Identification and application of functional RNAs

RNA assumes many roles in nature. As a structural entity, it is responsible for proxying genetic information, ferrying amino acids and organizing ribosome architecture. RNA also participates in several genetic regulatory mechanisms. Catalytic RNAs are responsible for the faithful modification of unprocessed transfer, ribosomal and messeger RNAs, and the assembly of proteins from amino acid monomers may be performed by RNA-derived catalytic residues in the ribosome. Previously researchers have developed methods for the isolation of unnatural RNA ligands and enzymes from random sequence pools. We have used these techniques in order to develop novel biosensors and biosensor components. RNA ligands (aptamers) were isolated from a random sequence pool that bind and inhibit ricin A-chain, a ribosome-inactivating protein and proposed biological warfare agent. In addition, ribozymes that were previously engineered to respond to a set of ligands were incorporated into a sensor platform for the first demonstration of an RNA-based detection system for the simultaneous detection of diverse analyte classes including DNA, proteins, peptides and small-molecules. We have also developed a set of computational tools in order to identify functional RNAs from both random sequence pools and genomic sequence databases. A computationally-accessible model was conceived in order to describe and predict the structural rearrangements undergone by allosteric ribozymes upon ligand binding, and the model was in turn used to select novel allosteric ribozymes from random sequence pools. In addition, we have used a structure-based search strategy in order to characterize well-folded regions in mRNAs with the goal of discovering additional examples of a novel class of genetic regulatory element, the riboswitches.