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.

Department of Analytical Chemistry University of Chemistry and Technology Prague Technická 5 166 28 Prague Czech Republic

Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland

Institute for Molecular Modeling and Simulation University of Natural Resources and Life Sciences Muthgasse 18 1190 Vienna Austria

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Nat Struct Mol Biol. 2007 Jan;14(1):37-44 PubMed

Chembiochem. 2007 Feb 12;8(3):306-14 PubMed

Biochemistry. 2000 Jul 18;39(28):8193-200 PubMed

Chemistry. 2001 Sep 3;7(17):3729-37 PubMed

RNA. 2014 Apr;20(4):516-27 PubMed

Annu Rev Biochem. 1995;64:435-61 PubMed

J Mol Biol. 2000 Feb 4;295(5):1211-23 PubMed

Methods Mol Biol. 2012;848:253-73 PubMed

RNA. 2005 Jan;11(1):1-6 PubMed

J Biomol NMR. 1998 Jul;12(1):1-23 PubMed

Biochemistry. 2009 Feb 24;48(7):1498-507 PubMed

Nucleic Acids Res. 2013 Feb 1;41(4):2489-504 PubMed

J Am Chem Soc. 2004 Jul 28;126(29):8908-9 PubMed

Dalton Trans. 2008 Oct 7;(37):4965-74 PubMed

Nucleic Acids Res. 2005 Nov 27;33(21):6674-87 PubMed

Dalton Trans. 2008 Feb 28;(8):1081-6 PubMed

Proc Natl Acad Sci U S A. 1983 Jul;80(14):4330-3 PubMed

J Mol Biol. 2008 Jan 11;375(2):572-80 PubMed

J Inorg Biochem. 1993 Jan;49(1):1-8 PubMed

Met Ions Life Sci. 2011;9:37-100 PubMed

Methods Enzymol. 2009;468:335-67 PubMed

EMBO J. 1998 Dec 1;17(23):7105-17 PubMed

RNA. 2000 Feb;6(2):199-205 PubMed

Science. 2008 Apr 4;320(5872):77-82 PubMed

FEBS Lett. 1998 Aug 21;433(3):301-6 PubMed

Chem Commun (Camb). 2005 Apr 28;(16):2069-79 PubMed

J Am Chem Soc. 2004 Jan 21;126(2):663-72 PubMed

J Mol Biol. 2005 Aug 12;351(2):371-82 PubMed

J Am Chem Soc. 2002 May 1;124(17):4595-601 PubMed

Biochemistry. 2014 Jan 28;53(3):579-90 PubMed

Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):988-1000 PubMed

Structure. 2007 Jul;15(7):761-72 PubMed

Biochemistry. 1997 Apr 22;36(16):4718-30 PubMed

Molecules. 2013 Nov 21;18(11):14414-29 PubMed

J Inorg Biochem. 2010 May;104(5):611-3 PubMed

Structure. 1996 Oct 15;4(10):1221-9 PubMed

RNA. 2007 Dec;13(12):2098-107 PubMed

Biochemistry. 1984 Oct 23;23(22):5262-71 PubMed

Nat Struct Mol Biol. 2004 Feb;11(2):187-92 PubMed

Genes Dev. 1999 Jul 1;13(13):1729-41 PubMed

Met Ions Life Sci. 2011;9:197-234 PubMed

Methods. 2001 Mar;23(3):201-5 PubMed

Met Ions Life Sci. 2013;11:191-274 PubMed

J Inorg Biochem. 1993 Feb 15;49(3):171-5 PubMed

Science. 1996 Mar 8;271(5254):1410-3 PubMed