SHAPE SELECTIVE DNA MINOR GROOVE LIGANDS

形状选择性 DNA 小沟配体

• 批准号: 2189060
• 负责人: SEAN M KERWIN
• 金额: $ 9.42万
• 依托单位: UNIVERSITY OF TEXAS AT AUSTIN
• 依托单位国家: 美国
• 财政年份: 1994
• 资助国家: 美国
• 起止时间: 1994-04-01 至 1999-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2189060
• 关键词: DNA; RNA directed DNA polymerase; chemical binding; chemical structure function; chemical synthesis; chromatography; ligands; nucleic acid biosynthesis; nucleic acid probes; nucleic acid sequence; nucleic acid structure

This proposal details our systematic approach to the design of new, sequence selective DNA minor groove binding compounds. Our approach differs from previous approaches in that we Wi" focus on the role of ligand shape, especially width, in molecular recognition of the minor groove of double-stranded DNA. We will address two specific questions: (a) What role does shape play in the interactions of small molecules with the minor groove? (b) How can we harness the role of ligand shape to rationally design ligands with predictable sequence and biochemical selectivities? Our focus on the role of shape in minor groove molecular recognition will specifically address the issues of the relative contribution of shape vis-a-vis hydrogen bonding and electrostatic contributions to molecular recognition, and the ability of the conformationally flexible minor groove of DNA to accommodate differently shaped ligands. As an application of this knowledge, we will specifically address the issues of sequence recognition and the ability of specific ligand/DNA complexes to effect DNA-processing enzymes that make contact with the minor groove, including Human Immunodeficiency Virus Type 1 (HIV-1) reverse transcriptase. Our long term goal is to have at hand a relatively small number of individual molecular building blocks, each of which possesses a well defined DNA binding specificity. These rigid molecular building blocks can then be assembled in a rational order to construct a DNA minor groove ligand that complements not only the electrostatic and hydrogen bonding environment of a particular sequence of DNA, but also its specific three-dimensional shape. We term such shape complementary DNA minor groove binding compounds morpholexins, because they read not only the lexis or "words" of the genetic code but also the morph or "shapes" of the regions in which these words reside. Specific aims of this work include: 1. The design and synthesis of two new classes of morpholexin units. Structural features of the ligands that will be addressed are: the width, the conformational flexibility, and the hydrogen bonding and electrostatic functionality. 2. The design and synthesis of linked morpholexins. These compounds will be designed to probe two specific linking motifs: a head-to-tail amide bond linker and a head-to-head alkynyldiol linker. 3. The evaluation of the DNA binding of these morpholexins. Two specific binding characteristics will be investigated: the sequence selectivity, and the relationship between the minor groove width and flexibility, and binding site selectivity. 4. The evaluation of the effect of these morpholexins on the DNA- directed DNA polymerization reaction catalyzed by HIV-1 reverse transcriptase. Specific investigations will focus on the correlation of particular DNA binding sites with specific effects of the resulting ligand/DNA complex on the strand displacement DNA synthesis catalyzed by HIV-1 reverse transcriptase.

该提案详细介绍了我们设计新的、 序列选择性 DNA 小沟结合化合物。我们的方法 与以前的方法不同的是，我们“关注”的角色 配体形状，特别是宽度，在次要分子的分子识别中 双链DNA的凹槽。我们将解决两个具体问题： (a) 形状在小分子相互作用中起什么作用 与小凹槽？ (b) 我们如何利用配体形状的作用 合理设计具有可预测序列和生化特征的配体 选择性？我们关注形状在小沟分子中的作用 认可将专门解决相关问题 形状相对于氢键和静电的贡献 对分子识别的贡献以及 DNA构象灵活的小沟可以容纳 不同形状的配体。作为这些知识的应用，我们 将专门解决序列识别和 特定配体/DNA 复合物影响 DNA 加工的能力 与小沟接触的酶，包括人类 1 型免疫缺陷病毒 (HIV-1) 逆转录酶。我们的长 长期目标是拥有数量相对较少的个人 分子构件，每个构件都拥有明确的 DNA 结合特异性。然后可以将这些刚性分子构建块 以合理的顺序组装构建DNA小沟配体 不仅补充了静电键和氢键 特定 DNA 序列的环境，以及其特定的 三维形状。 我们将这种形状称为互补DNA小分子 沟槽结合化合物吗啉，因为它们不仅读取 遗传密码的词汇或“单词”，还有遗传密码的变形或“形状” 这些词所在的区域。这项工作的具体目标 包括： 1. 两类新吗啉单元的设计与合成。 将要解决的配体的结构特征是： 宽度、构象灵活性以及氢键和 静电功能。 2.连接吗啉的设计与合成。这些化合物 将被设计来探测两个特定的连接基序：头对尾 酰胺键连接体和头对头炔二醇连接体。 3.评估这些吗啉蛋白的DNA结合。二 将研究特异性结合特征：序列 选择性，以及小槽宽度与 灵活性和结合位点选择性。 4. 评估这些吗啡肽对 DNA 的影响 HIV-1反向催化的定向DNA聚合反应 转录酶。具体调查将重点关注相关性 特定 DNA 结合位点及其产生的特定效果 链置换DNA合成催化的配体/DNA复合物 通过 HIV-1 逆转录酶。