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

在化学系生命过程化学（CLP）项目的支持下，纽约州立大学宾汉姆顿分校的Eriks Rozners教授和詹姆斯A。伊丽莎白敦学院的麦凯正在研究分子识别具有生物学意义的非编码核糖核酸（RNA）的新方法。随着CRISPR-Cas9等DNA编辑生化技术的出现，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，不到2%的脱氧核糖核酸（DNA）编码功能蛋白质，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、成像和功能调节对于生物技术的基础科学和实际应用非常有用。该项目旨在建立靶向双链RNA的新方法，这是RNA生物化学中长期存在的问题和实际限制。重要的是，该项目将通过跨越传统机构界限扩大跨学科合作研究，并通过研究和指导活动促进培训和发展多元化，具有全球竞争力的STEM（科学，技术，工程和数学）劳动力，从而扩大其影响。 合作继续5年的合作伙伴关系，建立了一个桥梁，伊丽莎白敦学院（主要是本科院校）的学生，特别是妇女，少数民族，和第一代大学生从本科学习过渡到高级研究生学习在研究型大学。工作将康廷改善本科生和研究生的STEM教育，并为有兴趣在主要本科院校探索职业生涯的研究生提供独特的培训。序列选择性RNA结合剂的开发对于理解非编码RNA的生物化学是重要的，并且可能强烈地影响基础RNA生物学以及生物技术和合成生物学中的实际应用。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的沃森-克里克碱基对的整个Hoogsteen面。这将通过开发新的核碱基和结合模式来实现，所述新的核碱基和结合模式将两条反向平行的PNA链置于大沟中，每条链与它们各自的RNA链氢键合。新的PNA的性质将使用合成有机化学进行优化，以促进对双链RNA的不同序列的识别，这有可能解决RNA分子识别中的一个长期存在的问题。如果成功，这项研究将使各种应用，如，成像和功能控制的监管RNA，设计核糖开关的合成生物学，和抑制生物学重要的RNA的基础研究。这个奖项反映了NSF的法定使命，并已被认为是值得的支持，通过评估使用基金会的智力价值和更广泛的影响审查标准。

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.