title: Metal interactions with a GAAA RNA tetraloop characterized by (31)P NMR and phosphorothioate substitutions.
abstract: A metal site in a 5'-GAAA-3' tetraloop, a stabilizing and phylogenetically conserved RNA motif, is explored using (31)P NMR spectroscopy and phosphorothioate modifications. Similar to previous reports [Legault, P., and Pardi, A. (1994) J. Magn. Reson., Ser. B 103, 82-86], the (31)P NMR spectrum of a 12-nucleotide stem-loop sequence 5'-GGCCGAAAGGCC-3' exhibits resolved features from each of the phosphodiester linkages. Titration with Mg(2+) results in distinct shifts of a subset of these (31)P features, which are assigned to phosphodiesters 5' to A6, A7, and G5. Titration with Co(NH(3))(6)(3+) causes only a slight upfield shift in the A6 feature, suggesting that changes caused by Mg(2+) are due to inner-sphere metal-phosphate coordination. R(p)-Phosphorothioate substitutions introduced enzymatically 5' to each of the three A residues of the tetraloop provide well-resolved (31)P NMR features that are observed to shift in the presence of Cd(2+) but not Mg(2+), again consistent with a metal-phosphate site. Analysis of (31)P NMR spectra using the sequence 5'-GGGCGAAAGUCC-3' with single phosphorothioate substitutions in the loop region, separated into R(p) and S(p) diastereomers, provides evidence for an inner-sphere interaction with the phosphate 5' to A7 but outer-sphere or structural effects that cause perturbations 5' to A6. Introduction of an R(p)-phosphorothioate 5' to A7 results in a distinct (31)P NMR spectrum, consistent with thermodynamic studies reported in the accompanying paper that indicate a unique structure caused by this substitution. On the basis of these results and existing structural information, a metal site in the 5'-GAAA-3' tetraloop is modeled using restrained molecular dynamics simulations.
authors.affiliation: Department of Chemistry, Texas A&M University, College Station, Texas 77842-3012, USA.
authors.forename: M
authors.initials: M
authors.lastname: Maderia
authors.forename: T E
authors.initials: TE
authors.lastname: Horton
authors.forename: V J
authors.initials: VJ
authors.lastname: DeRose
mesh_terms: D009682:Magnetic Resonance Spectroscopy; D008670:Metals / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D010761:Phosphorus Radioisotopes; D012313:RNA / Q000737:chemistry*
chemical_list: D008670:Metals; D010761:Phosphorus Radioisotopes; D012313:RNA