THEORETICAL ANALYSIS OF DNA SUPERHELICAL EQUILIBRIA

这项研究计划将开发出准确的理论方法 超螺旋DNA分子的二级结构平衡分析 千碱基长度和指定的序列，其中所有的转换 序列易受其影响的竞争。其中包括B-Z 过渡、十字拉伸、B-H过渡和股 分离。还将开发处理局部序列的方法 已知在实践中发生的影响，使 跃迁和平衡的计算。例子包括化学品 碱基配对的加合物、碱性位点或其他干扰，以及不完全的 易受影响的序列，如不精确的反向重复对称或 嘌呤-嘧啶交替反应。基于蒙特卡罗技术的方法 将为超螺旋二级结构的分析开发 高温或超长DNA序列中的转变 (约105个碱基对)。蒙特卡罗方法也将是 用于分析过渡和弯曲之间的相互作用 超螺旋DNA分子中的变形。过渡态理论 超螺旋跨构象反应的动力学将是 根据现有数据进行开发和测试。与多家公司合作 实验小组将阐明超螺旋DNA 构象转换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 复制启动中的分离；2)通过以下机制 超螺旋增强DNA对x-DNA单链断裂的敏感性 射线；3)端粒上的超螺旋十字形形成 序列及其在复制中的作用。发展起来的分析技术 在这项研究中，将用来从实验数据中推导出 重要的能量和构象参数决定了 超螺旋跃迁。序列修改的影响和 在超螺旋跃迁的能量学上将会发现不完善之处 在几个具体的案例中。这些将包括确定影响 在十字形挤压上违反了完美的反向重复对称性， 碱基甲基化对链分离的影响及能量学 在含有碱性中心或化学物质的分子中的链分离 加合物。将为以下对象计算过渡和不稳定配置文件 多种DNA来确定局部对特定基因的敏感性 转变与调控区域、突变热点、 染色体断裂点和其他生物活性部位。

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.