimensional structure; treatment strategy

The research combines computer simulation (energy optimization/expansion techniques, Monte-Carlo calculations, and normal-mode analysis) with a new naturally discrete model of DMAto examine the configurations and properties of supercoiled DMA,a topologically constrained form of the double helix subject to higher-order folding and compensatory strand twisting and the way that DMAexists in living cells. Base sequence-dependentfeatures of the long, threadlike polymer are incorporated in the theory and treated by numerical simulations. By combining analytical studies with computer simulations, we obtain complementary information and have a series of built-in checks and balances for assessing the significance of our findings. The computational results stimulate new theoretical developments, which in turn can be used to assess the validity of the calculations. The effects of the sugar-phosphate backbone and local chemical environment are treated implicitly with knowledge-based potentials extracted from high-resolution structures of double-helical DMAand, in representative cases, with explicit treatment of long-range forces. Our immediate goals are to study the sequence-dependent biophysical properties of DMA minicircles and loops and to establish the physico-chemical basis of in-vivo looping. The proposed studies aim to clarify the role of primary chemical features (base sequence), ligand binding (proteins), and levels of supercoiling (imposed constraints on base-pair positioning) on the overall folding of the double helix. We will extend our studies of DMA loops tethered to the Lac represser protein with the aim of gathering new insights into the role of the molecular assembly in the regulation of transcription and its potential applicability as a model of eukaryotic insulators. A second goal is to gain insight into the effect of DMAsequence and supercoiling on protein binding and consequent cellular function. Other issues to be addressed include: (1) the role of local sequence-dependent structure and ligand binding on large-scale configurational transitions of spatially constrained duplexes; (2) the competing effects of multiple proteins on the configurational properties of supercoiled molecules; and (3) the interplay of local and global structure in supercoiling dynamics.

这项研究结合了计算机模拟(能量优化/扩展技术、蒙特卡罗 计算和简正模分析)使用新的自然离散的DMA模型来检验 拓扑约束的双螺旋结构--超螺旋DMA的构型和性质 受制于高阶折叠和补偿性链扭曲以及活细胞中的DNA存在方式。 长的线状聚合物的碱基序列依赖的特征被结合在理论和 经过数值模拟处理。通过将分析研究与计算机模拟相结合，我们获得了 补充信息，并有一系列内置的制衡机制，用于评估重要性 我们的发现。计算结果刺激了新的理论发展，这反过来又可以 用于评估计算的有效性。糖-磷酸主链和局部的影响 用从高分辨率提取的基于知识的势来隐式处理化学环境 双螺旋DMA的结构，并在典型情况下，明确处理长程力。 我们的近期目标是研究DMA小环与序列相关的生物物理性质 并建立体内循环的物理化学基础。建议的研究旨在澄清 主要化学特征(碱基序列)、配体结合(蛋白质)和超螺旋水平的作用 (对碱基对定位施加限制)对双螺旋的整体折叠产生影响。我们将延长我们的 研究与Lac抑制蛋白相关的DMA环，目的是收集对 分子组装在转录调控中的作用及其作为模型的潜在适用性 真核绝缘体。第二个目标是深入了解DMA序列和超线圈对 蛋白质结合和由此产生的细胞功能。其他需要解决的问题包括：(1)地方政府的作用 大尺度空间构型跃迁的序列依赖结构和配基结合 限制双链；(2)多个蛋白质对构型性质的竞争影响 超螺旋分子；(3)局部结构和全局结构在超螺旋动力学中的相互作用。