Folding RNA: from AIDS to the Human Genome

描述（由申请人提供）：本研究的最终目标是表征指导RNA折叠的相互作用，并利用这些知识从其序列中可靠地预测RNA分子的结构。由于大多数疾病都是通过RNA介导的，而包括HIV在内的一些病毒的RNA基因组的二级结构在很大程度上是未知的，因此我们的研究结果可以导致合理的治疗设计。预测RNA结构的能力也将进一步解释人类基因组计划和其他测序工作所确定的序列。我们的研究结果也可能有助于打击生物恐怖主义，因为一旦基因组测序，它们可能提供一种快速设计治疗方法的方法，包括siRNA和反义化合物。通过对寡核苷酸热力学和结构性质的研究，为结构预测奠定了基础。特别强调的是，将放在内部循环的稳定性和结构的序列依赖性。与计算化学家的新合作将提供深入了解决定二级和局部三维结构的相互作用。通过自由能最小化的二级结构预测将增加来自序列比较、化学作图、寡核苷酸结合和NMR的约束，以部分补偿影响折叠的因素的不完整知识。特别是，将开发新的微阵列和纳米颗粒方法来测量和解释化学修饰的五聚体和六聚体与折叠RNA的结合。这将为设计一种通用的微阵列奠定基础，该微阵列可用于询问任何RNA的结构。化学作图和微阵列方法鉴定不在沃森-克里克对中的核苷酸。新的核磁共振辅助二级结构预测（NAPSS）方法使用未分配的光谱，通过识别典型碱基对区域（包括假结）来进一步限制折叠空间。预测方法的能力将通过尝试确定R2反转录转座子的5'编码区的323个核苷酸的二级结构来测试。在2006年，发现R2 RNA的该区域具有在将序列插入基因组期间暂时协调R2蛋白质的第二链DNA切割的新功能。初步结果表明，RNA含有一个新的假结。大多数疾病都是通过RNA介导的，包括艾滋病毒在内的一些病毒都有RNA基因组。本研究的目标是能够从其序列中可靠地预测RNA的结构，以便为合理设计靶向RNA的治疗方法提供基础。这些结果也可能有助于打击生物恐怖主义，因为一旦基因组测序，它们可能提供一种快速设计治疗方法的方法。

DESCRIPTION (provided by applicant): The ultimate goal of this research is to characterize the interactions directing RNA folding, and to use this knowledge to predict reliably the structures of RNA molecules from their sequences. Since most diseases are mediated through RNA, and some viruses, including HIV, have RNA genomes with largely unknown secondary structures, our results can lead to rational design of therapeutics. The ability to predict RNA structure should also further the interpretation of sequences determined by the Human Genome Project and other sequencing efforts. Our results may also contribute to fighting bioterrorism because they potentially provide a rapid way to design therapeutics, including siRNA and antisense compounds, once a genome has been sequenced. The foundation for structure prediction will be advanced by studies of the thermodynamic and structural properties of oligonucleotides. Particular emphasis will be placed on the sequence dependence of stability and structure for internal loops. New collaborations with computational chemists will provide insight into the interactions determining both secondary and local three dimensional structure. Secondary structure prediction by free energy minimization will be augmented with constraints from sequence comparison, chemical mapping, oligonucleotide binding, and NMR to partially compensate for incomplete knowledge of the factors affecting folding. In particular, new microarray and nanoparticle methods will be developed to measure and interpret binding of chemically modified pentamers and hexamers to folded RNA. The foundation will be laid for design of a universal microarray that can be used to interrogate the structure of any RNA. The chemical mapping and microarray methods identify nucleotides that are not in Watson-Crick pairs. The new NMR assisted prediction of secondary structure (NAPSS) method uses unassigned spectra to further restrict folding space by identifying regions of canonical base pairs, including pseudoknots. The power of the predictive methods will be tested by attempting to determine the secondary structure of 323 nucleotides of the 5' coding region of an R2 retrotransposon. In 2006, it was discovered that this region of R2 RNA has a novel function of temporally orchestrating second strand DNA cleavage by R2 protein during insertion of the sequence into a genome. Initial results indicate that the RNA contains a novel pseudoknot. Project Narrative (Relevance) Most diseases are mediated through RNA, and some viruses, including HIV, have RNA genomes. The goal of this research is to be able to predict reliably the structure of an RNA from its sequence in order to provide a foundation for rational design of therapeutics targeting RNA. The results may also help fight bioterrorism because they potentially provide a rapid way to design therapeutics once a genome has been sequenced.