title: Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs.
abstract: The structure of 5'-pppGGAC(GUAAUA)GUCC has been deduced from NMR data. The six-nucleotide hairpin loop is highly conserved in large subunit ribosomal RNA and confers unusual stability on RNA hairpins. Standard assignment methods, including through-bond strategies for backbone protons, were used to assign all 31P resonances and all but two of the non-exchangeable protons. The model calculated by restrained molecular dynamics shows that the loop adopts a specific structure stabilized by five non-canonical hydrogen bonds. An edge-to-edge G-A pair (hydrogen bonds G5 N3-A10 NH6, G5 H2-A1O N7 and A10 NH6-G5 O2') closes the hairpin loop. A trans 5' P-O bond at A7 reverses the direction of the backbone and is stabilized by two base-backbone hydrogen bonds (U6 NH3-U9 OP and U6 O2'-A8 N7). The only unstructured part of the loop is U9, which is completely unstacked and also the only phylogenetically variable position. The U6-A7-A8 "U-turn" reproduces hydrogen bonds and backbone torsion seen in the tRNA anticodon loop and TTpsiC loop, and in an internal loop of the hammerhead ribozyme. G-A is a common closing mismatch in ribosomal RNA hairpin loops. The U-turn and G-A pair found in this hexaloop structure may therefore be common structural units of RNA hairpin loops.
authors.affiliation: Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: S
authors.initials: S
authors.lastname: Huang
authors.forename: Y X
authors.initials: YX
authors.lastname: Wang
authors.forename: D E
authors.initials: DE
authors.lastname: Draper
mesh_terms: D001483:Base Sequence; D002241:Carbohydrates / Q000737:chemistry; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry*; D012335:RNA, Ribosomal / Q000737:chemistry*
chemical_list: D002241:Carbohydrates; D012329:RNA, Bacterial; D012335:RNA, Ribosomal