title: AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices.
abstract: This study reveals that AA and AG oppositions occur frequently at the ends of helices in RNA crystal and NMR structures in the PDB database and in the 16 S and 23 S rRNA comparative structure models, with the G usually 3' to the helix for the AG oppositions. In addition, these oppositions are frequently base-paired and usually in the sheared conformation, although other conformations are present in NMR and crystal structures. These A:A and A:G base-pairs are present in a variety of structural environments, including GNRA tetraloops, E and E-like loops, interfaced between two helices that are coaxially stacked, tandem G:A base-pairs, U-turns, and adenosine platforms. Finally, given structural studies that reveal conformational rearrangements occurring in regions of the RNA with AA and AG oppositions at the ends of helices, we suggest that these conformationally unique helix extensions might be associated with functionally important structural rearrangements.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
authors.forename: T
authors.initials: T
authors.lastname: Elgavish
authors.forename: J J
authors.initials: JJ
authors.lastname: Cannone
authors.forename: J C
authors.initials: JC
authors.lastname: Lee
authors.forename: S C
authors.initials: SC
authors.lastname: Harvey
authors.forename: R R
authors.initials: RR
authors.lastname: Gutell
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D018360:Crystallography, X-Ray; D019992:Databases as Topic; D004926:Escherichia coli / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000235:genetics*; D012338:RNA, Ribosomal, 23S / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S