Collaborative Research: Nucleobase-Modified PNA for Sequence Selective Triple-Helical Recognition of Non-Coding RNA

合作研究：核碱基修饰的 PNA 用于非编码 RNA 的序列选择性三螺旋识别

• 批准号: 2107900
• 负责人: Eriks Rozners
• 金额: $ 46.8万
• 依托单位: SUNY at Binghamton
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2107900&HistoricalAwards=false
• 关键词: Collaborative; Research; Nucleobase; Modified; PNA

With the support of the Chemistry of Life Processes (CLP) Program in the Division of Chemistry, Professors Eriks Rozners of SUNY Binghamton and James A. MacKay of Elizabethtown College are studying new methods for molecular recognition of biologically significant non-coding ribonucleic acid (RNA). With the onset of biochemical technologies such as CRISPR-Cas9 for DNA-editing, and the challenges associated with emerging pathogens such as the SARS-CoV-2 virus (novel coronavirus), RNA (ribonucleic acid) chemistry and biochemistry is at the forefront of research. We know that less than 2% of deoxyribonucleic acid (DNA) encodes for functional proteins, while over 70% of DNA is transcribed into RNA. The non-coding RNAs play important yet not fully understood roles in regulation of biological processes. Selective recognition, imaging, and functional regulation of such RNAs will be highly useful for fundamental science and practical applications in biotechnology. This project aims to establish new ways of targeting double-stranded RNA, which has been a long-standing problem and practical limitation in RNA biochemistry. Importantly, the project will be broader in its impact through expanding interdisciplinary collaborative research across traditional institutional boundaries and fostering the training and development of a diverse, globally competitive STEM (science, technology, engineering and mathematics) workforce through research and mentoring activities. The collaboration continues a 5 year partnership that has established a bridge for Elizabethtown College (a primarily undergraduate institution) students, especially women, minorities, and first generation college students for transitioning from undergraduate studies to advanced graduate studies at a research university. Work will contine toward improving STEM education of undergraduate and graduate students, and offer unique training for post-graduate students interested in exploring careers at a primarily undergraduate institution. The development of sequence-selective RNA binders is important for understanding the biochemistry of non-coding RNAs and may strongly impact fundamental RNA biology and practical applications in biotechnology and synthetic biology. This collaborative study will develop new derivatives of peptide nucleic acid (PNA) that are potentially capable of recognizing the entire Hoogsteen face of Watson-Crick base pairs of double-stranded RNA. This is to be achieved by development of new nucleobases and binding modes that place two anti-parallel PNA strands in the major groove, each hydrogen-bonding to their respective RNA strand. The properties of the new PNAs will be optimized using synthetic organic chemistry to promote recognition of diverse sequences of double-stranded RNA, which has the potential to solve a long-standing problem in molecular recognition of RNA. If successful, this research will enable a variety of applications, such as, imaging and functional control of regulatory RNA, designer riboswitches for synthetic biology, and inhibition of biologically important RNA for fundamental studies.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

在化学系生命过程化学（CLP）项目的支持下，纽约州立大学宾厄姆顿分校的erik Rozners教授和伊丽莎白镇学院的James A. MacKay教授正在研究生物学上重要的非编码核糖核酸（RNA）分子识别的新方法。随着用于dna编辑的CRISPR-Cas9等生物化学技术的出现，以及与SARS-CoV-2病毒（新型冠状病毒）等新兴病原体相关的挑战，RNA（核糖核酸）化学和生物化学处于研究的前沿。我们知道，只有不到2%的脱氧核糖核酸（DNA）编码功能性蛋白质，而超过70%的DNA被转录成RNA。非编码rna在生物过程的调控中发挥着重要但尚未完全理解的作用。这些rna的选择性识别、成像和功能调控将在生物技术的基础科学和实际应用中发挥重要作用。本项目旨在建立靶向双链RNA的新途径，这是RNA生物化学中一个长期存在的问题和实际限制。重要的是，通过扩大跨传统机构边界的跨学科合作研究，并通过研究和指导活动促进多样化、具有全球竞争力的STEM（科学、技术、工程和数学）劳动力的培训和发展，该项目将产生更广泛的影响。这项合作延续了5年的伙伴关系，为伊丽莎白镇学院（主要是一所本科院校）的学生，特别是女性、少数民族和第一代大学生，从本科学习过渡到研究型大学的高级研究生学习搭建了一座桥梁。我们将继续致力于改善本科生和研究生的STEM教育，并为有兴趣在本科院校探索职业的研究生提供独特的培训。序列选择性RNA结合物的开发对于理解非编码RNA的生物化学具有重要意义，并可能对基础RNA生物学以及生物技术和合成生物学的实际应用产生重大影响。这项合作研究将开发新的肽核酸（PNA）衍生物，这些衍生物可能能够识别双链RNA的Watson-Crick碱基对的整个Hoogsteen面。这是通过开发新的核碱基和结合模式来实现的，这些模式将两条反平行的PNA链置于主槽中，每条与各自的RNA链形成氢键。利用合成有机化学对新PNAs的性质进行优化，以促进对不同双链RNA序列的识别，这有可能解决长期存在的RNA分子识别问题。如果成功，这项研究将实现多种应用，例如，调控RNA的成像和功能控制，合成生物学的设计核糖开关，以及对基础研究中重要的生物学RNA的抑制。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

2-Guanidyl pyridine PNA nucleobase for triple-helical Hoogsteen recognition of cytosine in double-stranded RNA

2-胍基吡啶 PNA 核碱基用于双链 RNA 中胞嘧啶的三螺旋 Hoogsteen 识别

• DOI: 10.1039/d2cc02615e
• 发表时间: 2022
• 期刊: Chemical Communications
• 影响因子: 4.9
• 作者: Ryan, Christopher A.;Baskevics, Vladislavs;Katkevics, Martins;Rozners, Eriks
• 通讯作者: Rozners, Eriks

Nucleobase and Linker Modification for Triple‐Helical Recognition of Pyrimidines in RNA Using Peptide Nucleic Acids

使用肽核酸对 RNA 中嘧啶进行三螺旋识别的核碱基和接头修饰

• DOI: 10.1002/cbic.202300291
• 发表时间: 2023
• 期刊: ChemBioChem
• 影响因子: 3.2
• 作者: Kumpina, Ilze;Baskevics, Vladislavs;Nguyen, Khoi D.;Katkevics, Martins;Rozners, Eriks
• 通讯作者: Rozners, Eriks