Structure, dynamics, and function of the packaging RNA

描述（由申请人提供）：RNA在基本生物过程中充当信息载体、催化剂和调节剂，理解RNA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phi 29包装RNA（pRNA）的结构，构象动力学和功能机制来促进我们对RNA结构/功能关系的理解，pRNA在当今已知的最强大的生物马达-phi 29噬菌体的DNA包装马达中起着重要作用。 具体目标包括平行发展用于研究RNA结构和动力学的定点自旋标记（SDSL）技术，以及SDSL和其他方法用于研究pRNA结构和相互作用。SDSL利用连接到特定位点的氮氧部分来获得母体分子的结构和动力学信息，并且最近已显示能够提供RNA中的独特信息。由pRNA研究中的特定问题驱动的拟议RNA SDSL发展包括：（I）使用连接到任意序列的氮氧自由基建立核酸中的长程距离测量;以及（ii）建立第一个经验RNA SDSL线形库，用于从单个标记的氮氧自由基推断RNA结构信息。 这些发展将在包装RNA研究中找到应用。具体目标包括：（I）使用SDSL、NMR和计算建模的组合来研究pRNA中的结构和构象变化;以及（ii）通过分析pRNA官能团来绘制马达中的pRNA/蛋白质和pRNA/pRNA界面。 拟议的研究将揭示包装RNA结构和相互作用的信息，这将有助于理解phi 29包装的机制。据信，phi 29与许多其他双链DNA病毒（包括许多人类病原体）共享相同的DNA包装机制。了解phi 29包装运动功能将有助于开发对抗这些病毒的药理学方法。

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.