ArticleThe Journal of biological chemistry2011
The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine.
Article in The Journal of biological chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 39 citations in OpenAlex.
- Emergent Chemical Reactivity and Complexity of RNA Condensates.Angewandte Chemie (International ed. in English) · 2025Article
- Chemo-Enzymatic Generation of Highly Fluorescent Nucleoside Analogs Using Purine-Nucleoside Phosphorylase.Biomolecules · 2024Review
- Calculated pThe journal of physical chemistry. A · 2023Article
- Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids.Nucleic acids research · 2020Article
- Excited-State Proton Transfer in 8-Azapurines I: A Kinetic Analysis of 8-Azaxanthine Fluorescence.Molecules (Basel, Switzerland) · 2020Article
- Site-Selective Ribosylation of Fluorescent Nucleobase Analogs Using Purine-Nucleoside Phosphorylase as a Catalyst: Effects of Point Mutations.Molecules (Basel, Switzerland) · 2015Article
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- In vitro evolution of distinct self-cleaving ribozymes in diverse environments.Nucleic acids research · 2015Article
- Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path.Journal of the American Chemical Society · 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
- Enzymatic synthesis of highly fluorescent 8-azapurine ribosides using a purine nucleoside phosphorylase reverse reaction: variable ribosylation sites.Molecules (Basel, Switzerland) · 2013Article
- Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.The journal of physical chemistry letters · 2013Article
- Lewis acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme.Nucleic acids research · 2013Article
- pH-dependent dynamics of complex RNA macromolecules.Journal of chemical theory and computation · 2013Article
- The glmS ribozyme cofactor is a general acid-base catalyst.Journal of the American Chemical Society · 2012Article
- A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis.Journal of the American Chemical Society · 2012Article
- General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.Journal of the American Chemical Society · 2012Article
- Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent.Journal of chemical theory and computation · 2012Article
- Charged nucleobases and their potential for RNA catalysis.Accounts of chemical research · 2011Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Understanding how self-cleaving ribozymes mediate catalysis is crucial in light of compelling evidence that human and bacterial gene expression can be regulated through RNA self-cleavage. The hairpin ribozyme catalyzes reversible phosphodiester bond cleavage through a mechanism that does not require divalent metal cations. Previous structural and biochemical evidence implicated the amidine group of an active site adenosine, A38, in a pH-dependent step in catalysis. We developed a way to determine microscopic pK(a) values in active ribozymes based on the pH-dependent fluorescence of 8-azaadenosine (8azaA). We compared the microscopic pK(a) for ionization of 8azaA at position 38 with the apparent pK(a) for the self-cleavage reaction in a fully functional hairpin ribozyme with a unique 8azaA at position 38. Microscopic and apparent pK(a) values were virtually the same, evidence that A38 protonation accounts for the decrease in catalytic activity with decreasing pH. These results implicate the neutral unprotonated form of A38 in a transition state that involves formation of the 5'-oxygen-phosphorus bond.
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