SHAPE SELECTIVE DNA MINOR GROOVE LIGANDS

形状选择性 DNA 小沟配体

• 批准号: 2685031
• 负责人: SEAN M KERWIN
• 金额: $ 11.74万
• 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 2000-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2685031
• 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.

该建议详细介绍了我们的系统方法，用于设计新的， 序列选择性DNA小凹槽结合化合物。我们的方法 与以前的方法不同，我们专注于 配体形状，尤其是宽度，在分子识别中 双链DNA的凹槽。我们将解决两个具体问题： （a）在小分子的相互作用中形状扮演的角色 有小凹槽？ （b）我们如何利用配体形状的作用 具有可预测序列和生化的合理设计配体 选择性？我们专注于形状在小凹槽分子中的作用 认可将专门解决亲戚的问题 相对于氢键和静电的形状的贡献 对分子识别的贡献以及 DNA的构象柔性小凹槽可容纳 形状不同的配体。作为这些知识的应用，我们 将专门解决序列识别问题和 特定配体/DNA复合物实现DNA处理的能力 与小凹槽接触的酶，包括人 免疫缺陷病毒1型（HIV-1）逆转录酶。我们的漫长 术语目标是拥有相对较少的个人 分子构建块，每个块具有明确的DNA 结合特异性。这些刚性的分子构建块可以是 以合理的顺序组装来构建DNA小凹槽配体 这不仅补充了静电和氢键 特定DNA序列的环境，但也是其特定的环境 三维形状。 我们称这种形状互补的DNA小调 凹槽结合化合物形态素，因为它们不仅读 遗传密码的Lexis或“单词”，也是变形或“形状” 这些词所在的区域。这项工作的具体目标 包括： 1。两种新的形态素单元的设计和合成。 将要解决的配体的结构特征是： 宽度，构象柔韧性以及氢键和 静电功能。 2。链接的形态素的设计和合成。这些化合物 将设计用于探测两个特定的链接基线：一个从头到尾 酰胺债券接头和正面的Alkynyldiol链接器。 3。对这些形态素的DNA结合的评估。二 将研究特定的结合特征：序列 选择性，以及小凹槽宽度与 灵活性和结合位点的选择性。 4。评估这些形态素对DNA-的作用 HIV-1反向催化的定向DNA聚合反应 转录酶。具体调查将集中于相关性 特定的DNA结合位点具有所得的特定效果 链中的配体/DNA复合物在催化的链DNA合成上 通过HIV-1逆转录酶。