THEORETICAL ANALYSIS OF DNA SUPERHELICAL EQUILIBRIA

本研究计划将应用以前的理论方法 本研究者开发的用于分析 超螺旋基因组DNA序列。以前的强关联 在应激诱导的双链体不稳定（SIDD）位点之间发现， 将对特定类型的监管区域进行彻底调查。 将分析许多额外的DNA序列以确定SIDD 与转录活性区相关的性质，复制 起源，着丝粒，突变热点，染色体断裂点和 其他生物活动场所。每项的统计学显著性 协会将进行评估。目前的理论方法将是 扩展到治疗以下目前不适合分析的病例： 1)长DNA中的拓扑耦合诱导的超螺旋 可能受到核小体缠绕的限制，2）双链体不稳定诱导 通过转录因子等分子的近端结合，3） 对局部序列修饰的过渡行为的影响， 甲基化或错配的碱基，或无碱基位点，和4）竞争 在变性和其他特定的局部DNA 序列易受影响，如十字形挤出或过渡到 Z-或H-形式。蒙特卡罗方法将用于分析 在高温下B型DNA的稳定性 超螺旋与Richard Fye博士的现有合作， 专注于发展分析DNA的理论方法 超螺旋平衡，将继续。与两个合作 实验组，将研究超螺旋的热力学 DNA构象转换，以及它们在转录中的作用。

This research program will apply the theoretical methods previously developed by this investigator to the analysis of strand separation in superhelical genomic DNA sequences. The strong associations previously found between sites of stress-induced duplex destabilization (SIDD) and specific types of regulatory regions will be investigated thoroughly. Many additional DNA sequences will be analyzed to determine the SIDD properties associated to transcriptionally active regions, replication origins, centromeres, mutational hotspots, chromosomal breakpoints and other sites of biological activity. The statistical significance of each association will be assessed. The present theoretical methods will be extended to treat the following cases not currently amenable to analysis: 1) long DNAs in which the topological coupling induced by superhelicity may be limited by nucleosomal winding, 2) duplex destabilization induced by the proximal binding of molecules such as transcription factors, 3) effects on transition behavior of local sequence modifications such as methylated or mispaired bases, or abasic sites, and 4) competitions between denaturation and other transitions to which specific local DNA sequences are susceptible, such as cruciform extrusion or transition to Z- or to H-form. Monte Carlo methods will be used to analyze the stabilization of B-form DNA at high temperatures by positive supercoiling. The existing collaboration with Dr. Richard Fye, which focuses on the development of theoretical methods to analyze DNA superhelical equilibria, will be continued. Collaborations with two experimental groups, will investigate the thermodynamics of superhelical DNA conformational transitions, and the roles they play in transcription.