title: Nature of the ribosomal mRNA track: analysis of ribosome-binding sites containing different sequences and secondary structures.
abstract: The ribosomal mRNA track was investigated by toeprinting 30S ribosomes, in the presence or absence of tRNA, using a variety of different ribosome-binding sites. We found that: (1) the ribosome, by itself, recognizes the mRNA translational initiation site; (2) the ribosomal mRNA track makes extensive contact with mRNA independent of tRNA and the start codon; (3) ribosome-mRNA complexes are less stable than complexes containing tRNA; and (4) toeprinting can be used to analyze the contour of the ribosomal mRNA track, yielding information on its "height" as well as its "length" dimension. Examination of several ribosome-binding sites, including those containing very stable secondary structure, indicated that the "height" of the mRNA track is quite roomy, while the nucleotide distance between the site of Shine-Dalgarno annealing, the P site, and the 3'-edge of the mRNA track is fixed. The data suggest a mechanism for tethering regulatory elements to the ribosome during translation.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309.
authors.forename: S
authors.initials: S
authors.lastname: Ringquist
authors.forename: M
authors.initials: M
authors.lastname: MacDonald
authors.forename: T
authors.initials: T
authors.lastname: Gibson
authors.forename: L
authors.initials: L
authors.lastname: Gold
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D017931:DNA Primers; D004926:Escherichia coli / Q000378:metabolism; D008961:Models, Structural; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012194:RNA-Directed DNA Polymerase / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D017931:DNA Primers; D012333:RNA, Messenger; D012194:RNA-Directed DNA Polymerase