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

有了这个奖项，生命过程的化学计划正在资助宾厄姆顿大学的埃里克·罗兹纳斯和保罗·F·里德尔之间的合作努力。Agris在奥尔巴尼大学的研究，以开发新的方法来研究RNA分子，特别是那些所谓的非编码。RNA是存在于生命系统中的几种主要类型的生物聚合物之一，它在其中发挥重要功能。 其中最著名的功能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被称为编码（蛋白质）。 近年来，人们发现了许多非编码RNA，但其功能还不清楚。 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。 该提议建立在PI最近发现的基础上，即单链（ss）PNA可以与双链（ds）RNA形成三链体，其比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特定作用的更多细节，并可以在生物学和医学新工具的开发中产生更广泛的影响。该项目通过在跨学科研究领域为研究生和本科生提供均衡的实践培训，从而为这些学生未来的技术导向工作做好准备，从而产生更广泛的影响。研究的重点是开发PNA，DNA的合成类似物，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，并且这种结构的分子识别是一个困难的问题。设计使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，这是核酸的一个关键特征，在RNA的分子识别中没有得到充分利用。由于RNA的核碱基在双螺旋中已经是碱基配对的，所以对于dsRNA来说，最具选择性和最直接的序列读出将是大沟三螺旋的形成。肽核酸，PNA，在生理相关条件下与双链RNA形成高度稳定和序列选择性的三螺旋。本项目的具体目标是：（1）研究使用核碱基修饰的PNA对RNA的嘧啶-嘌呤混合片段的三螺旋识别;（2）研究阳离子肽缀合的PNA的RNA结合和细胞摄取;和（3）探索PNA-RNA三链体的分子识别，目的是利用结构信息为未来合理设计新的和更好的RNA结合剂。

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.