The Influence of Secondary Structure on the Folding and Catalysis of Functional RNAs

功能RNA具有错综复杂的三级结构，调节活性。RNA功能的一个限制是在分子水平上：它的四个碱基功能多样性很差。特别是，游离核苷酸不具有PKA的近中性，并且在生物pH下不能阳离子。另一方面，组氨酸和赖氨酸具有这些性质，这大大扩展了蛋白质的催化和识别能力。RNA中缺乏这种功能将极大地限制其功能。然而，一种可能性是，在折叠时，某些A和C的pKa值变得高度扰动，并转变为中性甚至更高。这个项目的中心焦点是理解二级结构在调节RNA功能特性中的重要性。我们将研究合作折叠的二级结构基序，这些基序可能具有强烈的pKA值。还将探讨二级结构折叠对三级结构功能稳定性的影响；假设在三级结构协同展开的条件下，增加二级结构稳定性会增加功能稳定性。因此，对RNA折叠中的协作性--孤立的二级结构以及相连的三级和二级结构--的理解贯穿了这项研究。最后，在假设稳定性通常来自静电相互作用的情况下，我们将探讨二级结构中异常稳定的分子起源。非线性泊松玻尔兹曼(NLPB)计算将被用来识别这种相互作用，这些将通过对模型序列的实验来参数化。更广泛的影响：该项目将使本科生参与出版物的研究和写作。已经制定了一项明确的计划，在未来识别和招收这些学生，让代表人数不足的群体的学生参与研究。该项目还涉及将分子概念和数学概念联系起来的课程改革。目标是使学生能够建立简单的分子模型，并从第一性原理推导出适当的方程式。将开发一套针对体现这些目标的一系列生物物理问题的模拟，并在互联网上提供。

Functional RNAs have intricate tertiary structures that mediate activity. One limitation to RNA function is found at the molecular level: its four bases have poor functional diversity. In particular, free nucleotides do not have pKa's near neutrality and cannot be cationic at biological pH. Histidine and lysine, on the other hand, possess these properties, which greatly expands the catalytic and recognition repertoire of proteins. Absence of such functionalities in RNA would greatly limit its function. One possibility, however, is that upon folding, pKa values for certain A's and C's become highly perturbed and shift to neutrality and beyond. The central focus of this project is on understanding the importance of secondary structure in modulating the functional properties of RNA. Cooperatively folding secondary structural motifs, which may possess strongly shifted pKa values, will be examined. The ability of secondary structure folding to influence the functional stability of tertiary structure will be explored as well; it is hypothesized that under conditions of cooperatively unfolding tertiary structure, increasing secondary structure stability will increase functional stability. Thus, the understanding of cooperativity in RNA folding-of isolated secondary structures and of linked tertiary and secondary structures-pervades this research. Lastly, the molecular origin of exceptional stability in secondary structures will be examined, with the hypothesis that stability often arises from electrostatic interactions. Non-linear Poisson Boltzmann (NLPB) calculations will be used to identify such interactions, and these will be parameterized by experiments on model sequences. Broader Impacts: This project will integrate undergraduates in the research and authorship of publications. A clear plan for identifying and recruiting these students in the future has been developed to involve students from underrepresented groups in the research. The project also involves curriculum reform by connecting molecular concepts and mathematical ones. A goal is to empower students to set up simple molecular models and derive appropriate equations from first principles. A set of simulations for a series of biophysical problems that embody these goals will be developed and made available on the Internet.