Towards solution of the RNA folding problem

描述(申请人提供)：RNA分子通常必须折叠成不同的三维结构才能发挥其生物学功能。这些折叠结构可以是大的或小的、长寿命的或瞬时的、和/或性质上稳定或不稳定的。RNA折叠的动力学特征是多条路径、中间体的数量以及经常(但不总是)路径上和/或路径外的动力学捕获物种。我们理解RNA是如何折叠的方法是确定哪些折叠途径在体外是可能的，目的是确定在体内发生的子集。我们通过计算将折叠的局部和全局测量整合到“结构-动力学”模型中，该模型描述了折叠反应的最早步骤。我们开发了高通量方法，用于获取毫秒时间和单核苷酸空间分辨率的时间进度曲线，使一般假设能够根据深入和广泛的实验数据进行测试。拟议的I组内含子研究试图通过批判性地比较系统发育相关的RNA分子的折叠和三级接触的温和系统扰动，建立RNA结构、稳定性和折叠动力学之间的定量关系。分析了结构与I组内含子催化核心同源的核糖开关的折叠，以确定这些不同的调控元件是否具有共同的折叠机制。为了了解物理环境和折叠环境之间的关系，我们探索了温度和离子条件等溶液变量对观察到的突现折叠行为的影响，以影响RNA的微观环境。最后，我们试图了解转录是如何影响RNA折叠的。与公共卫生相关：RNA对许多细胞过程的功能至关重要。它的正确折叠对于细胞的这些重要成分的生物学功能至关重要。然而，错误的RNA折叠与生理功能障碍和病理之间的联系才刚刚开始出现。我们相信，通过对模型系统(如I组核酶)的定量研究揭示的原理将直接适用于与人类病理相关的RNA结构和蛋白质-RNA组装。

DESCRIPTION (provided by applicant): RNA molecules often must fold into distinct three-dimensional structures to exert their biological function. These folded structures may be large or small, long-lived or transient, and/or stable or unstable in nature. The kinetics of RNA folding is characterized by multiple pathways, the population of intermediates and often (but not always) on- and/or off-pathway kinetically trapped species. Our approach to understanding how the RNA is folded is to determine which folding pathways are possible in vitro with the goal of determining the subset that occur in vivo. We computationally integrate local and global measures of folding into "structural-kinetic" models that characterize folding reactions from their earliest steps. Our development of high-throughput methods for the acquisition of time progress curves with millisecond time and single nucleotide spatial resolution allows general hypotheses to be tested against experimental data that is both deep and broad. The proposed studies of group I introns seek to establish quantitative relationships between RNA structure, stability and folding kinetics by critically comparing the folding of phylogenetically related RNA molecules and gentle systematic perturbation of tertiary contacts. The folding of a riboswitch whose structure is homologous to the catalytic core of group I intron is analyzed to determine if these different regulatory elements possess a common folding mechanism. We explore the effect on the observed emergent folding behavior solution variables such as temperature and ionic conditions that affect the microscopic environment of RNA in order to understand the relationships between the physical environment and folding environment. Lastly, we seek to understand how transcription affects RNA folding. PUBLIC HEALTH RELEVANCE: RNA is critical to the function of many cellular processes. Its correct folding is vital for the biological function of these important elements of the cell. However, the link between incorrect RNA folding and physiological malfunctions and pathologies is only started to emerge. We believe that the principles revealed by quantitative study of model systems such as the group I ribozymes will be directly applicable to RNA structures and protein-RNA assemblies linked to human pathologies.