title: The conformation of loop E of eukaryotic 5S ribosomal RNA.
abstract: The solution structure of a 27-nucleotide duplex, including the internal loop E from Xenopus laevis 5S ribosomal RNA, has been studied by two-dimensional NMR spectroscopy, followed by restrained molecular dynamics. The highly conserved internal loop closes to form a G.A base pair and a reverse-Hoogsteen A.U base pair. Extensive interstrand stacking between these uncommon base pairs provides a structural explanation for an interstrand ultraviolet-induced cross-link. A guanosine residue is bulged into the major groove and may form a base-triple with the adjacent reverse-Hoogsteen A.U pair. The structure of the less highly-conserved portion of the loop is less well-defined by the NMR data. A single-nucleotide deletion mutant has a very different, open conformation without mismatched base pairs [Varani, G., Wimberly, B., & Tinoco, I. Jr. (1989) Biochemistry 28, 7760-7772]. The implications of the structure for binding of the transcription factor TFIIIA and the cytotoxin alpha-sarcin are discussed.
authors.affiliation: Department of Chemistry, University of California, Berkeley 94720.
authors.forename: B
authors.initials: B
authors.lastname: Wimberly
authors.forename: G
authors.initials: G
authors.lastname: Varani
authors.forename: I
authors.initials: I
authors.lastname: Tinoco
mesh_terms: D000818:Animals; D001483:Base Sequence; D004591:Electrophoresis, Polyacrylamide Gel; D006367:HeLa Cells; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012341:RNA, Ribosomal, 5S / Q000737:chemistry* / Q000528:radiation effects; D014466:Ultraviolet Rays; D014982:Xenopus laevis
chemical_list: D012341:RNA, Ribosomal, 5S