Perturbation of Nucleotide Acidity in RNA Folding and Catalysis

RNA 折叠和催化中核苷酸酸度的扰动

• 批准号: 0100057
• 负责人: Scott Strobel
• 金额: $ 38万
• 依托单位: Yale University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-07-01 至 2005-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0100057&HistoricalAwards=false
• 关键词: Perturbation; Nucleotide; Acidity; RNA; Folding

With the support of the Organic and Macromolecular Chemistry Program, Professor Scott A. Strobel, of the Department of Molecular Biophysics and Biochemistry at Yale University, is undertaking a combinatorial approach to the exploration of acidity perturbations important for RNA structure and function. By exploiting the technique of Nucleotide Analog Interference Mapping, Professor Strobel simultaneously yet individually monitors the effect of incorporating a nucleotide analog at every position within an RNA molecule. After developing a set of nucleotide analogs which retain a full set of base functional groups, but which have altered acidity of the A- and C-imino groups, a variety of RNAs will be screened for functionally important protonation sites. These analogs will then be brought to bear on an investigation of potential base ionization events important for the catalytic activity of three self-processing ribozymes, specifically the hepatitis delta virus, the Varkud Satellite, and hairpin RNA enzymes.Many biochemical reactions are facilitated by "general" acid and/or base catalysis, wherein the reaction is assisted by a partial proton transfer somewhere along the reaction pathway. Since they possess acidic and basic groups of the appropriate strength, protein enzymes are well-suited to catalyze such reactions. Like proteins, large ribonucleic acid (RNA) molecules can also adopt complex structures and catalyze chemical reactions. However, unlike the protein enzymes, RNA does not contain acidic or basic groups which would be expected to participate in general acid or base catalysis. This implies that in particular circumstances, the acidity of a group within RNA must be substantially shifted by its specific, local microenvironment within the RNA molecule. With the support of the Organic and Macromolecular Chemistry Program, Professor Scott A. Strobel, of the Department of Molecular Biophysics and Biochemistry at Yale University, has developed a technique permitting the rapid analysis of the effects of multiple changes on the structure and properties of RNA. By developing a new set of "tools" for the application of this technique to the analysis of acidity effects, Professor Strobel will elucidate the molecular underpinnings of general acid and base catalysis by RNA, providing information about RNA structure and function and suggesting new ways to think about molecular evolution and catalysis.

在有机和高分子化学项目的支持下，Scott A.耶鲁大学分子生物物理和生物化学系的Strobel正在进行一种组合方法来探索对RNA结构和功能重要的酸性扰动。通过利用核苷酸类似物干扰图谱技术，Strobel教授同时但单独地监测在RNA分子内的每个位置掺入核苷酸类似物的效果。在开发出一组保留了全套碱基官能团但改变了A-和C-亚氨基酸性的核苷酸类似物后，将筛选各种RNA的功能重要的质子化位点。这些类似物，然后将承担对三个自加工核酶，特别是肝炎病毒，Varkud卫星，和发夹RNA酶的催化活性的重要的潜在的碱电离事件的调查。许多生化反应促进“一般”酸和/或碱催化，其中该反应是由部分质子转移沿着反应途径的某处协助。由于蛋白质酶具有适当强度的酸性和碱性基团，因此它们非常适合催化此类反应。像蛋白质一样，大的核糖核酸（RNA）分子也可以采用复杂的结构并催化化学反应。然而，与蛋白质酶不同，RNA不包含预期参与一般酸或碱催化的酸性或碱性基团。这意味着，在特定的情况下，RNA内基团的酸性必须通过RNA分子内特定的局部微环境而发生实质性变化。在有机与高分子化学项目的支持下，Scott A.耶鲁大学分子生物物理和生物化学系的Strobel开发了一种技术，可以快速分析多种变化对RNA结构和性质的影响。通过开发一套新的“工具”，将这种技术应用于分析酸度效应，Strobel教授将阐明RNA的一般酸和碱催化的分子基础，提供有关RNA结构和功能的信息，并提出思考分子进化和催化的新方法。