ArticleRNA (New York, N.Y.)2009
A class I ligase ribozyme with reduced Mg2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 21 citations in OpenAlex.
- Evolution of the substrate specificity of an RNA ligase ribozyme from phosphorimidazole to triphosphate activation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.Nature communications · 2018Article
- Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles.Bioinformatics (Oxford, England) · 2015Article
- Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Mapping L1 ligase ribozyme conformational switch.Journal of molecular biology · 2012Article
- Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2011Article
- The chemical origins of life and its early evolution: an introduction.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2011Article
- The structural basis of RNA-catalyzed RNA polymerization.Nature structural & molecular biology · 2011Article
- A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination.Nature structural & molecular biology · 2011Article
- Identification of dynamical hinge points of the L1 ligase molecular switch.RNA (New York, N.Y.) · 2010Article
- Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube.BMC evolutionary biology · 2010Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The class I ligase was among the first ribozymes to have been isolated from random sequences and represents the catalytic core of several RNA-directed RNA polymerase ribozymes. The ligase is also notable for its catalytic efficiency and structural complexity. Here, we report an improved version of this ribozyme, arising from selection that targeted the kinetics of the chemical step. Compared with the parent ribozyme, the improved ligase achieves a modest increase in rate enhancement under the selective conditions and shows a sharp reduction in [Mg(2+)] dependence. Analysis of the sequences and kinetics of successful clones suggests which mutations play the greatest part in these improvements. Moreover, backbone and nucleobase interference maps of the parent and improved ligase ribozymes complement the newly solved crystal structure of the improved ligase to identify the functionally significant interactions underlying the catalytic ability and structural complexity of the ligase ribozyme.
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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.