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.

该研究计划将以前采用理论方法 该研究者开发了分析链分离的 超螺旋基因组DNA序列。强大的联想以前 在压力引起的双甲化稳定部位（SIDD）和 特定类型的监管区域将进行彻底研究。 将分析许多其他DNA序列以确定SIDD 与转录活性区域相关的属性，复制 起源，中心粒，突变热点，染色体断点和 生物活性的其他部位。每个的统计意义 协会将进行评估。目前的理论方法将是 扩展以治疗以下情况当前无法分析的情况： 1）长DNA，其中拓扑耦合由超螺旋诱导 可能受到核小体绕组的限制，2）双链动稳定诱导的 通过分子（例如转录因子）的近端结合，3） 对局部序列修改的过渡行为的影响，例如 甲基化或误导的基地或无碱性地点，以及4）竞争 在变性与其他特定局部DNA的过渡之间 序列是易感的，例如十字形的挤出或过渡到 z-或h形式。蒙特卡洛方法将用于分析 在高温下稳定B形式DNA 超螺旋。与理查德·菲（Richard Fye）博士的现有合作 着重于分析DNA的理论方法的发展 超螺旋均衡将继续。与两个合作 实验组将研究超螺旋的热力学 DNA构象转变及其在转录中扮演的角色。