title: Detecting ligand binding to a small RNA target via saturation transfer difference NMR experiments in D(2)O and H(2)O.
abstract: A small RNA motif is used as a target for ligand-based NMR-screening by saturation transfer difference (STD) NMR experiments. The prerequisites for using a small RNA target in STD experiments, such as saturation time, frequency, and pulses, are discussed. We also show that it is of advantage to use D2O as solvent instead of H2O due to the reduced R1 relaxation rate in D2O. The 27-nucleotide model of the ribosomal A-site was known to bind the aminoglycoside paromomycin with high affinity. This binding interaction could be detected easily, proving the effectiveness of STD NMR experiments as a screening tool for RNA-ligand interactions.
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA.
authors.forename: Moriz
authors.initials: M
authors.lastname: Mayer
authors.forename: Thomas L
authors.initials: TL
authors.lastname: James
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism*; D017666:Deuterium Oxide / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010303:Paromomycin / Q000737:chemistry / Q000378:metabolism*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000378:metabolism*; D014867:Water / Q000737:chemistry
chemical_list: D000900:Anti-Bacterial Agents; D012335:RNA, Ribosomal; D014867:Water; D010303:Paromomycin; D017666:Deuterium Oxide