SEQUENCE-SPECIFIC RECOGNITION OF DNA BY A DIMER MOTIF

二聚体基序对 DNA 的序列特异性识别

• 批准号: 6613735
• 负责人: W David Wilson
• 金额: $ 19.31万
• 依托单位: GEORGIA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-07-01 至 2005-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6613735
• 关键词: DNA binding protein; DNA footprinting; X ray crystallography; amidines; benzimidazoles; biophysics; chemical synthesis; covalent bond; dimer; furans; heterocyclic compounds; intermolecular interaction; model design /development; molecular dynamics; mutant; nuclear magnetic resonance spectroscopy; nucleic acid sequence; nucleic acid structure; physical model; structural biology

As part of a drug discovery group to develop anti-opportunistic infection agents that are targeted to DNA-protein complexes, Dr. Wilson has developed unfused aromatic dications that bind in the DNA minor groove. Two of these compounds are now entering clinical trials. An additional exciting discovery from the minor-groove research is that one of the new compounds, a diamidine with a phenyl-furan-benzimidazole ring system (DB293), binds to mixed AT/GC sequences in DNA as a dimer. Initial NMR, DNAse I footprinting, and surface plasmon resonance results clearly support the hypothesis that DB293 binds in the minor groove at specific GC containing sequences of DNA in a highly cooperative manner as a stacked dimer. Previous studies have suggested that such complexes are not possible with dications and neither of the symmetric analogs of DB293 bind significantly to GC sequences. This proposal is built around the hypothesis that DB293 recognizes both strands of DNA and provides a new paradigm for design of compounds for recognition of specific DNA sequences. Such a recognition motif would require reevaluation of ideas on the limits for small molecule-DNA recognition. The general goal of the proposed research is to fully characterize the dimer-DNA binding motif and to develop models that will allow us to extend the mode to additional DNA sequences. A complementary approach utilizing biophysical and synthetic methods will be used to thoroughly characterize the dimer recognition mechanism. Information on the initial dimer complexes will then be used to design, synthesize and characterize the DNA interaction of new compounds with modified and/or extended dimer-DNA sequence recognition capability. Four specific aims will allow Dr. Wilson to achieve these goals: Aim 1: Determine the structural details of the DB293-dimer DNA complex by 2D NMR and x-ray methods if crystals can be obtained. Aim 2: Prepare analogs of DB293 and characterize their DNA interactions to determine what features of the molecular structure are essential for formation of the dimer motif. Aim 3: Modify the DB293-DNA dimer recognition sequence to determine what effect base pair changes have on dimer recognition and affinity. Aim 4: Use all of this information to define the dimer recognition rules for DB293.

作为发展反向运动的药物发现小组的一部分 威尔逊博士有针对DNA蛋白复合物的感染剂 开发的未使用的芳族散布在DNA小凹槽中结合。两个 这些化合物现在正在进入临床试验。另一个令人兴奋的 从次要研究中发现的是，其中一种是新化合物，一种 二氨基二氨基苯二氮唑唑环系统（DB293）与混合 DNA中的AT/GC序列作为二聚体。最初的NMR，DNase I足迹和 表面等离子体共振结果明显支持DB293的假设 在特定的GC中结合含DNA序列的特定GC。 高度合作的方式作为堆叠二聚体。先前的研究表明 这种复合物是不可能的 DB293的对称类似物与GC序列显着结合。该提议是 围绕DB293识别DNA链和 为设计特定DNA的化合物设计提供了新的范式 序列。这样的识别主题将需要重新评估关于 小分子-DNA识别的极限。拟议的一般目标 研究是为了充分表征二聚体-DNA结合基序并发展 将使我们能够将模式扩展到其他DNA序列的模型。一个 将使用生物物理和合成方法的补充方法 彻底表征二聚体识别机制。有关 然后，初始二聚体复合物将用于设计，合成和 表征新化合物与修改和/或扩展的新化合物的DNA相互作用 二聚体-DNA序列识别能力。四个具体目标将允许博士 威尔逊要实现这些目标：目标1：确定 DB293-DIMER DNA复合物通过2D NMR和X射线方法，如果可以是晶体 获得。目标2：准备DB293的类似物并表征其DNA 相互作用以确定分子结构的哪些特征 形成二聚体基序所必不可少的。 AIM 3：修改DB293-DNA二聚体 识别顺序以确定碱基对变化对二聚体的影响 认可和亲和力。目标4：使用所有这些信息来定义 DB293的二聚体识别规则。