RNA STRUCTURE DETERMINATION BY DOUBLE QUANTUM COHERENCE ESR

通过双量子相干 ESR 测定 RNA 结构

• 批准号: 7723903
• 负责人: Jack H Freed
• 金额: $ 0.35万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-01 至 2009-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7723903
• 关键词: Bacterial RNA; Base Pairing; Catalytic RNA; Code; Collaborations; Communication; Computer Retrieval of Information on Scientific Projects Database; DNA; Decompression Sickness; Electrons; Funding; Genetic; Genomics; Grant; HIV-1; Helix (Snails); Institution; Length; Measures; Nucleotides; Play; Purine Nucleotides; RNA; RNA Sequences; Research; Research Personnel; Resources; Ribosomal Frameshifting; Ribosomes; Role; Source; Spin Labels; Structure; Thiouridine; Translating; Uncertainty; United States National Institutes of Health; Viral; base; disorder control; ear helix; improved; insight; interest; molecular modeling; nuclear Overhauser enhancement; quantum; receptor; stem; three dimensional structure

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Studies of RNA are fundamental for the global genomics project. It plays a key role in translating genetic information stored in DNA and manifesting it via the ribosome machinery. The study of viral and bacterial RNA is an important component of RNA research and offers insights into disease control. There is a large, ongoing effort in RNA sequencing as well as efforts to obtain 3-D structures and their relation to RNA function. In our initial effort, we applied DQC ESR to measure end-to-end distances in A-form RNA. Three RNAs with 13, 16, and 26 base pairs were spin-labeled by 3-iodo-acetamido-proxyl attached to thiouridine. The 5'-5' distances were evaluated from DQC, yielding the distances between electron spins on 5-5' attached nitroxides of 40, 55, and 72¿, respectively, which agrees well with the proposed structures. A short communication describing the application of double-quantum filtered refocused primary echo (DQF-RPE) to 26 b.p. RNA is in press in J. Am. Chem. Soc. The ongoing collaboration with S.Butcher, is poised to combine NOE and DQC constraints to improve structure refinement. This will include the study of a 30 kDa RNA homodimer with a helical packing motif known as the tetraloop receptor. This motif plays an important role in tertiary structure formation in many different ribozymes. The second RNA structure of interest is derived from HIV-1 stem-loop domain involved in translational frameshifting (Staple and Butcher, NAR 2003, pdb code 1PJY). This RNA structure is essential for viral replication, but occurs in the context of a larger (45 nucleotide) RNA of unknown structure. The uncertainty in the structure is the relationship between the two helices, which are separated by a 3 nucleotide purine "hinge" region. The length of the molecule, based on molecular modeling, is approximately 71¿. However, this distance is unknown and may be less than 71¿ if the hinge region causes a bend between the two helices, as expected.

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 对RNA的研究是全球基因组学计划的基础。它在翻译储存在DNA中的遗传信息并通过核糖体机制表现出来方面发挥着关键作用。对病毒和细菌RNA的研究是RNA研究的重要组成部分，并为疾病控制提供了见解。在RNA测序以及获得三维结构及其与RNA功能的关系方面，有大量的持续努力。在我们最初的工作中，我们应用DQC ESR来测量A-型RNA中的端到端距离。三个具有13、16和26个碱基对的RNA被连接到硫脲上的3-碘-乙酰氨基-丙氧基自旋标记。从DQC计算了5‘-5’的距离，得到5-5‘连接的氮氧化物上的电子自旋距离分别为40、55和72？，这与所提出的结构很好地吻合。描述了双量子滤波再聚焦初级回波(DQF-RPE)在26b.p。《华尔街日报》刊登了《核糖核酸》。化学。SoC。正在进行的与S.Butcher的合作，准备将NOE和DQC约束结合起来，以改进结构改进。这将包括研究一种带有螺旋堆积基序的30 kDa RNA同源二聚体，称为Tetraloop受体。该基序在许多不同核酶的三级结构形成中起着重要作用。第二个感兴趣的RNA结构来自参与翻译框架转移的HIV-1茎环结构域(Staple和Butcher，NAR 2003，PDB代码1PJY)。这种RNA结构对病毒复制是必不可少的，但发生在结构未知的较大(45个核苷酸)RNA的背景下。结构上的不确定性是两个螺旋之间的关系，这两个螺旋被一个3核苷酸的嘌呤“铰链”区域分开。根据分子模型，该分子的长度约为71？然而，这个距离是未知的，如果铰链区域如预期的那样导致两个螺旋之间的弯曲，则可能小于71？