title: Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer.
abstract: BACKGROUND
  Aminoglycoside antibiotics can target RNA folds with micromolar affinity and inhibit biological processes ranging from protein biosynthesis to ribozyme action and viral replication. Specific features of aminoglycoside antibiotic-RNA recognition have been probed using chemical, biochemical, spectroscopic and computational approaches on both natural RNA targets and RNA aptamers identified through in vitro selection. Our previous studies on tobramycin-RNA aptamer complexes are extended to neomycin B bound to its selected RNA aptamer with 100 nM affinity.
  
  
  RESULTS
  The neamine moiety (rings I and II) of neomycin B is sandwiched between the major groove floor of a 'zippered-up' G.U mismatch aligned segment and a looped-out purine base that flaps over the bound antibiotic. Specific intermolecular hydrogen bonds are observed between the charged amines of neomycin B and base mismatch edges and backbone phosphates. These interactions anchor 2-deoxystreptamine ring I and pyranose ring II within the RNA-binding pocket.
  
  
  CONCLUSIONS
  The RNA aptamer complexes with tobramycin and neomycin B utilize common architectural principles to generate RNA-binding pockets for the bound aminoglycoside antibiotics. In each case, the 2-deoxystreptamine ring I and an attached pyranose ring are encapsulated within the major groove binding pocket, which is lined with mismatch pairs. The bound antibiotic within the pocket is capped over by a looped-out base and anchored in place through intermolecular hydrogen bonds involving charged amine groups of the antibiotic.
authors.affiliation: Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
authors.forename: L
authors.initials: L
authors.lastname: Jiang
authors.forename: A
authors.initials: A
authors.lastname: Majumdar
authors.forename: W
authors.initials: W
authors.lastname: Hu
authors.forename: T J
authors.initials: TJ
authors.lastname: Jaishree
authors.forename: W
authors.initials: W
authors.lastname: Xu
authors.forename: D J
authors.initials: DJ
authors.lastname: Patel
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry*; D002240:Carbohydrate Sequence; D005601:Framycetin / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009844:Oligosaccharides / Q000737:chemistry*; D011522:Protons; D012313:RNA / Q000737:chemistry*; D014031:Tobramycin / Q000737:chemistry
chemical_list: D000900:Anti-Bacterial Agents; D009844:Oligosaccharides; D011522:Protons; D005601:Framycetin; D012313:RNA; D014031:Tobramycin