Metal Ions in RNA Catalysis

Frederiksen, John K.; Fong, Robert; Piccirilli, Joseph A.

doi:10.1039/9781847558763-00260

Cited by 9 publications

(14 citation statements)

References 191 publications

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“…For example, NH 4 + supports catalysis although it is not a hard metal ion, and its proposed ionic radius is equivalent to or exceeds that of K + . [24] Nevertheless, these studies further demonstrate that metal ion identity can impact the overall apparent p K a of ribozyme self-cleavage as well as phosphate oxygen affinity, thus suggesting that metal ions can serve alternative roles supporting the mechanism of catalysis. We have previously proposed an acid-base mechanism of catalysis that invokes a proton relay within the catalytic core of the ribozyme.…”

Section: Resultsmentioning

confidence: 95%

Analysis of Metal Ion Dependence in glmS Ribozyme Self‐Cleavage and Coenzyme Binding

et al. 2010

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The bacterial glmS ribozyme is a mechanistically unique functional RNA among both riboswitches and RNA catalysts. Its self-cleavage activity is the basis of riboswitch regulation of glucosamine-6-phosphate (GlcN6P) production, and catalysis requires GlcN6P as a coenzyme. Previous work has shown that the ligand amine of GlcN6P is essential for glmS ribozyme self-cleavage as is its protonation state. Metal ions are also essential within the glmS ribozyme core for both structure and function of the ribozyme. Although metal ions do not directly promote catalysis, we show that metal ion identity and the varying physicochemical properties of metal ions impact the rate of glmS ribozyme self-cleavage. Specifically, these studies demonstrate that metal ion identity impacts the overall apparent pKa of ribozyme self-cleavage, and metal ion binding largely reflects phosphate oxygen affinity. Results suggest that metal ions serve alternative roles supporting the mechanism of catalysis.

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Section: Resultsmentioning

confidence: 95%

Analysis of Metal Ion Dependence in glmS Ribozyme Self‐Cleavage and Coenzyme Binding

et al. 2010

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“…Mg 2 þ Binding to Loop C Short. Since Mg 2 þ is always associated with RNA stabilizing the 3D structure, mediating interactions with other molecules, and its function in general [13 -15] [33] [34], it is intriguing to find out how the intracellular Mg 2 þ concentration can be precisely and specifically sensed by the mgtA riboswitch. Looking at the proposed stem loops individually allows a detailed analysis of their coordination in the helical parts as well as the GAAA tetraloop.…”

Section: Down Regulation Of Mgta At High Mgmentioning

confidence: 99%

Unusually High‐Affinity Mg²⁺ Binding at the AU‐Rich Sequence within the Antiterminator Hairpin of a Mg²⁺ Riboswitch

Korth

Sigel

2012

Chemistry & Biodiversity

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Mg2+-Responsive riboswitches represent a fascinating example of bifunctional RNAs that sense Mg2+ ions with high selectivity and autonomously regulate the expression of Mg2+-transporter proteins. The mechanism of the mgtA riboswitch is scarcely understood, and a detailed structural analysis is called for to study how this RNA can selectively recognize Mg2+ and respond by switching between two alternative stem loop structures. In this work, we investigated the structure and Mg2+-binding properties of the lower part of the antiterminator loop C from the mgtA riboswitch of Yersinia enterocolitica by solution NMR and report a discrete Mg2+-binding site embedded in the AU-rich sequence. At the position of Mg2+ binding, the helical axis exhibits a distinct kink accompanied by a widening of the major groove, which accommodates the Mg2+-binding pocket. An unusually large overlap between two adenine residues on the opposite strands suggests that the bending may be sequence-induced by strong stacking interactions, enabling Mg2+ to bind at this so-far not described metal-ion binding site.

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“…and Frederiksenetal. [104,108] bimetallic to ap urely Zn 2 + -dependent monometallic DNAzyme. [115] Later,e ven faster ands maller deoxyribozymes which requireZ n 2 + alone forc atalysis were identified by in vitro selection.…”

Section: Prebiotic Alternatives To Mg 2 + +mentioning

confidence: 99%

Nucleic Acid Catalysis under Potential Prebiotic Conditions

Vay

Salibi

Song

et al. 2019

Chemistry An Asian Journal

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Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial fort he emergence of primitive life 3.5-4b illion years ago. However,g eochemicalc onditions on early Earth must have differed greatlyf rom the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parame-ters, such as temperature,p H, and ionic composition, influence nucleic acidc atalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particularc atalytic RNAs (ribozymes) and DNAs( deoxyribozymes), under extreme and/or unusualc onditions that may relate to prebiotic environments.[a] Dr.

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Metal Ions in RNA Catalysis

Cited by 9 publications

References 191 publications

Analysis of Metal Ion Dependence in glmS Ribozyme Self‐Cleavage and Coenzyme Binding

Analysis of Metal Ion Dependence in glmS Ribozyme Self‐Cleavage and Coenzyme Binding

Unusually High‐Affinity Mg²⁺ Binding at the AU‐Rich Sequence within the Antiterminator Hairpin of a Mg²⁺ Riboswitch

Nucleic Acid Catalysis under Potential Prebiotic Conditions

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Metal Ions in RNA Catalysis

Cited by 9 publications

References 191 publications

Analysis of Metal Ion Dependence in glmS Ribozyme Self‐Cleavage and Coenzyme Binding

Analysis of Metal Ion Dependence in glmS Ribozyme Self‐Cleavage and Coenzyme Binding

Unusually High‐Affinity Mg2+ Binding at the AU‐Rich Sequence within the Antiterminator Hairpin of a Mg2+ Riboswitch

Nucleic Acid Catalysis under Potential Prebiotic Conditions

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Unusually High‐Affinity Mg²⁺ Binding at the AU‐Rich Sequence within the Antiterminator Hairpin of a Mg²⁺ Riboswitch