title: Studying metal ion binding properties of a three-way junction RNA by heteronuclear NMR.
abstract: Self-splicing group II introns are highly structured RNA molecules, containing a characteristic secondary and catalytically active tertiary structure, which is formed only in the presence of Mg(II). Mg(II) initiates the first folding step governed by the κζ element within domain 1 (D1κζ). We recently solved the NMR structure of D1κζ derived from the mitochondrial group II intron ribozyme Sc.ai5γ and demonstrated that Mg(II) is essential for its stabilization. Here, we performed a detailed multinuclear NMR study of metal ion interactions with D1κζ, using Cd(II) and cobalt(III)hexammine to probe inner- and outer-sphere coordination of Mg(II) and thus to better characterize its binding sites. Accordingly, we mapped (1)H, (15)N, (13)C, and (31)P spectral changes upon addition of different amounts of the metal ions. Our NMR data reveal a Cd(II)-assisted macrochelate formation at the 5'-end triphosphate, a preferential Cd(II) binding to guanines in a helical context, an electrostatic interaction in the ζ tetraloop receptor and various metal ion interactions in the GAAA tetraloop and κ element. These results together with our recently published data on Mg(II) interaction provide a much better understanding of Mg(II) binding to D1κζ, and reveal how intricate and complex metal ion interactions can be.
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.|Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic.
authors.forename: Simona
authors.initials: S
authors.lastname: Bartova
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.|Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
authors.forename: Maria
authors.initials: M
authors.lastname: Pechlaner
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. daniela.donghi@chem.uzh.ch.
authors.forename: Daniela
authors.initials: D
authors.lastname: Donghi
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. roland.sigel@chem.uzh.ch.
authors.forename: Roland K O
authors.initials: RK
authors.lastname: Sigel
mesh_terms: D001665:Binding Sites; D002104:Cadmium / Q000737:chemistry*; D003035:Cobalt / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D012313:RNA / Q000737:chemistry*
chemical_list: D002104:Cadmium; D003035:Cobalt; D012313:RNA; D008274:Magnesium
keywords: Metal ion binding; NMR; RNA