THEORETICAL ANALYSIS OF DNA SUPERHELICAL EQUILIBRIA

DNA超螺旋平衡的理论分析

• 批准号: 2749897
• 负责人: CRAIG J. BENHAM
• 金额: $ 16.62万
• 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/2749897
• 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.

本研究项目将应用前面的理论方法 由这位研究人员发展到分析链分离在 超螺旋基因组DNA序列。以前的强烈联想 在应激诱导的双链失稳(SIDD)和 将对特定类型的监管地区进行彻底调查。 许多额外的DNA序列将被分析以确定SIDD 与转录活性区域、复制相关的属性 起源、着丝粒、突变热点、染色体断裂点和 其他生物活性场所。每项指标的统计意义 将对协会进行评估。目前的理论方法将是 扩大到治疗目前无法分析的下列案件： 1)其中由超螺旋引起的拓扑耦合的长DNA 可能受到核小体卷曲的限制，2)诱导的双链失稳 通过转录因子等分子的近端结合，3) 局部序列修改对转换行为的影响，例如 甲基化或错配碱基，或基本位点，以及4)竞争 在变性和其他转变之间，特定的局部DNA 序列易受影响，例如十字形挤压或过渡到 Z形或H形。蒙特卡罗方法将被用来分析 正极在高温下稳定B型DNA的研究 超级卷曲。与理查德·费伊博士现有的合作， 专注于分析DNA的理论方法的发展 超螺旋平衡，将继续下去。与两家公司合作 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所起的作用。