TOPOLOGY GEOMETRY AND ENERGETICS OF CLOSED CIRCULAR DNA

本研究的总体目标是了解结构和 超螺旋DNA的动力学在下一个项目期间， 确定超螺旋DNA的三维结构 作为链接数的函数;在预测 沿着沿着 DNA的轮廓;并在阐明对DNA的影响后， 包裹在蛋白质表面的结构。具体目标分为 分为五类。(1)三级结构描述 超螺旋DNA本项目采用有限元法， 非线性结构力学，能量最小化被用来 预测每个连接数处的最稳定构型。扭动 和扭曲将被计算，结果将被用来预测 封闭DNA的流体动力学行为和平衡分布 拓扑异构体(2)超螺旋DNA螺旋重复序列的测定。 这涉及到测量的影响，对绕组数量， 将确定的回文序列挤压成十字形， 在适度升高的温度下局部变性。(3)当地的影响 在封闭的DNA中长距离扩散的结构元素。这一目标 是确定DNA局部结构对长距离 扩散位点特异性复合扩散步骤将被用作 分析工具。弯曲DNA序列以及蛋白质诱导的弯曲DNA 将使用序列。(4)DNA包裹在分段光滑的表面上。 将计算闭合圆的缠绕和表面扭曲 一系列不同几何形状的蛋白质上的DNA。的 文字将被分析为其分段组成部分和控制部分。 由于成对相互作用，包括 蛋白质复合物之间、连接体区域之间以及蛋白质 复合物和接头区。(5)蛋白质包裹对 闭合环状DNA的拓扑性质的后果 将蛋白质包裹的闭合环状DNA的连接数分解成 表面连接数和缠绕数的总和将在 详细将测量松弛的微型染色体的缠绕数， 温度的函数，以确定 热效应到包装和绕组组件，其次是一个 确定φ作为超螺旋密度的函数，以便 检验核小体畸变是由于 超螺旋的程度

The general objective of this research is to understand the structure and dynamics of supercoiled DNA. During the next project period emphasis will be upon determination of the three dimensional structure of supercoiled DNA as a function of the linking number; upon prediction of the interaction of local segments that are separated by a considerable distance along the contour of the DNA; and upon elucidation of the effects on the DNA structure of wrapping on a protein surface. The specific aims are divided into five categories. (1) Description of the tertiary structure of supercoiled DNA. This project applies the finite element method from nonlinear structural mechanics, with energy minimization being used to predict the most stable configuration at each linking number. The writhe and twist will be calculated, and the results will be used to predict the hydrodynamic behavior of closed DNA and the equilibrium distribution of topoisomers. (2) Determination of the helical repeat of supercoiled DNA. This involves measurement of the effect upon the winding number of extrusion of defined palindromic sequences into cruciforms and of limited local denaturation at moderately elevated temperatures. (3) Effect of local structural elements on long range diffusion in closed DNA. This objective is to determine the effects that DNA local structures have upon long-range diffusion. The site-specific recombination diffusion step will be used as an analytical tool. Bent DNA sequences as well as protein-induced bent DNA sequences will be employed. (4) DNA wrapped on piecewise smooth surfaces. Writhe and surface twist will be calculated for wrapping of closed circular DNA on a connected series of proteins of various geometric shapes. The writhe will be analyzed into its piecewise components and into the con- tributions due to pairwise interactions, including those between the protein complexes, between the linker regions, and between the protein complexes and the linker regions. (5) Effect of protein wrapping upon the topological properties of closed circular DNA. The consequences of decomposing the linking number of protein wrapped, closed circular DNA into the sum of the surface linking and winding numbers will be examined in detail. The winding number will be measured for relaxed minichromosomes as a function of temperature, in order to determine the partition of the thermal effects into wrapping and winding components, followed by a determination of phi as a function of the superhelix density, in order to test the hypothesis that nucleosome distortion results from increases in the extent of supercoiling.