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Studying metal ion binding properties of a three-way junction RNA by heteronuclear NMR

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Publication date 2016
Author Bartova Simona, Pechlaner Maria, Donghi Daniela, Sigel Roland K. O.,
Project Metal Ion-Guided Assembly and Structures of the Catalytic Core of Ribozymes
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Original article (peer-reviewed)

Journal JBIC Journal of Biological Inorganic Chemistry
Volume (Issue) 21(3)
Page(s) 319 - 328
Title of proceedings JBIC Journal of Biological Inorganic Chemistry
DOI 10.1007/s00775-016-1341-3

Open Access

Type of Open Access Publisher (Gold Open Access)


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.