This proposal focuses on the investigation of structure, and specific protein-nucleotide interactions of the RNA-binding domain of E. coli. rho protein. This protein plays an important role in the termination of transcription in prokaryotic organisms. Rho is particularly intriguing in that it binds equally well single- stranded DNA and single-stranded DNA however, it is only activated when bound to RNA. NMR spectroscopy methods will be used to determine the structures of-the rho RNA binding domain when bound to single stranded RNA and single stranded DNA. Various oligonucleotide ligands and protein mutations will be used to probe the specific interactions between the protein and nucleic acids to further the understand molecular mechanism of rho-dependent transcription termination. While much has been learned about DNA binding protein in recent years, relatively little is known about RNA binding proteins. Characterization of the binding interactions of rho with nucleic acids will be helpful in understanding RNA binding in other proteins since the RNA binding domain has structural homology with many prokaryotic and eukaryotic RNA-binding proteins.
