title: Identification of neomycin B-binding site in T box antiterminator model RNA.
abstract: The T box transcription antitermination mechanism regulates the expression of unique genes in many Gram-positive bacteria by responding, in a magnesium-dependent manner, to uncharged cognate tRNA base pairing with an antiterminator RNA element and other regions of the 5'-untranslated region. Model T box antiterminator RNA is known to bind aminoglycosides, ligands that typically bind RNA in divalent metal ion-binding sites. In this study, enzymatic footprinting and spectroscopic assays were used to identify and characterize the binding site of neomycin B to an antiterminator model RNA. Neomycin B binds the antiterminator bulge nucleotides in an electrostatic-dependent manner and displaces 3-4 monovalent cations, indicating that the antiterminator likely contains a divalent metal ion-binding site. Neomycin B facilitates rather than inhibits tRNA binding indicating that bulge-targeted inhibitors that bind the antiterminator via non-electrostatic interactions may be the more optimal candidates for antiterminator-targeted ligand design.
authors.affiliation: Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA.
authors.forename: Rajaneesh
authors.initials: R
authors.lastname: Anupam
authors.forename: Leyna
authors.initials: L
authors.lastname: Denapoli
authors.forename: Abigael
authors.initials: A
authors.lastname: Muchenditsi
authors.forename: Jennifer V
authors.initials: JV
authors.lastname: Hines
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002942:Circular Dichroism; D005601:Framycetin / Q000737:chemistry*; D008957:Models, Genetic; D012313:RNA / Q000737:chemistry* / Q000235:genetics*
chemical_list: D005601:Framycetin; D012313:RNA