CAREER: A Single Molecule Study of Alternative Folding of a Retroviral Untranslated RNA

职业生涯：逆转录病毒非翻译 RNA 选择性折叠的单分子研究

• 批准号: 1054449
• 负责人: Pan Li
• 金额: $ 50万
• 依托单位: SUNY at Albany
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-02-01 至 2017-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1054449&HistoricalAwards=false
• 关键词: CAREER; Single; Molecule; Study; Alternative

The objective of this CAREER project is to study folding and structure of a model retroviral 5'-untranslated leader RNA using single molecule methods. Two aspects of the RNA folding problem are exemplified by retroviral genomic RNAs. First, despite many possible conformations, a long viral RNA strand can adopt a well-defined structure under a given set of conditions. Second, large RNAs, such as the untranslated leader region of retroviruses, can rearrange into alternative folds in a timely fashion when triggered by different signals, such as those associated with host cell growth. To understand this intriguing structural stability and flexibility, the folding and structure transition of RNA will be studied one molecule at a time. Each RNA molecule will be stretched and relaxed like a rubber band using optical tweezers, with structure transitions revealed by extension of the molecule. The strategy of this project is to analyze alternative folding of individual domains, followed by examination of the entire leader RNA. Specifically, the TAR domain will be studied as an example of alternative secondary folding, whereas the DIS domain will be examined to understand structural rearrangements in RNA-RNA interactions. Characteristic folding patterns of these domains will be later used as fingerprints to interpret folding trajectories of the entire leader RNA. Furthermore, collaborations are established with theoreticians to interpret experimental data and to test physical models of RNA folding. Molecular dynamics simulations will be employed to examine RNA structure under tension at atomic levels. Statistical mechanical modeling is used to bridge the gap between single molecule and bulk observations. The broader impact of this project includes developing a new method to study alternative folding and structural rearrangement of large RNAs. In the post-genomic world, new models for RNA folding that extend beyond the most stable structure will be useful to predict versatile biological functions of untranslated RNAs from the ever-growing sequence database. This project with single-molecule study will provide direct observations necessary to calibrate the leading folding theories, and will foster close collaborations between biologists and physicists, experimentalists and theoreticians. The project will be conducted at the newly founded RNA Institute at SUNY Albany, providing long-term research opportunities in the RNA field for undergraduate and graduate students of diverse backgrounds. The project incorporates RNA structural biology and biophysics into teaching by participating in several graduate courses that are open to all students from the New York capital region institutions, including SUNY, Rensselaer Polytechnic Institute, New York State Department of Health, and Northeast Regional Forensics Institute. Techniques used in this research, such as stretching DNA, will be developed as lab demonstrations for undergraduate and graduate courses in various disciplines as well as ex-curricular scientific activities for high school students.

该职业项目的目的是使用单分子方法研究模型逆转录病毒5'-非翻译铅RNA的折叠和结构。 逆转录病毒基因组RNA例证了RNA折叠问题的两个方面。首先，尽管有许多可能的构象，但在给定的一组条件下，长长的病毒RNA链可以采用明确的结构。其次，大型RNA，例如逆转录病毒的未翻译领导者区域，当由不同信号触发时，例如与宿主细胞生长相关的信号时，可以及时重新排列替代折叠。为了了解这种有趣的结构稳定性和灵活性，将一次研究一个分子的RNA的折叠和结构过渡。每个RNA分子将使用光学镊子像橡皮筋一样拉伸和放松，并通过分子的扩展揭示了结构转变。该项目的策略是分析单个领域的替代折叠，然后检查整个领导者RNA。具体而言，将研究焦油结构域作为替代次级折叠的一个示例，而将检查DIS域以了解RNA-RNA相互作用中的结构重排。这些域的特征折叠模式将在后来用作指纹，以解释整个Leader RNA的折叠轨迹。此外，还与理论家建立了合作，以解释实验数据并测试RNA折叠的物理模型。将采用分子动力学模拟在原子水平的张力下检查RNA结构。统计机械建模用于弥合单分子和散装观测之间的间隙。该项目的更广泛影响包括开发一种新方法来研究大型RNA的替代折叠和结构重排。在基因组世界中，超出最稳定结构的RNA折叠的新模型将有助于预测不断增长的序列数据库中未翻译RNA的多功能生物学功能。该项目通过单分子研究将提供校准领先的折叠理论所需的直接观察，并将促进生物学家与物理学家，实验家和理论家之间的密切合作。该项目将在SUNY Albany的新成立的RNA研究所进行，为本科和研究生提供多种背景的RNA领域的长期研究机会。该项目将RNA结构生物学和生物物理学纳入教学中，通过参加几个研究生课程，这些课程向纽约首都地区机构的所有学生开放，包括纽约州立大学，纽约州伦斯勒理工学院，纽约州卫生局和东北地区福兰科学研究所。这项研究中使用的技术，例如拉伸DNA，将作为各种学科的本科和研究生课程以及高中生的外科科学活动开发。