Collaborative Research: Sequence Selective Recognition of Double-Stranded Non-Coding RNA via Triplex Forming PNA

合作研究：通过三链体形成 PNA 对双链非编码 RNA 进行序列选择性识别

• 批准号: 1407042
• 负责人: Paul Agris
• 金额: $ 15.52万
• 依托单位: SUNY at Albany
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-08-01 至 2019-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1407042&HistoricalAwards=false
• 关键词: Collaborative; Research; Sequence; Selective; Recognition

With this award, the Chemistry of Life Processes Program is funding a collaborative effort between Eriks Rozners of Binghamton University and Paul F. Agris at the University at Albany to develop new methods for the study of RNA molecules, specifically those termed non-coding. RNA is one of several major classes of biopolymers present in living systems where it plays important functions. One of the best known functions is of information transfer from DNA to proteins in the translation step of gene expression. The RNAs used in this process are called coding (of proteins). Recently many non-coding RNAs have been discovered although the function of these RNAs has not been identified yet. The proposal of Rozners and Agris describes a method for the identification of non-coding RNAs that have a double helix structure using peptide nucleic acids (PNAs). The proposal builds on the recent discovery made by the PIs that single stranded (ss) PNAs can form triplexes with double stranded (ds) RNA that are more stable than triplexes formed by PNA with DNA. These structures can help reveal more details about RNA and its specific roles in metabolism and cell function and can have a broader impact in the development of new tools for biology and medicine. The project is having a further broad impact by providing balanced hands-on training to several graduate and undergraduate students in an interdisciplinary research area, thus preparing these students for technology-oriented future work.The focus of the research is to develop PNAs, synthetic analogues of DNA, that bind double-stranded non-coding RNA with high sequence selectivity. Most non-coding RNAs fold in double-stranded conformations and molecular recognition of such structures is a difficult problem. Designing small molecules that selectively recognize RNA using hydrophobic or electrostatic interactions has been a challenging process. On the other hand, hydrogen bond mediated base pairing, which is a key feature of nucleic acids, has been underutilized in molecular recognition of RNA. Since the nucleobases of RNA are already base paired in the double helix, the most selective and straightforward sequence readout for ds RNA would be the major groove triple helix formation. Peptide nucleic acid, PNA, forms highly stable and sequence selective triple helices with double-stranded RNA at physiologically relevant conditions. The specific goals of this project are to: (1) study the triple helical recognition of mixed pyrimidine-purine tracts of RNA using nucleobase-modified PNA; (2) study the RNA binding and cellular uptake of PNA conjugated to cationic peptides; and (3) explore the molecular recognition of PNA-RNA triplexes with the goal of using the structural information for future rational design of new and better RNA binders.

凭借该奖项，生命过程化学项目正在资助宾厄姆顿大学的 Eriks Rozners 和奥尔巴尼大学的 Paul F. Agris 之间的合作，开发研究 RNA 分子（特别是非编码分子）的新方法。 RNA 是生命系统中存在的几大类生物聚合物之一，在生命系统中发挥着重要的功能。 最著名的功能之一是在基因表达的翻译步骤中从 DNA 到蛋白质的信息传递。此过程中使用的 RNA 称为（蛋白质）编码。 最近发现了许多非编码RNA，尽管这些RNA的功能尚未确定。 Rozners 和 Agris 的提案描述了一种使用肽核酸 (PNA) 鉴定具有双螺旋结构的非编码 RNA 的方法。 该提案基于 PI 最近的发现，即单链 (ss) PNA 可以与双链 (ds) RNA 形成三链体，比 PNA 与 DNA 形成的三链体更稳定。 这些结构可以帮助揭示有关 RNA 及其在代谢和细胞功能中的具体作用的更多细节，并且可以对生物学和医学新工具的开发产生更广泛的影响。该项目通过为跨学科研究领域的多名研究生和本科生提供平衡的实践培训，从而为这些学生为未来以技术为导向的工作做好准备，从而产生更广泛的影响。该研究的重点是开发 PNA，即 DNA 的合成类似物，能够以高序列选择性结合双链非编码 RNA。大多数非编码RNA以双链构象折叠，这种结构的分子识别是一个难题。设计利用疏水或静电相互作用选择性识别 RNA 的小分子一直是一个具有挑战性的过程。另一方面，氢键介导的碱基配对是核酸的一个关键特征，但在 RNA 的分子识别中尚未得到充分利用。由于 RNA 的核碱基在双螺旋中已经碱基配对，因此 ds RNA 最具选择性和最直接的序列读出将是主沟三螺旋的形成。肽核酸 (PNA) 在生理相关条件下与双链 RNA 形成高度稳定且序列选择性的三螺旋。本项目的具体目标是：（1）研究利用核碱基修饰的PNA对RNA混合嘧啶-嘌呤束的三螺旋识别； (2) 研究与阳离子肽缀合的PNA的RNA结合和细胞摄取； (3) 探索 PNA-RNA 三链体的分子识别，目标是利用结构信息来合理设计新的、更好的 RNA 结合剂。