ArticleRNA (New York, N.Y.)2001
Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping.
Article in RNA (New York, N.Y.), 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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Who cites it
22 citing papers in PubMed, 46 citations in OpenAlex.
- Molecular targets of aspirin and cancer prevention.British journal of cancer · 2014Review
- Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.Proteins · 2014Article
- Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.The journal of physical chemistry letters · 2013Article
- pH-dependent dynamics of complex RNA macromolecules.Journal of chemical theory and computation · 2013Article
- Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent.Journal of chemical theory and computation · 2012Article
- The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine.The Journal of biological chemistry · 2011Article
- Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data.RNA (New York, N.Y.) · 2011Article
- Catalytic importance of a protonated adenosine in the hairpin ribozyme active site.Biochemistry · 2010Article
- Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.Biochemistry · 2009Article
- Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.RNA (New York, N.Y.) · 2009Article
- The linear form of a group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility.RNA (New York, N.Y.) · 2009Article
- Fluorine substituted adenosines as probes of nucleobase protonation in functional RNAs.Journal of the American Chemical Society · 2008Article
- Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.RNA (New York, N.Y.) · 2008Article
- Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis.Journal of the American Chemical Society · 2008Article
- Mutational inhibition of ligation in the hairpin ribozyme: substitutions of conserved nucleobases A9 and A10 destabilize tertiary structure and selectively promote cleavage.RNA (New York, N.Y.) · 2008Article
- Dissecting RNA folding by nucleotide analog interference mapping (NAIM).Nature protocols · 2008Article
- Ribozyme catalysis revisited: is water involved?Molecular cell · 2007Review
- Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.Biochemistry · 2006Article
- Functional identification of catalytic metal ion binding sites within RNA.PLoS biology · 2005Article
- The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure.Nucleic acids research · 2005Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Tertiary structure in globular RNA folds can create local environments that lead to pKa perturbation of specific nucleotide functional groups. To assess the prevalence of functionally relevant adenosine-specific pKa perturbation in RNA structure, we have altered the nucleotide analog interference mapping (NAIM) approach to include a series of a phosphorothioate-tagged adenosine analogs with shifted N1 pKa values. We have used these analogs to analyze the hairpin ribozyme, a small self-cleaving/ligating RNA catalyst that is proposed to employ a general acid-base reaction mechanism. A single adenosine (A10) within the ribozyme active site displayed an interference pattern consistent with a functionally significant base ionization. The exocyclic amino group of a second adenosine (A38) contributes substantially to hairpin catalysis, but ionization of the nucleotide does not appear to be important for activity. Within the hairpin ribozyme crystal structure, A10 and A38 line opposite edges of a solvent-excluded cavity adjacent to the 5'-OH nucleophile. The results are inconsistent with the model of ribozyme chemistry in which A38 acts as a general acid-base catalyst, and suggest that the hairpin ribozyme uses an alternative mechanism to achieve catalytic rate enhancement that utilizes functional groups within a solvent-excluded cleft in the ribozyme active site.
Indexed as
Identifiers
11680850PMC1370189W2125158708What 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.