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

通过这一奖项，生命过程化学项目资助了宾厄姆顿大学的Eriks Rozners和奥尔巴尼大学的Paul F.Agis之间的合作努力，以开发研究RNA分子的新方法，特别是那些被称为非编码的方法。RNA是存在于生命系统中的几种主要生物聚合物之一，在这些系统中它发挥着重要的功能。最广为人知的功能之一是在基因表达的翻译步骤中将信息从DNA转移到蛋白质。在这个过程中使用的RNA被称为(蛋白质的)编码。最近，许多非编码RNA被发现，尽管这些RNA的功能尚未确定。Rozners和Agis的建议描述了一种使用肽核酸(PNA)识别具有双螺旋结构的非编码RNA的方法。这项建议是基于PIs最近的发现，即单链(Ss)PNA可以与双链(DS)RNA形成三链，比PNA和DNA形成的三链更稳定。这些结构有助于揭示更多关于RNA及其在新陈代谢和细胞功能中的具体作用的细节，并可以在开发新的生物和医学工具方面产生更广泛的影响。该项目正在产生更广泛的影响，在一个跨学科的研究领域为几名研究生和本科生提供平衡的动手培训，从而为这些学生未来的技术工作做好准备。研究的重点是开发PNA，这是一种合成的DNA类似物，可以结合具有高序列选择性的双链非编码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困难的问题。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，作为核酸的一个关键特征，氢键介导的碱基配对在RNA的分子识别中一直没有得到充分的利用。由于RNA的碱基已经在双螺旋中配对，所以ds RNA最选择性和最直接的序列读出将是主要的沟槽三螺旋形成。多肽核酸，PNA，在生理条件下与双链RNA形成高度稳定和序列选择性的三螺旋。本项目的具体目标是：(1)研究利用碱基修饰的PNA对混合的嘧啶-嘌呤RNA链的三螺旋识别；(2)研究阳离子多肽与PNA的结合和细胞摄取；以及(3)探索PNA-RNA三链的分子识别，目的是利用结构信息为未来合理设计新的更好的RNA结合剂提供依据。

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.