title: Mapping the inside of the ribosome with an RNA helical ruler.
abstract: The structure of ribosomal RNA (rRNA) in the ribosome was probed with hydroxyl radicals generated locally from iron(II) tethered to the 5' ends of anticodon stem-loop analogs (ASLs) of transfer RNA. The ASLs, ranging in length from 4 to 33 base pairs, bound to the ribosome in a messenger RNA-dependent manner and directed cleavage to specific regions of the 16S, 23S, and 5S rRNA chains. The positions and intensities of cleavage depended on whether the ASLs were bound to the ribosomal A or P site, and on the lengths of their stems. These data predict the three-dimensional locations of the rRNA targets relative to the positions of A- and P- site transfer RNAs inside the ribosome.
authors.affiliation: Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA.
authors.forename: S
authors.initials: S
authors.lastname: Joseph
authors.forename: B
authors.initials: B
authors.lastname: Weiser
authors.forename: H F
authors.initials: HF
authors.lastname: Noller
mesh_terms: D000926:Anticodon; D001482:Base Composition; D001483:Base Sequence; D004492:Edetic Acid / Q000031:analogs & derivatives / Q000378:metabolism; D005296:Ferrous Compounds / Q000378:metabolism; D017665:Hydroxyl Radical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009942:Organometallic Compounds / Q000378:metabolism; D015347:RNA Probes; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000378:metabolism; D012341:RNA, Ribosomal, 5S / Q000737:chemistry / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism*; D012360:RNA, Transfer, Phe / Q000737:chemistry / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism
chemical_list: D000926:Anticodon; D005296:Ferrous Compounds; D009942:Organometallic Compounds; D015347:RNA Probes; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S; D012341:RNA, Ribosomal, 5S; D012360:RNA, Transfer, Phe; D017665:Hydroxyl Radical; C042007:1-(4-bromoacetamidobenzyl)EDTA; D012343:RNA, Transfer; D004492:Edetic Acid