Structure, dynamics, and function of the packaging RNA

描述（申请人提供）：RNA在重要的生物过程中充当信息载体、催化剂和调节剂，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来推进我们对RNA结构/功能关系的理解，phi29包装RNA （pRNA）在当今已知的最强大的生物马达- phi29噬菌体的DNA包装马达中起着重要作用。

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.