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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 1H, 15N, 13C, and 31P 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.

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Acknowledgments

Financial support by the Swiss National Science Foundation (Project Funding to RKOS and Ambizione Fellowship PZ00P2_136726 to DD), by the Scientific Exchange Program between Switzerland and the New Member States of the EU (Sciex Fellowship 13.326 to SB), by an ERC Starting Grant (MIRNA to RKOS), and by the University of Zurich is gratefully acknowledged.

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Correspondence to Daniela Donghi or Roland K. O. Sigel.

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Bartova, S., Pechlaner, M., Donghi, D. et al. Studying metal ion binding properties of a three-way junction RNA by heteronuclear NMR. J Biol Inorg Chem 21, 319–328 (2016). https://doi.org/10.1007/s00775-016-1341-3

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  • DOI: https://doi.org/10.1007/s00775-016-1341-3

Keywords

  • RNA
  • Metal ion binding
  • NMR