SHAPE SELECTIVE DNA MINOR GROOVE LIGANDS

形状选择性 DNA 小沟配体

• 批准号: 2189061
• 负责人: SEAN M KERWIN
• 金额: $ 9.77万
• 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/2189061
• 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.

这份提案详细说明了我们设计新的、 序列选择性DNA小槽结合化合物。我们的方法 与以前的方法不同之处在于，我们将重点放在 配基形状，尤其是宽度，在分子识别中的次要作用 双链DNA的凹槽。我们将回答两个具体问题： (A)形状在小分子相互作用中起什么作用 用小凹槽吗？(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性的配体 选择性？我们对形状在微小沟槽分子中的作用的关注 表彰将具体解决亲属的问题 形状对氢键和静电的贡献 对分子识别的贡献，以及 DNA的构象柔性的小槽，以适应 形状不同的配体。作为对这一知识的应用，我们 将具体解决序列识别和 特异性配体/DNA复合体影响DNA加工的能力 与小凹槽接触的酶，包括人类 免疫缺陷病毒1型(HIV-1)逆转录酶。我们的龙 任期目标是手头有相对较少数量的个人 分子构建块，每个构建块都具有明确定义的DNA 结合专一性。然后，这些坚硬的分子构建块可以 有序组装构建DNA小沟槽配体 这不仅是对静电和氢键的补充 特定DNA序列的环境，也是其特定的 三维形状。我们称这种形状为互补的DNA小 沟槽结合化合物吗啡，因为它们不仅能读到 词汇或遗传密码的“词”，也包括词形或形状 这些单词所在的区域。这项工作的具体目标 包括： 1.两类新吗啡肽单元的设计与合成。 将讨论的配体的结构特征如下： 宽度、构象柔性以及氢键和 静电功能。 2.键合吗啡肽的设计与合成。这些化合物 将探索两个特定的链接主题：首尾相接 酰胺键连接剂和头对头的炔基二醇连接剂。 3.对这些吗啡肽的DNA结合力进行了评价。二 将研究特定的结合特征：序列 以及小槽宽度与选择性的关系。 灵活性和结合部位的选择性。 4.评价吗啡肽对DNA的影响。 HIV-1逆转录催化的定向DNA聚合反应 转录酶。具体调查将集中在相关性上 特定的DNA结合位点与由此产生的特定效果 配体/DNA络合物催化的链置换DNA合成 通过HIV-1逆转录酶。