RNA-protein interactions are critical to many cellular processes including the regulation of gene expression. A great deal of genetic and biochemical data exists for several RNA-protein systems; however, the structural principles that govern RNA specific recognition by RNA binding proteins are poorly understood. The bacteriophage R17 contains one of the most well characterized RNA-protein interactions. The coat protein of R17 binds tightly and specifically to an RNA hairpin containing the translation start site of the viral replicase gene. This study will focus on the application of hetero-nuclear magnetic resonance (NMR) spectroscopy to probe the structural elements that give rise to this interaction. Structural data will be generated for the RNA hairpins in the absence and presence of R17 coat protein. We will also investigate the structure and-dynamics of loop and stem variants that show different degrees of protein binding affinity. Because RNA molecules have the ability to fold to form unique secondary and tertiary structures, RNA binding proteins are forced to distinguish between a diverse array of three dimensional shapes -- each possessing a precise electrostatic arrangement The R17 system represents a convenient model that will allow us to identify a few of the structural components employed by RNA molecules to confer specificity to RNA-protein interactions. The principles governing molecular recognition in the R17 system should be relevant to RNA-protein interactions in eukaryotic cells. The principles discovered here may be used in the preparation of RNA or protein ligands designed to perform a specific task such as site specific cleavage of a nucleic acid fragment in vivo or in vitro.
