title: Structure of a U.U pair within a conserved ribosomal RNA hairpin.
abstract: A conserved hairpin corresponding to nt 1057-1081 of large subunit rRNA (Escherichia coli numbering) is part of a domain targeted by antibiotics and ribosomal protein L11. The stem of the hairpin contains a U.U juxtaposition, found as either U.U or U.C in virtually all rRNA sequences. This hairpin has been synthesized and most of the aromatic and sugar protons were assigned by two-dimensional proton NMR. Distances and sugar puckers deduced from the NMR data were combined with restrained molecular dynamics calculations to deduce structural features of the hairpin. The two U residues are stacked in the helix, form one NH3-O4 hydrogen bond and require an extended backbone conformation (trans alpha and gamma) at one of the U nucleotides. The hairpin loop, UAGAAGC closed by a U-A pair, is the same size as tRNA anticodon loops, but not as well ordered.
authors: Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
authors: Y X
authors: YX
authors: Wang
authors: S
authors: S
authors: Huang
authors: D E
authors: DE
authors: Draper
mesh_terms: D000926:Anticodon; D001483:Base Sequence; D002241:Carbohydrates / Q000737:chemistry; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics; D006859:Hydrogen / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010759:Phosphorus Isotopes; D011522:Protons; D012329:RNA, Bacterial / Q000737:chemistry*; D012335:RNA, Ribosomal / Q000737:chemistry*; D014498:Uracil / Q000737:chemistry*
chemical_list: D000926:Anticodon; D002241:Carbohydrates; D010759:Phosphorus Isotopes; D011522:Protons; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D014498:Uracil; D006859:Hydrogen