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In vitro selection of a viomycin-binding RNA pseudoknot

M G Wallis1, B Streicher, H Wank

  • 1Institute of Microbiology and Genetics University of Vienna Dr. Bohrgasse 9, A-1030, Vienna, Austria.

Chemistry & Biology
|May 1, 1997
PubMed
Summary
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Viomycin, an antibiotic, selectively binds to specific RNA pseudoknots. Researchers identified a conserved RNA motif crucial for viomycin binding, revealing the molecular basis for its action.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • RNA Biology

Background:

  • Viomycin is a peptide antibiotic that inhibits crucial cellular processes like protein synthesis and RNA self-splicing.
  • Its mechanism involves interaction with RNA molecules, including the human hepatitis delta virus ribozyme.

Purpose of the Study:

  • To elucidate the molecular mechanisms of RNA recognition and binding by viomycin.
  • To identify novel RNA structures that interact with viomycin.

Main Methods:

  • In vitro selection (SELEX) was employed to isolate viomycin-binding RNA molecules.
  • Structural probing, mutational analysis, and chemical footprinting were used to characterize the RNA-viomycin interaction.

Main Results:

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  • A highly conserved 14-nucleotide RNA motif was identified in over 90% of selected molecules.
  • This motif forms a stem-loop structure with a pseudoknot, identified as the primary antibiotic-binding site.
  • The conserved sequence and pseudoknot structure are essential for viomycin binding.

    • Conclusions:

    • Viomycin exhibits strong selectivity for specific RNA pseudoknots.
    • The identified RNA motif represents a key structural element for viomycin recognition and binding.
    • This finding provides insight into the molecular basis of viomycin's antibiotic activity.