ReviewMethods (San Diego, Calif.)2009
Identification of catalytic metal ion ligands in ribozymes.
Review in Methods (San Diego, Calif.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed, 70 citations in OpenAlex.
- Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension.Journal of the American Chemical Society · 2024Article
- Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.Journal of chemical information and modeling · 2023Article
- Decoding on the ribosome depends on the structure of the mRNA phosphodiester backbone.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme.Biochemistry · 2018Article
- Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2018Article
- Phosphodiester models for cleavage of nucleic acids.Beilstein journal of organic chemistry · 2018Review
- Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA.Journal of the American Chemical Society · 2017Article
- The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme.Nature chemical biology · 2017Article
- Characterization of kinesin switch I mutations that cause hereditary spastic paraplegia.PloS one · 2017Article
- Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes.Inorganica chimica acta · 2016Article
- The Role of Correlation and Solvation in Ion Interactions with B-DNA.Biophysical journal · 2016Article
- Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes.PloS one · 2016Article
- An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.RNA (New York, N.Y.) · 2016Article
- Heavy atom labeled nucleotides for measurement of kinetic isotope effects.Biochimica et biophysica acta · 2015Review
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics.Analytical 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
- Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson-Boltzmann approach.Biopolymers · 2014Article
- Nucleic acid catalysis: metals, nucleobases, and other cofactors.Chemical reviews · 2014Review
- Experimental approaches for measuring pKa's in RNA and DNA.Methods in enzymology · 2014Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Site-bound metal ions participate in the catalytic mechanisms of many ribozymes. Understanding these mechanisms therefore requires knowledge of the specific ligands on both substrate and ribozyme that coordinate these catalytic metal ions. A number of different structural and biochemical strategies have been developed and refined for identifying metal ion binding sites within ribozymes, and for assessing the catalytic contributions of the metal ions bound at those sites. We review these approaches and provide examples of their application, focusing in particular on metal ion rescue experiments and their roles in the construction of the transition state models for the Tetrahymena group I and RNase P ribozymes.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.