title: Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.
abstract: RNA molecules with high affinity for immobilized Ni2+ were isolated from an RNA pool with 50 randomized positions by in vitro selection-amplification. The selected RNAs preferentially bind Ni2+ and Co2+ over other cations from first series transition metals. Conserved structure motifs, comprising about 15 nt, were identified that are likely to represent the Ni2+ binding sites. Two conserved motifs contain an asymmetric purine-rich internal loop and probably a mismatch G-A base pair. The structure of one of these motifs was studied with proton NMR spectroscopy and formation of the G-A pair at the junction of helix and internal loop was demonstrated. Using Ni2+ as a paramagnetic probe, a divalent metal ion binding site near this G-A base pair was identified. Ni2+ ions bound to this motif exert a specific stabilization effect. We propose that small asymmetric purine-rich loops that contain a G-A interaction may represent a divalent metal ion binding site in RNA.
authors.affiliation: Laboratorium für Biochemie, Universität Bayreuth, Germany.
authors.forename: H P
authors.initials: HP
authors.lastname: Hofmann
authors.forename: S
authors.initials: S
authors.lastname: Limmer
authors.forename: V
authors.initials: V
authors.lastname: Hornung
authors.forename: M
authors.initials: M
authors.lastname: Sprinzl
mesh_terms: D000225:Adenine; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D006147:Guanine; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009532:Nickel / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D011522:Protons; D011687:Purines / Q000737:chemistry*; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D014466:Ultraviolet Rays
chemical_list: D011522:Protons; D011687:Purines; D006147:Guanine; D012313:RNA; D009532:Nickel; D000225:Adenine