RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide

J Mol Biol. 1996 Oct 4;262(4):421-36. doi: 10.1006/jmbi.1996.0526.


The codon-anticodon interaction on the ribosome occurs in the A site of the 30 S subunit. Aminoglycoside antibiotics, which bind to ribosomal RNA in the A site, cause misreading of the genetic code and inhibit translocation. Biochemical studies and nuclear magnetic resonance spectroscopy were used to characterize the interaction between the aminoglycoside antibiotic paromomycin and a small model oligonucleotide that mimics the A site of Escherichia coli 16 S ribosomal RNA. Upon chemical modification, the RNA oligonucleotide exhibits an accessibility pattern similar to that of 16 S rRNA in the 30 S subunit. In addition, the oligonucleotide binds specifically aminoglycoside antibiotics. The antibiotic binding site forms an asymmetric internal loop, caused by non-canonical base-pairs. Nucleotides that are important for binding of paromomycin were identified by performing quantitative footprinting on oligonucleotide sequence variants and include the C1407.G1494 base-pair, and A.U base-pair at positions 1410/1490, and nucleotides A1408, A1493 and U1495. The asymmetry of the internal loop, which requires the presence of a nucleotide in position 1492, is also crucial for antibiotic binding. Introduction into the oligonucleotide of base changes that are known to confer aminoglycoside resistance in 16 S rRNA result in weaker binding of paromomycin to the oligonucleotide. Oligonucleotides homologous to eukaryotic rRNA sequences show reduced binding of paromomycin, suggesting a physical origin for the species-specific action of aminoglycosides.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Aminoglycosides / metabolism*
  • Autoradiography
  • DNA Footprinting
  • Drug Resistance, Microbial / genetics
  • Magnetic Resonance Spectroscopy
  • Nucleic Acid Conformation
  • Paromomycin / metabolism
  • RNA, Bacterial / chemistry*
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / metabolism*
  • RNA, Ribosomal, 16S / chemistry
  • Species Specificity
  • Structure-Activity Relationship


  • Aminoglycosides
  • RNA, Bacterial
  • RNA, Ribosomal
  • RNA, Ribosomal, 16S
  • Paromomycin