ArticleRNA (New York, N.Y.)2005
Characterization of a native hammerhead ribozyme derived from schistosomes.
Article in RNA (New York, N.Y.), 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 77 citations in OpenAlex.
- The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design.RNA (New York, N.Y.) · 2020Article
- Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution.Nucleic acids research · 2019Article
- Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme.RNA (New York, N.Y.) · 2019Article
- Bulky cations greatly increase the turnover of a native hammerhead ribozyme.RSC advances · 2019Article
- Compartmentalised RNA catalysis in membrane-free coacervate protocells.Nature communications · 2018Article
- Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations.Biochemistry · 2017Article
- Nucleic acid catalysis: metals, nucleobases, and other cofactors.Chemical reviews · 2014Review
- Computational selection and experimental validation of allosteric ribozymes that sense a specific sequence of human telomerase reverse transcriptase mRNAs as universal anticancer therapy agents.Nucleic acid therapeutics · 2013Article
- RNA catalysis through compartmentalization.Nature chemistry · 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
- Site-specific platinum(II) cross-linking in a ribozyme active site.Journal of the American Chemical Society · 2012Article
- Ground-state coordination of a catalytic metal to the scissile phosphate of a tertiary-stabilized Hammerhead ribozyme.RNA (New York, N.Y.) · 2012Article
- Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme.Journal of chemical theory and computation · 2011Article
- Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations.RNA (New York, N.Y.) · 2010Article
- Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from?Molecules (Basel, Switzerland) · 2010Article
- Enhanced product stability in the hammerhead ribozyme.Biochemistry · 2010Article
- Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae).BMC evolutionary biology · 2010Article
- The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme.Biochemistry · 2009Article
- Identification of catalytic metal ion ligands in ribozymes.Methods (San Diego, Calif.) · 2009Review
- Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme.RNA (New York, N.Y.) · 2008Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A recent re-examination of the role of the helices surrounding the conserved core of the hammerhead ribozyme has identified putative loop-loop interactions between stems I and II in native hammerhead sequences. These extended hammerhead sequences are more active at low concentrations of divalent cations than are minimal hammerheads. The loop-loop interactions are proposed to stabilize a more active conformation of the conserved core. Here, a kinetic and thermodynamic characterization of an extended hammerhead sequence derived from Schistosoma mansoni is performed. Biphasic kinetics are observed, suggesting the presence of at least two conformers, one cleaving with a fast rate and the other with a slow rate. Replacing loop II with a poly(U) sequence designed to eliminate the interaction between the two loops results in greatly diminished activity, suggesting that the loop-loop interactions do aid in forming a more active conformation. Previous studies with minimal hammerheads have shown deleterious effects of Rp-phosphorothioate substitutions at the cleavage site and 5' to A9, both of which could be rescued with Cd2+. Here, phosphorothioate modifications at the cleavage site and 5' to A9 were made in the schistosome-derived sequence. In Mg2+, both phosphorothioate substitutions decreased the overall fraction cleaved without significantly affecting the observed rate of cleavage. The addition of Cd2+ rescued cleavage in both cases, suggesting that these are still putative metal binding sites in this native sequence.
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