UC Irvine

RNA is capable of storing genetic information and facilitating catalysis, two fundamental requirements of life. Present day cells use DNA as the main receptacle of genetic information and proteins to enable a majority of functions in the cell. RNA serves as the intermediate between DNA and proteins and possesses the capabilities of both. The vast functionality of RNA has led to the hypothesis that RNA predates both DNA and proteins as one of the earliest molecules necessary and responsible for the evolution of cells. RNA is involved in many important biological processes required for gene expression including mRNA splicing and translation which ultimately lead to protein production. The extent to which RNA is implicated in biological processes remains open to discovery. Many well characterized RNAs capable of catalysis (ribozymes) and metabolite binding (aptamers) have been discovered throughout nature, but their biological significance has not been fully elucidated. New tools to probe and tune expression of RNA would be beneficial in uncovering the roles and capabilities of RNA in vivo and in vitro.

The scope of the work herein focuses on designing novel tools by laboratory evolution of RNA. The main objectives are to develop RNA based tools capable of tracing RNA by luminescence, tuning expression of RNA (by a riboswitch), and improving methods for in vitro RNA discovery. Improving methods for RNA discovery is crucial to expanding the molecular tools available to study RNA and its biological targets. A luminescent RNA based tracer will provide direct analytic feedback of expression as well as a method to follow the localization of RNAs of interest. Riboswitches are RNA-based expression systems that alter expression based on binding to a target; a riboswitch can be coupled with an RNA to tune and study the expression of the target RNA. These novel RNA tools will aid in uncovering the informational and functional significance of the RNA they are coupled with, providing new methods to discover the biological roles of RNA. Such advancements will result in not only a better understanding of RNA biology in vivo, but also produce important insights both in elucidating the possible roles of RNA in life, and in employing RNA in a multitude of reactions in vitro.