THEORETICAL ANALYSIS OF DNA SUPERHELICAL EQUILIBRIA

这项研究计划将开发准确的理论方法， 分析超螺旋DNA分子的二级结构平衡 的长度和特定的序列，其中所有的转换 序列容易受到的竞争。 其中包括B-Z 过渡、十字形拉伸、B-H过渡和线束 分居 还将开发处理局部序列的方法 已知在实践中发生的效应，使能量学复杂化， 过渡和平衡的计算。 实例包括化学 加合物、无碱基位点或碱基配对的其他破坏，以及不完全的 敏感序列如不精确的反向重复对称或 嘌呤-嘧啶交替 基于蒙特卡罗技术的方法 将被开发用于分析超螺旋二级结构 在高温下或在极长的DNA序列中的转变 （约105个碱基对）。 蒙特卡罗方法也将 用于分析过渡和弯曲之间的相互作用 超螺旋DNA分子的变形。 过渡态理论 超螺旋构象转换反应的动力学将是 并根据现有数据进行了测试。 与多个 实验小组将阐明超螺旋DNA 构象转变在正常和病理过程中起作用。 这些项目包括研究：1）超螺旋链的作用 复制起始的分离; 2） 超螺旋性增强了DNA对单链断裂的敏感性， 射线，和; 3）在正痘病毒端粒的超螺旋十字形形成 序列及其在复制中的作用。 分析技术的发展 在这项研究中，将用于从实验数据推导出的值 重要的能量和构象参数 超螺旋跃迁 序列修饰的影响， 在超螺旋跃迁的能量学上， 在几个具体的案例中。 这些将包括确定影响 十字形挤压的完美反向重复对称的违反， 碱基甲基化对链分离的影响， 指含有脱碱基位点或化学物质的分子中的链分离 加合物 转换和不稳定的配置文件将计算为 各种DNA，以确定当地的敏感性， 转换与调控区，突变热点， 染色体断裂点和其他生物活性位点。

This research program will develop accurate theoretical methods for analyzing secondary structural equilibria in superhelical DNA molecules of kilobase length and specified sequence, in which all transitions compete to which the sequence is susceptible. These include B-Z transitions, cruciform extrusions, B-H transitions, and strand separation. Methods also will be developed for handling local sequence effects, known to occur in practice, that complicate the energetics of transitions and the calculation of equilibria. Examples include chemical adducts, abasic sites or other disruptions of base pairing, and imperfect susceptible sequences such as imprecise inverted repeat symmetry or purine-pyrimidine alternation. Methods based on Monte Carlo techniques will be developed for the analysis of superhelical secondary structural transitions at high temperatures or in extremely long DNA sequences (approximately 105 base pairs). Monte Carlo methods also will be developed to analyze the interplay between transitions and bending deformations in superhelical DNA molecules. Transition state theories of the kinetics of superhelical transconformation reactions will be developed and tested against available data. Collaborations with several experimental groups will illuminate roles that superhelical DNA conformational transitions play in normal and pathological processes. These include projects examining: 1) the role of superhelical strand separation in the initiation of replication; 2) mechanisms by which superhelicity enhances DNA sensitivity to single strand breakage by x- rays, and; 3) superhelical cruciform formation at orthopoxviral telomere sequences and its role in replication. The analytic techniques developed in this research will be used to deduce from experimental data the values of important energetic and conformational parameters governing superhelical transitions. The effects of sequence modifications and imperfections on the energetics of superhelical transitions will be found in several specific cases. These will include determining the influence of violations of perfect inverted repeat symmetry on cruciform extrusion, the effects of base methylation on strand separation, and the energetics of strand separation in molecules containing abasic sites or chemical adducts. Transition and destabilization profiles will be calculated for a variety of DNAs to determine how local susceptibilities to specific transitions correlate with regulatory regions, mutational hotspots, chromosomal breakpoints and other sites of biological activity.