CAREER: Determining The Fundamental Rules of RNA Tertiary Contact Formation

University Of Nebraska-Lincoln, Lincoln NE

Investigators

Abstract

This award is funded in part under the American Rescue Plan Act of 2021 (Public Law 117-2). Structured ribonucleic acids (RNAs) play critical roles in cellular functions, underlie the function of RNA viruses, and serve as blueprints for new artificial machines such as biosensors, biomolecular scaffolds, and regulators of synthetic biosynthesis pathways. RNA structure is composed of discrete and modular RNA motifs – helices, junctions, and loops. Functional RNAs often contain long-range tertiary contacts between two or more RNA motifs that lock RNA strands into well-defined structures required for function. This project aims to understand how tertiary contacts form in RNA structure. Tertiary contacts are the “glue” of RNA structure allowing them to form complex 3D structures. This project will decipher the rules of their formation, ultimately generating the first predictive model of tertiary contact formation. In conjunction, the program seeks to educate the next generation of scientists and the public in RNA folding and structure by engaging students and citizen scientists in novel science-based video games that allow participants to directly contribute to research outcomes. This will entail a new course on the molecular design of biomolecules that employ scientific videos games, which will allow students to design new biomolecules that will be experimentally tested in the lab. Findings from this integrated research and education program will have important long-term applications in harnessing RNA structure to build the next generation of RNA biosensors and therapeutics. Structured RNAs fold into complex 3D conformations that perform fundamental biological processes. These RNAs often contain long-range tertiary contacts between two or more RNA motifs that lock RNA strands into well-defined structures required for function. Currently, there is no method that can reliably predict tertiary contact formation. Predicting tertiary contacts is challenging as it is unknown which motifs will form tertiary contacts and whether it is possible for these motifs to be brought into proximity to form an interaction. This program seeks to develop the first predictive model of tertiary contact formation. Towards this goal the PI will use novel 3D RNA design and massively multiplexed biochemical assays to identify which motifs can form tertiary contacts; determine the 3D conformational flexibility of RNA elements that permit tertiary contact partners to be brought into proximity to interact, and build tertiary contact formation model and utilize it to improve the activity of a ribozyme. The development of a predictive model of tertiary contact formation will improve the fundamental understanding of structural mechanisms of RNA-regulated processes such as gene expression, protein translation, and mRNA splicing. This project is jointly funded by the Molecular Biophysics Cluster of the Molecular and Cellular Biosciences Division in the Directorate of Biological Sciences and by the Established Program to Stimulate Competitive Research (EPSCoR). 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.