RNA Folding and RNA-Protein Binding Analyzed by Fluorescence Anisotropy and Resonance Energy Transfer

Abstract

Ribonucleic acids (RNA) perform a host of functions in all living things. The vast majority of these roles are associated with diverse aspects of gene expression, including but not limited to delivery of genetic information between the genome (usually DNA) and protein synthetic machinery, coordination of processing events on nascent RNA molecules, and delivery of amino acids to translating ribosomes, which themselves are largely composed of RNA. More recent concepts in RNA metabolism include cis-regulation of gene expression by riboswitches1 and trans-regulation through small, non-coding RNAs2. Over the past two decades, a large body of work has described catalytic functions for many RNA molecules, from small structured RNAs capable of self-cleavage to the peptidyltransfer functions of ribosomes3,4. Finally, the heterogeneous nature of RNA structure and its amenability to reiterative selection procedures has prompted significant biotechnological interest in RNA aptamers. These are generally short RNA sequences that exhibit high affinity and selectivity for specific molecular targets, and show considerable promise as tools for diagnostic sensing and modulation of biomolecular function5,6