ArticleRNA (New York, N.Y.)2007
Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme.
Article in RNA (New York, N.Y.), 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 30 citations in OpenAlex.
- Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants.Biology · 2023Review
- Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations.Biochemistry · 2017Article
- Chemistry and Biology of Self-Cleaving Ribozymes.Trends in biochemical sciences · 2015Review
- Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.Biochemistry · 2015Article
- Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density.Biochemistry · 2015Article
- Endogenous polyamine function--the RNA perspective.Nucleic acids research · 2014Review
- Active-site monovalent cations revealed in a 1.55-Å-resolution hammerhead ribozyme structure.Journal of molecular biology · 2013Article
- Lewis acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme.Nucleic acids research · 2013Article
- Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.Progress in molecular biology and translational science · 2013Review
- Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction.Biochemistry · 2011Review
- Binding of kinetically inert metal ions to RNA: the case of platinum(II).Metal ions in life sciences · 2011Review
- Metal ions: supporting actors in the playbook of small ribozymes.Metal ions in life sciences · 2011Review
- Metal binding and substrate positioning by evolutionarily invariant U6 sequences in catalytically active protein-free snRNAs.RNA (New York, N.Y.) · 2010Article
- Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from?Molecules (Basel, Switzerland) · 2010Article
- The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme.Biochemistry · 2009Article
- Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation.Journal of molecular biology · 2009Article
- Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.The journal of physical chemistry. B · 2008Article
- Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation.Journal of the American Chemical Society · 2008Article
- Dissecting metal ion-dependent folding and catalysis of a single DNAzyme.Nature chemical biology · 2007Article
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Divalent ion sensitivity of hammerhead ribozymes is significantly reduced when the RNA structure includes appropriate tertiary stabilization. Therefore, we investigated the activity of the tertiary stabilized "RzB" hammerhead ribozyme in several nondivalent ions. Ribozyme RzB is active in spermidine and Na(+) alone, although the cleavage rates are reduced by more than 1,000-fold relative to the rates observed in Mg(2+) and in transition metal ions. The trivalent cobalt hexammine (CoHex) ion is often used as an exchange-inert analog of hydrated magnesium ion. Trans-cleavage rates exceeded 8 min(-1) in 20 mM CoHex, which promoted cleavage through outersphere interactions. The stimulation of catalysis afforded by the tertiary structural interactions within RzB does not require Mg(2+), unlike other extended hammerhead ribozymes. Site-specific interaction with at least one Mg(2+) ion is suggested by CoHex competition experiments. In the presence of a constant, low concentration of Mg(2+), low concentrations of CoHex decreased the rate by two to three orders of magnitude relative to the rate in Mg(2+) alone. Cleavage rates increased as CoHex concentrations were raised further, but the final fraction cleaved was lower than what was observed in CoHex or Mg(2+) alone. These observations suggest that Mg(2+) and CoHex compete for binding and that they cause misfolded structures when they are together. The results of this study support the existence of an alternate catalytic mechanism used by nondivalent ions (especially CoHex) that is distinct from the one promoted by divalent metal ions, and they imply that divalent metals influence catalysis through a specific nonstructural role.
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