Theoretical Aspects of DNA Supercoiling

该研究结合了计算机模拟（能量优化/扩展技术，蒙特-卡罗 计算，和正常模式分析）与一个新的自然离散模型的DMA检查 超螺旋DMA的构型和性质，双螺旋的拓扑约束形式 受到高阶折叠和补偿链扭曲和DMA存在于活细胞中的方式的影响。 长的线状聚合物的碱基序列依赖性特征被纳入理论， 通过数值模拟进行处理。通过分析研究与计算机模拟相结合，我们得到 补充资料，并有一系列内置的检查和平衡，以评估的重要性 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-磷酸骨架和局部的影响 化学环境处理隐式与知识为基础的潜力提取的高分辨率 双螺旋DMA结构，并在代表性的情况下，明确治疗的长程力。 我们的近期目标是研究DMA微环的序列依赖性生物物理特性， 环，并建立体内成环的物理化学基础。拟议的研究旨在澄清 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的影响。我们将扩大我们的 研究DMA环拴在Lac阻遏蛋白的目的是收集新的见解， 分子组装在转录调控中的作用及其作为转录调控模型的潜在适用性 真核绝缘体第二个目标是深入了解DMA序列和超螺旋对 蛋白质结合和随后的细胞功能。其他有待解决的问题包括：（1）地方政府的作用 序列依赖结构和配体结合对大规模空间构型转变的影响 限制性双链体;（2）多个蛋白质的竞争效应对构象特性的影响， 超螺旋分子;（3）超螺旋动力学中局部和全局结构的相互作用。

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.