Folding RNA: from AIDS to the Human Genome

描述(由申请人提供)：这项研究的最终目标是表征指导RNA折叠的相互作用，并利用这一知识根据其序列可靠地预测RNA分子的结构。由于大多数疾病是通过RNA介导的，而一些病毒，包括HIV，具有基本上未知的二级结构的RNA基因组，我们的结果可以导致合理的治疗设计。预测RNA结构的能力也应该进一步解释由人类基因组计划和其他测序工作确定的序列。我们的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疗法的方法，包括siRNA和反义化合物。通过对寡核苷酸的热力学和结构性质的研究，将为结构预测奠定基础。将特别强调内部环路的稳定性和结构的顺序依赖性。与计算化学家的新合作将提供对决定二级和局部三维结构的相互作用的洞察。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、寡核苷酸结合和核磁共振的约束，以部分弥补对影响折叠的因素的不完全了解。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，该微阵列可以用于询问任何RNA的结构。化学图谱和微阵列方法识别不在Watson-Crick对中的核苷酸。新的核磁共振辅助二级结构预测(NAPSS)方法使用未分配的谱，通过识别包括假结在内的正则碱基对区域来进一步限制折叠空间。将通过尝试确定R2反转录转座子5‘编码区的323个核苷酸的二级结构来测试预测方法的能力。2006年，人们发现R2 RNA的这个区域具有一种新的功能，在序列插入基因组的过程中，R2蛋白可以暂时地协调R2蛋白对第二链DNA的切割。初步结果表明，该RNA含有一个新的伪结。项目简介(相关性)大多数疾病是通过RNA介导的，包括艾滋病毒在内的一些病毒具有RNA基因组。本研究的目的是能够从RNA的序列中可靠地预测其结构，为合理设计针对RNA的治疗药物提供基础。这些结果还可能有助于打击生物恐怖主义，因为一旦基因组测序完成，它们可能会提供一种快速设计疗法的方法。

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.