HIV frameshift site RNA structure and ligand binding

描述(申请人提供)：HIV POL基因的表达完全依赖于程序化的翻译移码。移码是由一种RNA元件介导的，它包括一个光滑的位点和一个高度保守的下游结构。下游的RNA结构刺激通过一种未知的机制进行帧转移。其目标是在原子水平上了解移码位点RNA的结构和功能。布彻博士将确定HIV-1 M组以及HIV-2和SIV-SMM的移码位点RNA的核磁共振结构。这些结构被广泛认为是开发新疗法的有吸引力的靶点。因此，作为第二代具有增强特异性的RNA结合配体的合理开发的一步，将确定HIV-1移码位点RNA与一种新的具有抗HIV活性的小分子--胍基新霉素B结合的结构。最后，为了更广泛地了解移码位点RNA的结构和功能，我们将利用光反应对RNA进行修饰，以探讨其与激光诱导的交联翻译机制的相互作用。所得到的数据将被映射到核糖体和移码部位的RNA结构，以 生成移帧交互组件的第一个视图。 具体目标是： 1.确定了整个HIV-1移码位点(FS)RNA的核磁共振结构。 2.研究了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.确定艾滋病毒FS RNA和翻译机制之间的相互作用部位。

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.