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 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.
Wallis
M G
MG
Institute of Microbiology and Genetics University of Vienna Dr. Bohrgasse 9, A-1030, Vienna, Austria.
Streicher
B
B
Wank
H
H
von Ahsen
U
U
Clodi
E
E
Wallace
S T
ST
Famulok
M
M
Schroeder
R
R
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*
D000900:Anti-Bacterial Agents; D015347:RNA Probes; D007854:Lead; D012313:RNA; C015563:tuberactinomycin; D004776:Enviomycin; D014756:Viomycin