Methods to Detect and Characterize Metal Ion Binding Sites in RNA

Erat, Michèle C.; Sigel, Roland K. O.

doi:10.1039/9781849732512-00037

Cited by 42 publications

(12 citation statements)

References 226 publications

(195 reference statements)

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“…The higher the charge density, the stronger the interaction with water, and the more difficult it will be to dehydrate the metal ion [52]. Being rather small (~0.65 Å) Mg 2+ has a high charge density and is therefore surrounded by six ordered water molecules in octahedral coordination [52,79]. In contrast, K + (1.3 Å radius) is accompanied by eight or nine less ordered waters [52].…”

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confidence: 99%

Metal ion induced heterogeneity in RNA folding studied by smFRET

Börner

Kowerko

Miserachs

et al. 2016

Coordination Chemistry Reviews

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More than two decades investigating nucleic acids and ribonucleic acids (RNA) by single molecule Förster Resonance Energy Transfer (smFRET) have passed. It turned out that sample heterogeneity in structure and function of RNA molecules as well as folding intermediates, kinetic subpopulations, and interconversion rates of conformational states of RNA biomolecules, all of which are usually hidden in ensemble type experiments, are often observed characteristics. Besides proteins, metal ions play a crucial role in RNA folding and dynamics, as well as RNA/RNA or RNA/DNA interactions. RNA molecules form discrete conformational intermediates before reaching the native three-dimensional fold, whereby metal ions guide the folding pathway by changing the energetic barriers between local and global minima in the energy landscape. Here we review recent advances in the characterization of the role of metal ions in folding and function of nucleic acid structures by means of smFRET. Subsequently, the workflow of smFRET data analysis is described and exemplified by the metal ion-depending folding and dynamics of the group IIB intron from S. cerevisiae and RNA-RNA binding kinetics of this ribozyme's 5'-splice site formation.

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confidence: 99%

Metal ion induced heterogeneity in RNA folding studied by smFRET

Börner

Kowerko

Miserachs

et al. 2016

Coordination Chemistry Reviews

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“…K(I) is the most abundant intracellular monovalent metal ion, and is often associated to RNA for charge neutralization, while Mg(II) is considered a true RNA cofactor, and may be involved in catalysis in the so-called two-metal-ion mechanism [55]. There are different ways to investigate the interactions between metal ions and RNA [56,57]. Biochemical and spectroscopic techniques used to study such interactions include, for instance, metal ion induced cleavage experiments, sulphur rescue and nucleotide analogue interference mapping experiments, X-ray crystallography, EPR and NMR spectroscopy, and have been recently reviewed [56,57].…”

Section: Rna Structure and Its Intrinsic Need For Metal Ionsmentioning

confidence: 99%

Covalent and non-covalent binding of metal complexes to RNA

Alberti

Zampakou

Donghi

2016

Journal of Inorganic Biochemistry

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Targeting nucleic acids with metal complexes is an exciting and widely explored field of research. Following the discovery of the anticancer drug cisplatin, a number of metal complexes have been designed, synthesised, and tested for their DNA binding properties. On the contrary, the interaction of metal complexes with RNA has been much less investigated. RNA is an essential biomolecule, involved in a variety of crucial cellular functions, which offers a much wider structural diversity than DNA. As such, RNA represents an attractive target for the design and the development of structure-selective therapeutic and diagnostic agents. A few recent publications describe the ability of various metal complexes to interact with RNA, and the binding of cisplatin and derivatives to RNA is being currently investigated. This short review offers an overview of some recent advances on both covalent and non-covalent interactions of metal complexes with RNA and addresses the potential of targeting RNA non-duplex structures.

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“…Due to their physiological abundance, divalent metal ions like Mg 2+ help to assemble the active tertiary structure of the polyanionic RNA not only by shielding the negatively charged sugar-phosphate backbone but also by facilitating specific tertiary interactions within nucleobases (Misra and Draper, 1998; Pyle, 2002; Woodson, 2005). These metal ion interactions are mediated either through an inner sphere or an outer sphere co-ordination where the contacts to the RNA are made directly or via water molecules, respectively (Erat and Sigel, 2011; Schnabl et al, 2011). …”

Section: Introductionmentioning

confidence: 99%

Tb3+-Cleavage Assays Reveal Specific Mg2+ Binding Sites Necessary to Pre-fold the btuB Riboswitch for AdoCbl Binding

2017

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Riboswitches are RNA elements that bind specific metabolites in order to regulate the gene expression involved in controlling the cellular concentration of the respective molecule or ion. Ligand recognition is mostly facilitated by Mg2+ mediated pre-organization of the riboswitch to an active tertiary fold. To predict these specific Mg2+ induced tertiary interactions of the btuB riboswitch from E. coli, we here report Mg2+ binding pockets in its aptameric part in both, the ligand-free and the ligand-bound form. An ensemble of weak and strong metal ion binding sites distributed over the entire aptamer was detected by terbium(III) cleavage assays, Tb3+ being an established Mg2+ mimic. Interestingly many of the Mn+ (n = 2 or 3) binding sites involve conserved bases within the class of coenzyme B12-binding riboswitches. Comparison with the published crystal structure of the coenzyme B12 riboswitch of S. thermophilum aided in identifying a common set of Mn+ binding sites that might be crucial for tertiary interactions involved in the organization of the aptamer. Our results suggest that Mn+ binding at strategic locations of the btuB riboswitch indeed facilitates the assembly of the binding pocket needed for ligand recognition. Binding of the specific ligand, coenzyme B12 (AdoCbl), to the btuB aptamer does however not lead to drastic alterations of these Mn+ binding cores, indicating the lack of a major rearrangement within the three-dimensional structure of the RNA. This finding is strengthened by Tb3+ mediated footprints of the riboswitch's structure in its ligand-free and ligand-bound state indicating that AdoCbl indeed induces local changes rather than a global structural rearrangement.

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Methods to Detect and Characterize Metal Ion Binding Sites in RNA

Cited by 42 publications

References 226 publications

Metal ion induced heterogeneity in RNA folding studied by smFRET

Metal ion induced heterogeneity in RNA folding studied by smFRET

Covalent and non-covalent binding of metal complexes to RNA

Tb3+-Cleavage Assays Reveal Specific Mg2+ Binding Sites Necessary to Pre-fold the btuB Riboswitch for AdoCbl Binding

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