ArticleProceedings of the National Academy of Sciences of the United States of America2005
Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- Hydrogel-Bead Particles Enable Activity-Based Identification of Nucleic Acid Aptamer Enzyme Inhibitors.Analytical chemistry · 2025Article
- Evolution Driven Microscale Combinatorial Chemistry in Intracellular Mimicking Droplets to Engineer Thermostable RNA for Cellular Imaging.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Ultrahigh-Throughput Enzyme Engineering and Discovery inChemical reviews · 2023Review
- Pushing the Limits of Nucleic Acid Function.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Review
- Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey.Angewandte Chemie (International ed. in English) · 2021Review
- A GTP-synthesizing ribozyme selected by metabolic coupling to an RNA polymerase ribozyme.Science advances · 2021Article
- Water/Oil Emulsions with Controlled Droplet Sizes forACS omega · 2021Article
- Multiplexed Enzyme Activity-Based Probe Display via Hybridization.ACS combinatorial science · 2020Article
- Compartmentalised RNA catalysis in membrane-free coacervate protocells.Nature communications · 2018Article
- High-throughput screening of biomolecules using cell-free gene expression systems.Synthetic biology (Oxford, England) · 2018Review
- Chemoselective Coupling Preserves the Substrate Integrity of Surface-Immobilized Oligonucleotides for Emulsion PCR-Based Gene Library Construction.ACS combinatorial science · 2017Article
- Improving the odds: Influence of starting pools on in vitro selection outcomes.Methods (San Diego, Calif.) · 2016Review
- Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes.Trends in biochemical sciences · 2016Review
- Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications.Chemical Society reviews · 2016Review
- Oligonucleotide Functionalised Microbeads: Indispensable Tools for High-Throughput Aptamer Selection.Molecules (Basel, Switzerland) · 2015Review
- Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment.Nucleic acids research · 2015Article
- Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions.RNA (New York, N.Y.) · 2015Article
- Cell-free synthetic biology: thinking outside the cell.Metabolic engineering · 2012Review
- DNA-catalyzed reductive amination.Angewandte Chemie (International ed. in English) · 2011Article
- The shape-shifting quasispecies of RNA: one sequence, many functional folds.Physical chemistry chemical physics : PCCP · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In vitro compartmentalization (IVC) has previously been used to evolve protein enzymes. Here, we demonstrate how IVC can be applied to select RNA enzymes (ribozymes) for a property that has previously been unselectable: true intermolecular catalysis. Libraries containing 10(11) ribozyme genes are compartmentalized in the aqueous droplets of a water-in-oil emulsion, such that most droplets contain no more than one gene, and transcribed in situ. By coencapsulating the gene, RNA, and the substrates/products of the catalyzed reaction, ribozymes can be selected for all enzymatic properties: substrate recognition, product formation, rate acceleration, and turnover. Here we exploit the complementarity of IVC with systematic evolution of ligands by exponential enrichment (SELEX), which allows selection of larger libraries (>/=10(15)) and for very small rate accelerations (k(cat)/k(uncat)) but only selects for intramolecular single-turnover reactions. We selected approximately 10(14) random RNAs for Diels-Alderase activity with five rounds of SELEX, then six to nine rounds with IVC. All selected ribozymes catalyzed the Diels-Alder reaction in a truly bimolecular fashion and with multiple turnover. Nearly all ribozymes selected by using eleven rounds of SELEX alone contain a common catalytic motif. Selecting with SELEX then IVC gave ribozymes with significant sequence variations in this catalytic motif and ribozymes with completely novel motifs. Interestingly, the catalytic properties of all of the selected ribozymes were quite similar. The ribozymes are strongly product inhibited, consistent with the Diels-Alder transition state closely resembling the product. More efficient Diels-Alderases may need to catalyze a second reaction that transforms the product and prevents product inhibition.
Indexed as
Identifiers
What 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.