Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.
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.
Hofmann
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HP
Laboratorium für Biochemie, Universität Bayreuth, Germany.
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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
D011522:Protons; D011687:Purines; D006147:Guanine; D012313:RNA; D009532:Nickel; D000225:Adenine