ArticleJournal of the American Chemical Society2012
A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.Nucleic acids research · 2026Article
- Self-cleaving ribozymes: substrate specificity and synthetic biology applications.RSC chemical biology · 2021Review
- The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry.Nucleic acids research · 2019Article
- Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme.Nature communications · 2017Article
- Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.Biophysical chemistry · 2017Article
- The structure of anRNA (New York, N.Y.) · 2017Article
- Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity.Nucleic acids research · 2016Article
- Facile synthesis of a 3-deazaadenosine phosphoramidite for RNA solid-phase synthesis.Beilstein journal of organic chemistry · 2016Article
- A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class.Angewandte Chemie (International ed. in English) · 2015Article
- Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.Biochemistry · 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
- Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme.Journal of the American Chemical Society · 2014Article
- Experimental approaches for measuring pKa's in RNA and DNA.Methods in enzymology · 2014Article
- Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis.RNA biology · 2013Article
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7 authors.
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Abstract
One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman crystallography to directly measure pK(a) values for the Ade38 N1 imino group of a hairpin ribozyme in distinct conformational states. A transition-state analogue gave a pK(a) value of 6.27 ± 0.05, which agrees strikingly well with values measured by pH-rate analyses. To identify the chemical attributes that contribute to the shifted pK(a), we determined crystal structures of hairpin ribozyme variants containing single-atom substitutions at the active site and measured their respective Ade38 N1 pK(a) values. This approach led to the identification of a single interaction in the transition-state conformation that elevates the base pK(a) > 0.8 log unit relative to the precatalytic state. The agreement of the microscopic and macroscopic pK(a) values and the accompanying structural analysis supports a mechanism in which Ade38 N1(H)+ functions as a general acid in phosphodiester bond cleavage. Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity.
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