IN-VITRO SELECTION OF A VIOMYCIN-BINDING RNA PSEUDOKNOT

Background: The peptide antibiotic viomycin inhibits ribosomal protein synthesis, group I intron self-splicing and self-cleavage of the huma n hepatitis delta virus ribozyme. To understand the molecular basis of RNA binding and recognition by viomycin, we isolated a variety of nov el viomycin-binding RNA molecules using in vitro selection. Results: M ore than 90% of the selected RNA molecules shared one continuous highl y conserved region of 14 nucleotides. Mutational analyses, structural probing, together with footprinting experiments by chemical modificati on, and Pb2+-induced cleavage showed that this conserved sequence harb ours the antibiotic-binding site and forms a stem-loop structure, More over, the loop is engaged in a long-range interaction forming a pseudo knot. Conclusions: A comparison between the novel viomycin-binding mot if and the natural RNA target sites for viomycin showed that all these segments forma pseudoknot al the antibiotic-binding site. We therefor e conclude that this peptide antibiotic has a strong selectivity for p articular RNA pseudoknots.