Theoretical Aspects of DNA Supercoiling

描述（由申请人提供）：该研究将计算机模拟（能量优化/扩展技术、蒙特卡罗计算和正态分析）与一种新的自然离散的DMA模型结合起来，研究超螺旋DMA的结构和性质，这是一种受高阶折叠和补偿链扭曲约束的双螺旋结构的拓扑形式，以及DMA在活细胞中的存在方式。长，线状聚合物的碱基序列依赖特征被纳入理论并通过数值模拟处理。通过将分析研究与计算机模拟相结合，我们获得了互补的信息，并有一系列内置的检查和平衡来评估我们发现的重要性。计算结果刺激了新的理论发展，反过来又可以用来评估计算的有效性。糖-磷酸主链和局部化学环境的影响隐含地通过从双螺旋DMA的高分辨率结构中提取的基于知识的电位来处理，并且在有代表性的情况下，通过明确地处理远程力。我们的直接目标是研究序列依赖的DMA微环和环的生物物理特性，并建立体内环的物理化学基础。提出的研究旨在阐明主要化学特征（碱基序列），配体结合（蛋白质）和超卷曲水平（对碱基对定位施加限制）在双螺旋整体折叠中的作用。我们将扩展我们对连接在Lac抑制蛋白上的DMA环的研究，目的是收集关于分子组装在转录调节中的作用及其作为真核绝缘体模型的潜在适用性的新见解。第二个目标是深入了解DMA序列和超卷曲对蛋白质结合和随之产生的细胞功能的影响。其他需要解决的问题包括：(1)局部序列依赖结构和配体结合在空间受限双链的大规模构型转变中的作用；(2)多种蛋白质对超卷曲分子构型特性的竞争效应；(3)超线圈动力学中局部结构与全局结构的相互作用。

DESCRIPTION (provided by applicant): The research combines computer simulation (energy optimization/expansion techniques, Monte-Carlo calculations, and normal-mode analysis) with a new naturally discrete model of DMA to 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 DMA exists in living cells. Base sequence-dependent features 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 DMA and, 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 DMA sequence 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.