HIV frameshift site RNA structure and ligand binding

描述（由申请方提供）：HIV Pol基因的表达完全依赖于程序性-1翻译移码。移码由RNA元件介导，该RNA元件包括滑动位点和高度保守的下游结构。下游RNA结构通过未知的机制刺激移码。其目的是发展一个原子水平的理解的结构和功能的移码位点RNA。Butcher博士将确定HIV-1 M组以及HIV-2和SIV-SMM的移码位点RNA的NMR结构。这些结构被广泛认为是开发新疗法的有吸引力的靶标。因此，作为合理开发具有增强特异性的第二代RNA结合配体的一个步骤，将确定与具有抗HIV活性的新型小分子胍基新霉素B结合的HIV-1移码位点RNA的结构。最后，为了更广泛地了解移码位点RNA的结构和功能，将使用光反应性RNA修饰来探测其与翻译机器通过激光诱导的交联的相互作用。所得到的数据将被映射到核糖体和移码位点RNA结构， 产生移码交互的第一个视图。 具体目标是： 1.确定整个HIV-1移码位点（FS）RNA的NMR结构。 2.研究胍基糖苷结合的结构和热力学效应。 3.确定HIV-2和SIV-SMM FS RNA的结构。 4.确定HIV FS RNA和翻译机制之间的相互作用位点。

DESCRIPTION (provided by applicant): The expression of HIV Pol genes is entirely dependent upon a programmed -1 translational frameshift. Frameshifting is mediated by an RNA element that includes a slippery site and a highly conserved, downstream structure. The downstream RNA structure stimulates frameshifting through an unknown mechansim. The objective is to develop an atomic-level understanding of the structure and function of the frameshift site RNA. Dr. Butcher will determine the NMR structures of the frameshift site RNAs from HIV-1 group M, as well as from HIV-2 and SIV-SMM. These structures are broadly recognized to be attractive targets for the development of new therapeutics. Therefore, as a step towards the rational development of second generation RNA binding ligands with enhanced specificity, the structure of the HIV-1 frameshift site RNA bound to a novel small molecule with anti-HIV activity, guanidino neomycin B will be determined. Finally, in order to more broadly understand the structure and function of the frameshift site RNA, photoreactive RNA modifications will be used to probe its interactions with the translational machinery by laser-induced cross-linking. The resulting data will be mapped to the ribosomal and frameshift site RNA structures to produce the first view of the frameshifting interaction. The specific aims are: 1. Determine the NMR structure of the entire HIV-1 frameshift site (FS) RNA. 2. Investigate the structural and thermodynamic effects of guanidino glycoside binding. 3. Determine the structure of the HIV-2 and SIV-SMM FS RNAs. 4. Identify sites of interaction between the HIV FS RNA and translational machinery.