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

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 kappa I element within domain 1 (D1 kappa I ). We recently solved the NMR structure of D1 kappa I derived from the mitochondrial group II intron ribozyme Sc.ai5 gamma and demonstrated that Mg(II) is essential for its stabilization. Here, we performed a detailed multinuclear NMR study of metal ion interactions with D1 kappa I , 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 H-1, N-15, C-13, and P-31 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 zeta tetraloop receptor and various metal ion interactions in the GAAA tetraloop and kappa element. These results together with our recently published data on Mg(II) interaction provide a much better understanding of Mg(II) binding to D1 kappa I , and reveal how intricate and complex metal ion interactions can be.