RNA Dynamics by Solution and Solid State Deuterium NMR

通过溶液和固态氘 NMR 进行 RNA 动力学分析

• 批准号: 0642253
• 负责人: Gabriele Varani
• 金额: $ 62.62万
• 依托单位: University of Washington
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-03-01 至 2011-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0642253&HistoricalAwards=false
• 关键词: RNA; Dynamics; Solution; Solid; State

The objective of this project is to investigate nucleic acids dynamics by applying solution and solid-state NMR conjointly to a paradigmatic system, the HIV-1 TAR. RNA dynamics will be described more comprehensively than it has been possible so far by analyzing the experimental results obtained by the two NMR methods through a common theoretical framework. The concomitant use of the two spectroscopies will allow a wider range of time scales and sites than would be possible by using either technique in isolation, and to compare dynamics of RNA in solution and the solid. The central hypothesis underlying this project is that motion is an important aspect of nucleic acid function and HIV TAR provides an eloquent demonstration of this premise. Its structure and molecular interactions have been studied extensively, yet the molecular basis for TAR recognition by Tat protein is poorly understood because of complex conformational dynamics in the protein and RNA. Both solution and solid state NMR are powerful methods to study dynamics, but each has limitations. Solution relaxation data are poorly sensitive to motions that occur at certain rates, while solid-state deuterium lineshape analysis requires singly deuterated samples. Therefore, it is necessary to develop new methods to collect and analyze the experimental results to understand in quantitative detail how motion contributes to molecular recognition in nucleic acids. By analyzing the two set of spectroscopic results through the same theoretical framework, it will be possible to gain qualitatively and quantitatively new insight into the nature of the motions within TAR RNA that underlie its recognition by Tat protein and therefore its function in gene regulation. The new tools to study functional dynamics in nucleic acids developed in this project will be broadly applicable to other nucleic acid and even to proteins.This project is highly interdisciplinary, crossing the areas of physical chemistry, molecular biology, biochemistry, molecular pharmacology and molecular virology. Therefore, it provides many opportunities for scientific collaborations and for exposing undergraduate and graduate students to interdisciplinary research. It provides fertile grounds for training future leaders in the development and application of NMR methods to study biological systems. An important aspect of the PI's research group is the presence of a majority of female students and a number of under-represented minorities. One of the PIs supervises every summer a high school student from an under-represented minority group through the University of Washington Genome and STAR programs aimed at increasing recruitment of under-represented minority students to the science

该项目的目的是通过将溶液和固态NMR结合应用于一个范例系统HIV-1 TAR来研究核酸动力学。RNA动力学将更全面地描述比它已经可能到目前为止，通过分析实验结果得到的两种NMR方法通过一个共同的理论框架。同时使用这两种光谱将允许更广泛的时间尺度和网站比可能通过使用任何一种技术在隔离，并比较动态的RNA在溶液和固体。该项目的核心假设是运动是核酸功能的一个重要方面，HIV TAR为这一前提提供了有力的证明。它的结构和分子相互作用已被广泛研究，但由于蛋白质和RNA中复杂的构象动力学，对达特蛋白识别TAR的分子基础知之甚少。溶液和固体核磁共振都是研究动力学的有力方法，但都有局限性。溶液弛豫数据对以一定速率发生的运动不敏感，而固态氘线形分析需要单氘样品。因此，有必要开发新的方法来收集和分析实验结果，以定量地详细了解运动如何有助于核酸中的分子识别。通过相同的理论框架分析两组光谱结果，将有可能获得定性和定量的新见解TAR RNA内的运动的性质，其识别达特蛋白，因此其在基因调控中的功能的基础。本项目所开发的核酸功能动力学研究新工具将广泛适用于其他核酸甚至蛋白质，本项目是一个跨学科的研究项目，涉及物理化学、分子生物学、生物化学、分子药理学和分子病毒学等多个领域。因此，它为科学合作和本科生和研究生进行跨学科研究提供了许多机会。它为培养未来的领导者在开发和应用核磁共振方法来研究生物系统提供了肥沃的土壤。PI研究小组的一个重要方面是女生占大多数，少数民族代表人数不足。每年夏天，其中一名PI通过华盛顿大学的基因组和星星计划监督一名来自代表性不足的少数民族的高中生，这些计划旨在增加代表性不足的少数民族学生对科学的招募