THEORETICAL ANALYSIS OF DNA SUPERHELICAL EQUILIBRIA

DNA超螺旋平衡的理论分析

• 批准号: 2184482
• 负责人: CRAIG J. BENHAM
• 金额: $ 11.02万
• 依托单位: MOUNT SINAI SCHOOL OF MEDICINE OF CUNY
• 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 1996-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2184482
• 关键词: DNA; DNA damage; DNA methylation; DNA replication; DNA replication origin; analytical method; artificial intelligence; chemical kinetics; chemical structure function; computer assisted sequence analysis; computer data analysis; computer simulation; conformation; mathematical model; method development; model design /development; molecular size; nucleic acid sequence; nucleic acid structure; radiation genetics; structural biology; telomere; thermodynamics; virus genetics

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.

该研究计划将开发准确的理论方法 分析超螺旋DNA分子中的二级结构平衡 千个酶长度和指定序列，其中所有过渡 竞争序列易感的。 这些包括B-Z 过渡，十字形挤出，B-H过渡和链 分离。 还将开发用于处理本地序列的方法 效果，已知在实践中发生，使能量学复杂化 过渡和平衡的计算。 例子包括化学 加合物，无asic网站或基本配对的其他干扰和不完美 易感序列，例如不精确的反复对称性或 嘌呤 - 吡啶胺的交替。 基于蒙特卡洛技术的方法 将开发用于分析超螺旋二级结构 高温或极长的DNA序列的过渡 （大约105个碱基对）。 蒙特卡洛方法也将是 开发用于分析过渡与弯曲之间的相互作用 超螺旋DNA分子的变形。 过渡状态理论 超螺旋透射反应的动力学将是 根据可用数据开发和测试。 与几个合作 实验组将阐明超螺旋DNA的角色 构象转变在正常和病理过程中发挥作用。 这些包括研究：1）超螺旋链的作用 在复制开始时分离； 2）机制 超螺旋性增强了DNA对单链破裂的敏感性，x- 射线，并且； 3）在正托端粒上的超螺旋十字形形成 序列及其在复制中的作用。 开发了分析技术 在这项研究中，将用于从实验数据中推导值 重要的充满活力和构象参数 超螺旋过渡。 序列修改和 将发现有关超螺旋过渡的能量学的缺陷 在某些特定情况下。 这些将包括确定影响 在十字形挤出上违反了完美的反复重复对称性， 碱甲基化对链分离和能量学的影响 包含无碱性位点或化学的分子中的链分离 加合物。 将计算过渡和不稳定概况 各种DNA来确定当地对特定的敏感性 过渡与调节区域，突变热点相关， 染色体断点和生物活性的其他部位。