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: 6163488
• 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 2004-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6163488
• 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.

作为药物发现小组的一部分，开发反机会主义 针对DNA-蛋白质复合体的感染剂，威尔逊博士 形成了结合在DNA小槽中的未融合的芳香族化合物。其中两个 这些化合物现在正在进行临床试验。另一件令人兴奋的事 次要凹槽研究的发现是其中一种新化合物，一种 联胺具有苯基-呋喃-苯并咪唑环系(DB293)，与混合物结合 DNA中的AT/GC序列为二聚体。初始核磁共振、DNase I足迹和 表面等离子体共振结果清楚地支持了DB293的假设 在含有DNA序列的特定GC处结合在小沟中 高度合作的方式作为堆叠二聚体。此前的研究表明， 这样的复合体是不可能有口述的，而且两个 DB293的对称类似物与GC序列显著结合。这项建议是 建立在DB293识别DNA和DNA链的假设基础上 为设计识别特定DNA的化合物提供了一种新的范例 序列。这样的承认主题将需要重新评估关于 小分子的极限--DNA识别。建议的总体目标是 研究是充分表征二聚体-DNA结合基序并开发 这些模型将允许我们将模式扩展到额外的DNA序列。一个 将使用利用生物物理和合成方法的互补方法 深入研究二聚体的识别机制。有关的资料 然后，初始二聚体络合物将用于设计、合成和 表征具有修饰和/或扩展的新化合物的DNA相互作用 二聚体-DNA序列识别能力。四个具体的目标将允许博士。 威尔逊为实现这些目标：目标1：确定 DB293-二聚体DNA络合物的二维核磁共振和X-射线分析 获得。目的2：制备DB293类似物并鉴定其DNA 相互作用，以确定分子结构的哪些特征 对形成二聚体基序是必不可少的。目的3：修饰DB293-DNA二聚体 确定碱基对变化对二聚体有什么影响的识别序列 认可度和亲和力。目标4：使用所有这些信息来定义 DB293的二聚体识别规则。