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，我们将”关注的作用， 配体的形状，特别是宽度，在分子识别的次要 双链DNA的凹槽。我们将讨论两个具体问题： (a)形状在小分子的相互作用中扮演什么角色 有小沟的吗(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物化学性质的配体， 选择性？我们关注形状在小沟分子中的作用 承认将具体解决相对的问题， 形状对氢键和静电的贡献 对分子识别的贡献，以及 构象灵活的DNA小沟，以适应 不同形状的配体。作为这些知识的应用，我们 将专门讨论序列识别和 特异性配体/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。我们漫长 长期目标是手头有相对较少的个人， 分子构建模块，每个模块都具有明确的DNA 结合特异性然后，这些刚性分子构建块可以被 以合理的顺序组装以构建DNA小沟配体， 它不仅补充了静电和氢键 一个特定的DNA序列的环境，而且其特定的 三维形状。 我们称这种形状为互补DNA小分子 沟结合化合物morpholexins，因为他们不仅阅读 遗传密码的词汇或“单词”， 这些词所在的区域。这项工作的具体目标 包括以下步骤： 1.两类新型吗啉结合素单元的设计与合成。 将被解决的配体的结构特征是： 宽度、构象柔性和氢键， 静电功能性 2.连接型吗啉蛋白的设计与合成。这些化合物 将被设计成探测两个特定的连接基序：一个头到尾的连接基序， 酰胺键连接基和头对头炔基二醇连接基。 3.这些morpholexins的DNA结合的评价。两 将研究特异性结合特征：序列 选择性，以及小沟宽度和 柔性和结合位点选择性。 4.评价这些形态蛋白对DNA的影响， HIV-1逆转录酶催化的DNA定向聚合反应 录酶具体调查将重点关注相关性 特定的DNA结合位点， 配体/DNA复合物对链置换DNA合成的催化作用 HIV-1逆转录酶。