Metal ion binding to an RNA internal loop

• Published in: Inorganica Chimica Acta 2016-10, Vol.452, p.104-110
• Main Authors: Bartova, Simona, Alberti, Elena, Sigel, Roland K.O., Donghi, Daniela
• Format: Article
• Language: English
• Subjects: Binding sites; Cobalt; Metal ion binding; Metal ions; NMR; NMR spectroscopy; Nuclear magnetic resonance; Potassium perchlorates; Ribonucleic acid; RNA; Spectrum analysis; Splicing
• ISSN: 0020-1693; 1873-3255
• DOI: 10.1016/j.ica.2016.02.050

Metal ions are crucial for both RNA structure and function. In this work heteronuclear NMR was exploited to study the metal ion binding sites of an RNA internal loop. Besides Mg(II), cobalt(III)hexammine and Cd(II) were used to investigate outer- and inner-sphere coordination, respectively. [Display omitted] •Metal ion binding to an RNA internal loop was studied by 1H, 15N, 31P and 113Cd NMR.•Mg(II) inner- and outer-sphere binding probed with cobalt(III)hexammine and Cd(II).•Cd(II) macrochelate was observed at the 5′-end triphosphate.•All three metal ions bind to the internal loop.•The use of KCl or KClO4 in Cd(II) titrations leads to significant differences. Studying the interaction of metal ions with RNA is challenging because of the fast dynamics of the system and the intricate interplay between structural and functional roles of metal ions. NMR spectroscopy is an exceptional tool to investigate such interactions in solution and allows for a detailed description of both metal ion binding sites and binding modes in complex and dynamic RNA structures. We recently applied heteronuclear NMR to study the metal ion binding properties of a three-way junction RNA (D1κζ) which plays an important role in group II intron splicing, and observed metal ion binding in both κ and ζ regions of the construct. Here we concentrate in more detail on the ζ region (D1ζ) using NMR to investigate the interaction with Mg(II), Cd(II) and cobalt(III)hexammine. Our data confirm Cd(II) induced macrochelate formation at the 5′-end triphosphate, suggest an overall similar behaviour for the two divalent metal ions, but with much clearer changes in chemical shifts upon Cd(II) addition, and reveal only little changes upon cobalt(III)hexammine addition, allowing to discriminate between inner- and outer-sphere binding. Moreover, we observed distinct differences when we titrated the sample with Cd(II) in the presence of either KCl or KClO4 as background monovalent salt.