title: In vitro selection of a viomycin-binding RNA pseudoknot.
abstract: BACKGROUND
  The peptide antibiotic viomycin inhibits ribosomal protein synthesis, group I intron self-splicing and self-cleavage of the human hepatitis delta virus ribozyme. To understand the molecular basis of RNA binding and recognition by viomycin, we isolated a variety of novel viomycin-binding RNA molecules using in vitro selection.
  
  
  RESULTS
  More than 90% of the selected RNA molecules shared one continuous highly conserved region of 14 nucleotides. Mutational analyses, structural probing, together with footprinting experiments by chemical modification, and Pb2+-induced cleavage showed that this conserved sequence harbours the antibiotic-binding site and forms a stem-loop structure. Moreover, the loop is engaged in a long-range interaction forming a pseudoknot.
  
  
  CONCLUSIONS
  A comparison between the novel viomycin-binding motif and the natural RNA target sites for viomycin showed that all these segments form a pseudoknot at the antibiotic-binding site. We therefore conclude that this peptide antibiotic has a strong selectivity for particular RNA pseudoknots.
authors.affiliation: Institute of Microbiology and Genetics University of Vienna Dr. Bohrgasse 9, A-1030, Vienna, Austria.
authors.forename: M G
authors.initials: MG
authors.lastname: Wallis
authors.forename: B
authors.initials: B
authors.lastname: Streicher
authors.forename: H
authors.initials: H
authors.lastname: Wank
authors.forename: U
authors.initials: U
authors.lastname: von Ahsen
authors.forename: E
authors.initials: E
authors.lastname: Clodi
authors.forename: S T
authors.initials: ST
authors.lastname: Wallace
authors.forename: M
authors.initials: M
authors.lastname: Famulok
authors.forename: R
authors.initials: R
authors.lastname: Schroeder
mesh_terms: D000900:Anti-Bacterial Agents / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D003001:Cloning, Molecular; D017124:Conserved Sequence; D004776:Enviomycin / Q000031:analogs & derivatives / Q000378:metabolism; D006801:Humans; D007854:Lead / Q000737:chemistry; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism*; D015347:RNA Probes; D014756:Viomycin / Q000378:metabolism*
chemical_list: D000900:Anti-Bacterial Agents; D015347:RNA Probes; D007854:Lead; D012313:RNA; C015563:tuberactinomycin; D004776:Enviomycin; D014756:Viomycin