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: 6387193
• 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/6387193
• 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.

作为一个药物发现小组的一部分， 针对DNA-蛋白质复合物的感染剂，威尔逊博士 发展了结合在DNA小沟中的未稠合的芳香二价阳离子。两 这些化合物目前正进入临床试验阶段。另一个令人兴奋的 小沟研究的发现是，一种新的化合物， 联脒与苯基呋喃苯并咪唑环系统（DB293），结合到混合 DNA中的AT/GC序列作为二聚体。初始NMR，DNA酶I足迹，和 表面等离子体共振结果清楚地支持DB293 结合在小沟中的特定GC含有DNA序列， 高度协同的方式作为堆叠的二聚体。以前的研究表明 这样的复合体是不可能的， DB293的对称类似物与GC序列显著结合。这项建议是 DB293可以识别DNA的两条链， 为设计识别特定DNA的化合物提供了新的范例 序列的这样一个承认的主题将需要重新评估关于 小分子DNA识别的极限。建议的总目标 研究的目的是充分表征二聚体-DNA结合基序， 这些模型将允许我们将该模式扩展到其他DNA序列。一 将使用利用生物物理和合成方法的补充方法 以彻底表征二聚体识别机制。信息 然后将初始二聚体复合物用于设计、合成和 表征新化合物与修饰的和/或延伸的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。 威尔逊实现这些目标：目标1：确定结构的细节， 如果晶体可以，通过2D NMR和X射线方法测定DB293-二聚体DNA复合物 得到了目的2：制备DB293类似物并表征其DNA 相互作用来确定分子结构的特征 对于二聚体基序的形成至关重要。目的3：修饰DB293-DNA二聚体 识别序列，以确定碱基对变化对二聚体的影响 识别和亲和力。目标4：使用所有这些信息来定义 DB293的二聚体识别规则。