ArticleRNA (New York, N.Y.)2006
Extraordinary rates of transition metal ion-mediated ribozyme catalysis.
Article in RNA (New York, N.Y.), 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 86 citations in OpenAlex.
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2.Nucleic acids research · 2024Article
- Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis.Biochemistry · 2023Article
- Pushing the Limits of Nucleic Acid Function.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Review
- Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates, including Mechanistic Considerations.Molecules (Basel, Switzerland) · 2022Review
- Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium.Non-coding RNA · 2020Article
- Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution.Nucleic acids research · 2019Article
- Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations.Biochemistry · 2017Article
- Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.Biochemistry · 2016Article
- Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.Biochemistry · 2015Article
- In vitro evolution of distinct self-cleaving ribozymes in diverse environments.Nucleic acids research · 2015Article
- Nucleic acid catalysis: metals, nucleobases, and other cofactors.Chemical reviews · 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
- A versatile cis-blocking and trans-activation strategy for ribozyme characterization.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
- Folding of the hammerhead ribozyme: pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change.RNA (New York, N.Y.) · 2012Article
- The importance of peripheral sequences in determining the metal selectivity of an in vitro-selected Co(2+) -dependent DNAzyme.Chembiochem : a European journal of chemical biology · 2012Article
- Structure-based search reveals hammerhead ribozymes in the human microbiome.The Journal of biological chemistry · 2011Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
In pre-steady-state, fast-quench kinetic analysis, the tertiary-stabilized hammerhead ribozyme "RzB" cleaves its substrate RNA with maximal measured k (obs) values of approximately 3000 min(-1) in 1 mM Mn(2+) and approximately 780 min(-1) in 1 mM Mg(2+) at 37 degrees C (pH 7.4). Apparent pKa for the catalytic general base is approximately 7.8-8.5, independent of the corresponding metal hydrate pKa, suggesting potential involvement of a nucleobase as general base as suggested previously from nucleobase substitution studies. The pH-rate profile is bell-shaped for Cd(2+), for which the general catalytic acid has a pKa of 7.3 +/- 0.1. Simulations of the pH-rate relation suggest a pKa for the general catalytic acid to be approximately 9.5 in Mn(2+) and >9.5 in Mg(2+). The acid pKa's follow the trend in the pKa of the hydrated metal ions but are displaced by approximately 1-2 pH units in the presence of Cd(2+) and Mn(2+). One possible explanation for this trend is direct metal ion coordination with a nucleobase, which then acts as general acid.
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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.