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Metal ion binding to an RNA internal loop


Bartova, Simona; Alberti, Elena; Sigel, Roland K O; Donghi, Daniela (2016). Metal ion binding to an RNA internal loop. Inorganica Chimica Acta, 452:104-110.

Abstract

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.

Abstract

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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Chemistry
Dewey Decimal Classification:540 Chemistry
Language:English
Date:2016
Deposited On:24 Oct 2016 10:56
Last Modified:29 May 2017 07:25
Publisher:Elsevier
ISSN:0020-1693
Publisher DOI:https://doi.org/10.1016/j.ica.2016.02.050

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