Metal-Ion Interactions with Nucleic Acids and Their Constituents

Sigel, Roland K. O.; Sigel, Helmut

doi:10.1016/b978-0-08-097774-4.00317-x

Cited by 19 publications

(28 citation statements)

References 419 publications

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“…S4). G•C base pairs but also A•U tracks have been shown previously to bind divalent ions (Korth and Sigel 2012;Sigel and Sigel 2013). In the following, we now focus our analysis of the chemical shift changes on the 11-nt loop region and their comparison in the absence and in the presence of IBS1 (Fig.…”

Section: Mgmentioning

confidence: 99%

“…In Figure 6B, the major groove of the EBS1•IBS1 helix is visible as a tunnel of dense negative potential, which makes it an appealing candidate for metal ion binding with N7 and O6 of G14 and G63 and O4 of U64 being possible coordinating atoms. Indeed, G•U wobble pairs such as G14•U64 often attract Mg 2+ ions to bind in their major groove (Allain and Varani 1995;Sigel and Sigel 2013 …”

Section: Mgmentioning

confidence: 99%

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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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Section: Mgmentioning

confidence: 99%

Section: Mgmentioning

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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“…In most cases, such a competent structure can be achieved by Mg 2+ -assisted folding of the riboswitch. Mg 2+ favors the formation and stabilization of the tertiary structure of the polyanionic RNA by reducing the strong electrostatic repulsions experienced by the closely positioned phosphodiester groups (Pyle 2002;Draper 2004;Woodson 2005;Freisinger and Sigel 2007;Sigel and Pyle 2007;Chu et al 2008;Sigel and Sigel 2013). Divalent metal ions like Mg 2+ have been reported to be playing indispensable roles in the case of riboswitches in the formation of an active tertiary structure (Lemay et al 2006;Noeske et al 2007b;Serganov et al 2009;Haller et al 2011a;Jenkins et al 2011;Ramesh et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Mg²⁺-induced conformational changes in the btuB riboswitch from E. coli

Choudhary

Sigel

2013

RNA

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Mg2+ has been shown to modulate the function of riboswitches by facilitating the ligand-riboswitch interactions. The btuB riboswitch from Escherichia coli undergoes a conformational change upon binding to its ligand, coenzyme B 12 (adenosylcobalamine, AdoCbl), and down-regulates the expression of the B 12 transporter protein BtuB in order to control the cellular levels of AdoCbl. Here, we discuss the structural folding attained by the btuB riboswitch from E. coli in response to Mg 2+ and how it affects the ligand binding competent conformation of the RNA. The btuB riboswitch notably adopts different conformational states depending upon the concentration of Mg 2+ . With the help of in-line probing, we show the existence of at least two specific conformations, one being achieved in the complete absence of Mg 2+ (or low Mg 2+ concentration) and the other appearing above ∼0.5 mM Mg 2+ . Distinct regions of the riboswitch exhibit different dissociation constants toward Mg 2+ , indicating a stepwise folding of the btuB RNA. Increasing the Mg 2+ concentration drives the transition from one conformation toward the other. The conformational state existing above 0.5 mM Mg 2+ defines the binding competent conformation of the btuB riboswitch which can productively interact with the ligand, coenzyme B 12 , and switch the RNA conformation. Moreover, raising the Mg 2+ concentration enhances the ratio of switched RNA in the presence of AdoCbl. The lack of a AdoCbl-induced conformational switch experienced by the btuB riboswitch in the absence of Mg 2+ indicates a crucial role played by Mg 2+ for defining an active conformation of the riboswitch.

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“…1) [4,5]. While always being interested to understand the binding equilibrium down to the atomic coordination pattern [6], he also characterized weak interactions between metal ions and nucleotides in the past two decades, and transferred his findings to the situation in larger nucleic acid structures, where metal ions play a crucial role for structure and catalysis [7].…”

Section: Celebrating Helmut Sigelmentioning

confidence: 99%