TOPOLOGY GEOMETRY AND ENERGETICS OF CLOSED CIRCULAR DNA

这项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，重点将是 超螺旋DNA三维结构的测定 作为链接数的函数；在预测 沿路相隔相当远的局部线段 DNA的轮廓；以及在阐明对DNA的影响时 蛋白质表面包裹的结构。具体目标是有分歧的 分为五个类别。(1)三级结构描述 超螺旋DNA。本项目采用有限元方法，从 非线性结构力学，能量最小化用于 预测每个链接数的最稳定构型。《扭曲》 和扭度将被计算，结果将被用来预测 闭合DNA的流体力学行为及其平衡分布 拓扑异构体。(2)超螺旋DNA螺旋重复序列的测定。 这涉及对卷绕数量的影响的测量 将定义的回文序列挤压成十字形和有限的 在适度高温下局部变性。(3)局部效应 闭合DNA中长程扩散的结构元素。这一目标 就是确定DNA局部结构对长程 扩散。特定部位的重组扩散步骤将被用作 一种分析工具。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。 将计算闭合圆形的缠绕扭度和曲面扭转度 DNA存在于各种几何形状的一系列相连的蛋白质上。这个 Writhe将被分析成它的分段组件并进入Conn- 由于两两相互作用而产生的贡献，包括 蛋白质复合体，连接区之间和蛋白质之间 复合体和连接区。(5)蛋白质包装对果肉品质的影响 闭合环状DNA的拓扑性质其后果是 将包裹的蛋白质的连接数、闭合的环状DNA分解成 将在中检查表面连接数和缠绕数之和 细节。松弛的微染色体的缠绕数将被测量为 温度的函数，以确定 热效应进入包装和缠绕组件，然后是 测定作为超螺旋密度的函数的phi，以便 检验核小体扭曲是由核小体数目增加引起的假设 超级卷曲的程度。

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.