Perturbation of Nucleotide Acidity in RNA Folding and Catalysis

在有机化学和高分子化学计划的支持下，耶鲁大学分子生物物理和生物化学系的Scott A.Strobel教授正在进行一种组合方法来探索对RNA结构和功能至关重要的酸度扰动。通过利用核苷酸类似干扰图谱技术，斯特罗贝尔教授同时还单独监测了在RNA分子中的每个位置加入核苷酸类似物的效果。在开发了一组保留了全套碱性官能团但改变了A-和C-亚氨基的酸性的核苷酸类似物后，将筛选各种RNA以寻找功能上重要的质子化位点。然后，这些类似物将用于研究对三种自处理核酶的催化活性重要的潜在碱基电离事件，特别是丁型肝炎病毒、Varkud卫星和发夹RNA酶。许多生化反应是由“一般的”酸和/或碱催化促进的，其中反应是由反应路径上某个地方的部分质子转移辅助的。因为它们具有适当强度的酸性和碱性基团，所以蛋白质酶非常适合催化这种反应。与蛋白质一样，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，与蛋白质酶不同的是，RNA不包含酸性或碱性基团，这些基团有望参与一般的酸或碱催化。这意味着在特定情况下，RNA分子中某个基团的酸性必须因其特定的局部微环境而发生显著变化。在有机化学和高分子化学计划的支持下，耶鲁大学分子生物物理和生物化学系的Scott A.Strobel教授开发了一种技术，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”，将这项技术应用于酸度效应的分析，斯特罗贝尔教授将阐明RNA对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。

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.