Structure, dynamics, and function of the packaging RNA

包装 RNA 的结构、动力学和功能

• 批准号: 7143580
• 负责人: Peter Z Qin
• 金额: $ 27.42万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-01 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7143580
• 关键词: RNA; X ray crystallography; adenosine triphosphate; circular dichroism; computational biology; conformation; electron spin resonance spectroscopy; high performance liquid chromatography; hydroxyl group; intermolecular interaction; method development; molecular biology information system; nitrogen oxides; nuclear magnetic resonance spectroscopy; nucleic acid structure

DESCRIPTION (provided by applicant): RNA acts as information carriers, catalysts, and regulators in essential biological processes, and understanding RNA structure and function is intimately linked to combating diseases. The long-term objectives of this project is to advance our understanding of the RNA structure/function relationship via studying structure, conformational dynamics, and mechanism of function, in the phi29 packaging RNA (pRNA) that plays essential roles in the most powerful biological motor known today - the DNA packaging motor of the phi29 bacteriophage. The specific aims involve a parallel development of the site-directed spin labeling (SDSL) technique for studying RNA structure and dynamics, and application of SDSL and other methods to study pRNA structure and interaction. SDSL utilizes a nitroxide moiety attached to specific sites to obtain structural and dynamic information of the parent molecule, and has recently been shown to be able to provide unique information in RNA. Proposed RNA SDSL developments, which are driven by specific questions in pRNA studies, include: (I) establishing long-range distance measurements in nucleic acids using nitroxides attached to arbitrary sequences; and (ii) establishing the first empirical RNA SDSL line shape library for deducing RNA structural information from singly labeled nitroxides. These developments will find applications in packaging RNA studies. Specific aims includes: (I) studying structure and conformational changes in the pRNA using a combination of SDSL, NMR, and computational modeling; and (ii) mapping pRNA/protein and pRNA/pRNA interfaces in the motor via analyzing pRNA functional groups. The proposed studies will reveal information on packaging RNA structure and interaction that will aid in understanding the mechanism of phi29 packaging. It is believed that phi29 shares the same DNA packaging mechanism with many other double stranded DNA viruses, including a number of human pathogens. Understanding phi29 packaging motor function will aid in developing pharmacological approaches to combat these viruses.

描述（由申请人提供）：RNA 在重要的生物过程中充当信息载体、催化剂和调节器，了解 RNA 的结构和功能与对抗疾病密切相关。该项目的长期目标是通过研究 phi29 包装 RNA (pRNA) 的结构、构象动力学和功能机制，增进我们对 RNA 结构/功能关系的理解，phi29 包装 RNA (pRNA) 在最强大的生物马达中发挥着重要作用今天已知的 - phi29 噬菌体的 DNA 包装马达。 具体目标包括并行开发用于研究RNA结构和动力学的定点自旋标记（SDSL）技术，以及应用SDSL和其他方法来研究pRNA结构和相互作用。 SDSL 利用附着在特定位点上的硝基氧部分来获取母体分子的结构和动态信息，并且最近已被证明能够提供 RNA 中的独特信息。拟议的 RNA SDSL 开发是由 pRNA 研究中的具体问题驱动的，包括：(I) 使用附着在任意序列上的硝基氧在核酸中建立长距离测量； (ii) 建立第一个经验性 RNA SDSL 线形库，用于从单标记硝基氧推断 RNA 结构信息。 这些进展将在包装 RNA 研究中得到应用。具体目标包括： (I) 结合 SDSL、NMR 和计算模型研究 pRNA 的结构和构象变化； (ii) 通过分析 pRNA 功能组绘制运动中 pRNA/蛋白质和 pRNA/pRNA 界面的图谱。 拟议的研究将揭示有关包装 RNA 结构和相互作用的信息，这将有助于理解 phi29 包装的机制。据信，phi29 与许多其他双链 DNA 病毒（包括许多人类病原体）具有相同的 DNA 包装机制。了解 phi29 包装运动功能将有助于开发对抗这些病毒的药理学方法。