RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. Academic Article uri icon

Overview

MeSH

  • Autoradiography
  • DNA Footprinting
  • Drug Resistance, Microbial
  • Magnetic Resonance Spectroscopy
  • Nucleic Acid Conformation
  • Paromomycin
  • RNA, Ribosomal, 16S
  • Species Specificity
  • Structure-Activity Relationship

MeSH Major

  • Aminoglycosides
  • RNA, Bacterial
  • RNA, Ribosomal

abstract

  • 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 date

  • October 4, 1996

has subject area

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

Research

keywords

  • Journal Article

Identity

Language

  • eng

Digital Object Identifier (DOI)

  • 10.1006/jmbi.1996.0526

PubMed ID

  • 8893854

Additional Document Info

start page

  • 421

end page

  • 436

volume

  • 262

number

  • 4