title: Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA.
abstract: 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.
authors.affiliation: Department of Chemistry and the Skaggs Institute of Chemical Biology The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037, USA wong@scripps.edu
authors.forename: C H
authors.initials: CH
authors.lastname: Wong
authors.forename: M
authors.initials: M
authors.lastname: Hendrix
authors.forename: E S
authors.initials: ES
authors.lastname: Priestley
authors.forename: W A
authors.initials: WA
authors.lastname: Greenberg
mesh_terms: D000900:Anti-Bacterial Agents / Q000378:metabolism / Q000494:pharmacology*; D006863:Hydrogen-Ion Concentration; D007612:Kanamycin / Q000378:metabolism / Q000494:pharmacology; D008745:Methylation; D009355:Neomycin / Q000378:metabolism / Q000494:pharmacology; D009994:Osmolar Concentration; D010303:Paromomycin / Q000378:metabolism / Q000494:pharmacology; D012329:RNA, Bacterial / Q000187:drug effects* / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D007612:Kanamycin; D010303:Paromomycin; D009355:Neomycin