title: Severe axial bending of RNA induced by the U1A binding element present in the 3' untranslated region of the U1A mRNA.
abstract: The 3' untranslated region of the U1A mRNA contains a binding site for the U1A protein that consists of two asymmetric internal bulges. The bulges each comprise a loop of seven unpaired bases opposing a single base (termed a U1A box). The seven-base loops are located on opposite strands, distributed in a symmetrical manner about the intervening four-base duplex. We have investigated the global conformation of this binding element. Comparison of electrophoretic mobilities of RNA duplexes interrupted by a single U1A box with a series of duplexes of the same length containing oligoadenine bulges indicates that the individual boxes cause a substantial kinking of the helix axis, estimated to be 90 (+/- 10) degrees. A series of RNA duplexes were constructed containing a U1A box separated from an A5 bulge by a duplex section of length between 3 and 21 bp. It was found that the electrophoretic mobilities of these species varied sinusoidally, indicating that the U1A box introduces a defined kink into the RNA helix, rather than a point of flexibility. Electrophoretic experiments with the complete U1A binding element suggest that the axial trajectories of the two U1A boxes combine to give an approximately in-line, 180 degrees change in duplex direction.
authors.affiliation: Department of Biochemistry, University Dundee, UK.
authors.forename: R J
authors.initials: RJ
authors.lastname: Grainger
authors.forename: A I
authors.initials: AI
authors.lastname: Murchie
authors.forename: D G
authors.initials: DG
authors.lastname: Norman
authors.forename: D M
authors.initials: DM
authors.lastname: Lilley
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D004591:Electrophoresis, Polyacrylamide Gel; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry / Q000235:genetics; D012330:RNA, Double-Stranded / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry*; D016601:RNA-Binding Proteins; D017412:Ribonucleoprotein, U1 Small Nuclear / Q000235:genetics* / Q000378:metabolism
chemical_list: D009843:Oligoribonucleotides; D012330:RNA, Double-Stranded; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D017412:Ribonucleoprotein, U1 Small Nuclear; C075339:U1A protein