RUI: Examining Non-Canonical Interactions in Small RNA Motifs

Colorado College, Colorado Springs CO

Investigators

Abstract

Intellectual Merit: RNA molecules play important roles in all aspects of gene expression as well as many other cellular processes. Inside the cell, RNA molecules form distinct structures to interact with DNA, proteins, other RNAs and with various metabolites to carry out these functions. RNA molecules contain various recurrent structural features or motifs. This project aims to increase understanding of the details of bonding within recurrent RNA motifs and to elucidate rules for RNA structure formation. Colorado College undergraduates will measure the stabilities of small RNA structures using thermodynamic methods, including thermal denaturation and isothermal calorimetry. Particular regions of RNA will then be modified, and RNA stabilities before and after the modification will be compared to identify key contributors to bonding for each structural motif. Improved understanding of the general rules for structure formation will improve our ability to get greater information from the genome databases, to predict the structures formed by RNA in the cell and to elucidate their functions and mechanisms of action. Detailed thermodynamic parameters for recurrent RNA structures that guide and stabilize the folding of RNA as it is transcribed will improve our understanding of RNA folding, as these structures may serve as nucleation sites for the formation of higher-order structures. Broader Impact: Broader impacts of this work include the scientific impact of improved knowledge of RNA structural motifs and recruitment and training of undergraduates in current research methods both inside and outside of the classroom. The laboratories in biochemistry courses are being modified to introduce research methodology to the students in the classroom. In nucleic acids biochemistry course, students will design an RNA-based project and apply their thermodynamic knowledge to understanding RNA structures. This project will strengthen their understanding of thermodynamics and RNA structure and function along introducing them to RNA research. Undergraduate students will be presented with an option to do research starting in their introductory classes. Up to eight undergraduate students will work in the research laboratory and participate in developing and testing hypotheses on small RNA structure and function. Women and minority students from biochemistry classes will be given priority to do research in the laboratory. In addition, undergraduate students will be provided opportunities to participate in outreach work with Longfellow and Audubon Elementary Schools. Elementary school students will learn the basic principles of science by testing hypothesis on concepts such as solubility and density. Students will make a positive contribution to the society by using their scientific knowledge to provide information about RNA to the general public on topics such as HIV's life cycle and its treatment; this in turn makes science relevant to their lives. The science outreach projects to the community are specifically designed to raise the scientific literacy of the general public. Sharing of equipment and expertise with University of Colorado, Colorado Springs will build bridges locally and will benefit all involved. High school students and teachers from Pine Creek High School will also participate in RNA research during the summer. Quantitative methods will be introduced into biology courses at Pine Creek High School.