THEORETICAL ANALYSIS OF DNA SUPERHELICAL EQUILIBRIA

DNA超螺旋平衡的理论分析

• 批准号: 2459436
• 负责人: CRAIG J. BENHAM
• 金额: $ 16.46万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 1993
• 资助国家: 美国
• 起止时间: 1993-08-01 至 2000-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2459436
• 关键词: DNA; DNA damage; DNA replication origin; analytical method; centromere; chemical stability; chemical structure function; computer assisted sequence analysis; computer program /software; computer simulation; conformation; fungal genetics; gene mutation; genetic regulatory element; genetic transcription; mathematical model; method development; nucleic acid denaturation; nucleic acid sequence; nucleic acid structure; open reading frames; statistics /biometry; temperature; thermodynamics; virus genetics

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.

本研究计划将应用先前的理论方法 由该研究人员开发用于分析链分离 超螺旋基因组DNA序列。之前的强关联 发现在应力诱导双链体不稳定（SIDD）位点和 对特定类型的监管区域进行深入调查。 许多额外的 DNA 序列将被分析以确定 SIDD 与转录活性区域、复制相关的特性 起源、着丝粒、突变热点、染色体断点和 其他生物活性位点。每个的统计显着性 协会将被评估。目前的理论方法将是 扩展到治疗目前无法分析的以下病例： 1）长DNA，其中由超螺旋引起的拓扑耦合 可能受到核小体缠绕的限制，2) 诱导的双链体不稳定 通过转录因子等分子的近端结合，3) 对局部序列修饰的转换行为的影响，例如 甲基化或错配碱基，或无碱基位点，以及 4) 竞争 变性和其他转变之间的特定局部DNA 序列是敏感的，例如十字形挤出或过渡 Z-或H-形式。蒙特卡罗方法将用于分析 B 型 DNA 在高温下的稳定性 超螺旋。与 Richard Fye 博士的现有合作， 专注于 DNA 分析理论方法的发展 超螺旋平衡，将继续。与两人合作 实验小组将研究超螺旋的热力学 DNA 构象转变及其在转录中发挥的作用。