Characterization of Metal Ion-Nucleic Acid Interactions in Solution

Pechlaner, Maria; Sigel, Roland K. O.

doi:10.1007/978-94-007-2172-2_1

Cited by 53 publications

(36 citation statements)

References 328 publications

(366 reference statements)

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“…Ligand exchange in earth alkaline metal aquo complexes occurs at very high rates (10 6 Hz ≤ k ex ≤ 10 9 Hz) (34). On the other end of the spectrum, M 2+ that are site-specifically bound to RNA are believed to exchange on a timescale of milliseconds because they are (partially) dehydrated and/or the cation makes two or more direct contacts to the RNA (chelation) (2,35).…”

Section: +mentioning

confidence: 99%

“…M n+ ions have been identified in numerous nucleic acid structures, and they typically display millimolar affinities for their binding sites (34,36,37). As a consequence, these sites are not fully occupied at physiological M n+ concentrations, providing a possible explanation for the heterogeneity observed in the majority of single-molecule studies addressing DNA and RNA folding.…”

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confidence: 99%

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Cation-induced kinetic heterogeneity of the intron–exon recognition in single group II introns

Kowerko

König

Skilandat

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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RNA is commonly believed to undergo a number of sequential folding steps before reaching its functional fold, i.e., the global minimum in the free energy landscape. However, there is accumulating evidence that several functional conformations are often in coexistence, corresponding to multiple (local) minima in the folding landscape. Here we use the 5′-exon-intron recognition duplex of a self-splicing ribozyme as a model system to study the influence of Mg 2+ NA folding is a hierarchical process that depends on the sequential formation of secondary and tertiary structures. As the RNA phosphate-sugar backbone is negatively charged, structural compaction creates electrostatic repulsion, which must be overcome by positive charges. The majority of negative charges are nonspecifically screened by the ion atmosphere, typically a set of dynamically exchanging M + ions (1). An estimated 10-20% of negative charge is, however, compensated by M n+ that bind site-specifically to the RNA molecule, in particular, Mg 2+ (2). One RNA molecule that is known to harbor several specific M 2+ binding sites is the self-splicing group II intron Sc.ai5γ from the yeast mitochondrial cox1 (cytochrome oxidase 1) gene (3). It is one of the largest known RNA enzymes, and both its folding pathway and catalysis are strictly dependent on Mg 2+. In turn, the splicing reaction is inhibited by small amounts of Ca 2+ (4). Site specificity of the two sequential transesterfication reactions is ensured by proper base pairing between distal exon-binding sites (5′ cleavage, EBS1 and 2; 3′ cleavage, EBS3) and intron-binding sites (IBS1, 2, and 3) (5).Single-molecule Förster resonance energy transfer (smFRET), i.e., distance-dependent energy transfer between a single pair of fluorophores, is ideally suited to study the cation-dependent conformational dynamics of single RNA molecules (6, 7). If different conformations lead to distinctly different transfer efficiencies, smFRET unveils the entire folding pathway, reports on the relative occurrence of all conformations present in the ensemble, and provides detailed information on the rates at which they interconvert (7). This is important because simple two-state folding is rarely observed in experimental data (8, 9). Rather, the vast conformational space sampled by biomolecules often results not only in folding intermediates but also in kinetic traps and/or multiple native states. In an smFRET experiment, individual molecules consequently display different behaviors that may or may not persist over the observation period (10). Heterogeneity has been precedented for a number of RNA molecules, including group I introns (11, 12), the hairpin ribozyme (13-17), and RNase P RNA (18). In addition, heterogeneity has been reported for different . However, the molecular basis of the phenomenon is often enigmatic, and its quantitative characterization is challenging (21).Here we use the 5′-exon-intron recognition site of the Sc.ai5γ ribozyme to study Mg 2+ -and Ca 2+ -mediated RNA-RNA structure formation by smFRET. ...

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Section: +mentioning

confidence: 99%

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confidence: 99%

Cation-induced kinetic heterogeneity of the intron–exon recognition in single group II introns

Kowerko

König

Skilandat

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…The electrostatic surface potentials of d3 ′ EBS1 and d3 ′ EBS1•IBS1 were calculated with the PDB2PQR version 1.8 webserver (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) (Dolinsky et al 2004) and visualized with the APBS Tools2 plugin (Baker et al 2001) for PYMOL (http://www.pymol.org). H]-NOESY spectra recorded at 298 K as described earlier (Erat and Sigel 2011;Pechlaner and Sigel 2012). MgCl 2 was added in steps of 0, 0.5, 1, 1.5, 2, 2.5, 3, 4, 5, 6, 6.5, and 7 mM to d3 ′ EBS1 and in steps of 0, 0.5, 1, 2 3, 4, 5, 6, 7, 8, and 10 …”

Section: Nmr Spectroscopymentioning

confidence: 99%

NMR structure of the 5′ splice site in the group IIB intron Sc.ai5γ—conformational requirements for exon–intron recognition

Kruschel

Skilandat

Sigel

2014

RNA

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A crucial step of the self-splicing reaction of group II intron ribozymes is the recognition of the 5 ′ exon by the intron. This recognition is achieved by two regions in domain 1 of the intron, the exon-binding sites EBS1 and EBS2 forming base pairs with the intron-binding sites IBS1 and IBS2 located at the end of the 5 ′ exon. The complementarity of the EBS1•IBS1 contact is most important for ensuring site-specific cleavage of the phosphodiester bond between the 5 ′ exon and the intron. Here, we present the NMR solution structures of the d3 ′ hairpin including EBS1 free in solution and bound to the IBS1 7-mer. In the unbound state, EBS1 is part of a flexible 11-nucleotide (nt) loop. Binding of IBS1 restructures and freezes the entire loop region. Mg 2+ ions are bound near the termini of the EBS1•IBS1 helix, stabilizing the interaction. Formation of the 7-bp EBS1•IBS1 helix within a loop of only 11 nt forces the loop backbone to form a sharp turn opposite of the splice site, thereby presenting the scissile phosphate in a position that is structurally unique.

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“…The most abundant divalent metal ion in living cells, Mg 2+ (10), has the same number of electrons as H 2 O and Na + and is mostly spectroscopically silent. Consequently, it is difficult to localize Mg 2+ and to differentiate single Mg 2+ ions from H 2 O or Na + by X-ray, NMR, or other spectroscopic methods.…”

Section: Introductionmentioning

confidence: 99%

MINAS—a database of Metal Ions in Nucleic AcidS

Schnabl

Suter

Sigel

2011

Nucleic Acids Research

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Correctly folded into the respective native 3D structure, RNA and DNA are responsible for uncountable key functions in any viable organism. In order to exert their function, metal ion cofactors are closely involved in folding, structure formation and, e.g. in ribozymes, also the catalytic mechanism. The database MINAS, Metal Ions in Nucleic AcidS (http://www.minas.uzh.ch), compiles the detailed information on innersphere, outersphere and larger coordination environment of >70 000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 Å radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids.

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Characterization of Metal Ion-Nucleic Acid Interactions in Solution

Cited by 53 publications

References 328 publications

Cation-induced kinetic heterogeneity of the intron–exon recognition in single group II introns

Cation-induced kinetic heterogeneity of the intron–exon recognition in single group II introns

NMR structure of the 5′ splice site in the group IIB intron Sc.ai5γ—conformational requirements for exon–intron recognition

MINAS—a database of Metal Ions in Nucleic AcidS

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