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

有了这个奖项，生命过程化学项目资助了宾厄姆顿大学的erik Rozners和奥尔巴尼大学的Paul F. Agris之间的合作，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发挥重要作用的几种主要生物聚合物之一。在基因表达的翻译步骤中，最著名的功能之一是从DNA到蛋白质的信息传递。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，但这些非编码rna的功能尚未确定。Rozners和Agris的提案描述了一种利用肽核酸（PNAs）识别具有双螺旋结构的非编码rna的方法。该建议建立在pi最近发现的基础上，即单链PNAs可以与双链RNA形成三联体，这比PNA与DNA形成的三联体更稳定。这些结构可以帮助揭示更多关于RNA的细节及其在代谢和细胞功能中的特定作用，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几名研究生和本科生提供平衡的实践培训，从而为这些学生将来从事以技术为导向的工作做好准备，从而产生进一步广泛的影响。研究的重点是开发PNAs， DNA的合成类似物，结合双链非编码RNA具有高序列选择性。大多数非编码rna以双链结构折叠，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的核碱基已经在双螺旋结构中进行碱基配对，因此对ds RNA最具选择性和最直接的序列读出将是主要的凹槽三螺旋结构。肽核酸（PNA）在生理相关条件下与双链RNA形成高度稳定、序列选择性强的三螺旋结构。本课题的具体目标是：(1)利用核碱基修饰的PNA研究对RNA混合嘧啶-嘌呤束的三螺旋识别；(2)研究阳离子多肽结合PNA的RNA结合和细胞摄取；(3)探索RNA -RNA三联体的分子识别，目的是利用结构信息来合理设计新的和更好的RNA结合物。

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.