Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA

Chem Biol. 1998 Jul;5(7):397-406. doi: 10.1016/s1074-5521(98)90073-4.


Background: Aminoglycoside antibiotics bind to the A-site of the decoding region of 16S RNA in the bacterial ribosome, an interaction that is probably responsible for their activity. A detailed study of the specificity of aminoglycoside binding to A-site RNA would improve our understanding of their mechanism of antibiotic activity.

Results: We have studied the binding specificity of several aminoglycosides with model RNA sequences derived from the 16S ribosomal A-site using surface plasmon resonance. The 4,5-linked (neomycin) class of aminoglycosides showed specificity for wild-type A-site sequences, but the 4,6-linked class (kanamycins and gentamicins), generally showed poor specificity for the same sequences. Methylation of a cytidine in the target RNA, as found in the Escherichia coli ribosome, had negligible effects on aminoglycoside binding.

Conclusions: Although both 4,5- and 4, 6-linked aminoglycosides target the same ribosomal site, they appear to bind and effect antibiotic activity in different manners. The aminoglycosides might recognize different RNA conformations or the interaction might involve different RNA tertiary structures that are not equally sampled in our ribosome-free model. These results imply that models of ribosomal RNA must be carefully designed if the data are expected to accurately reflect biological activity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / metabolism
  • Anti-Bacterial Agents / pharmacology*
  • Hydrogen-Ion Concentration
  • Kanamycin / metabolism
  • Kanamycin / pharmacology
  • Methylation
  • Neomycin / metabolism
  • Neomycin / pharmacology
  • Osmolar Concentration
  • Paromomycin / metabolism
  • Paromomycin / pharmacology
  • RNA, Bacterial / drug effects*
  • RNA, Bacterial / metabolism
  • RNA, Ribosomal, 16S / drug effects*
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 16S / metabolism


  • Anti-Bacterial Agents
  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • Kanamycin
  • Paromomycin
  • Neomycin