ArticleNucleic acids research2015
High-throughput assay and engineering of self-cleaving ribozymes by sequencing.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
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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.
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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.
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Who cites it
30 citing papers in PubMed, 59 citations in OpenAlex.
- Mammalian therapeutic riboswitches: Engineering and custom ligands.Molecular therapy. Nucleic acids · 2026Review
- Engineering aptamer dimers (apdimers) for optimization of synthetic riboswitches.Nucleic acids research · 2026Article
- Systematic discovery of novel ribozymes with gene silencing properties from global deep-sea RNA viromes.Frontiers in microbiology · 2026Article
- Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity.RNA (New York, N.Y.) · 2025Article
- CHiTA: A scarless high-throughput pipeline for characterization of ribozymes.Methods (San Diego, Calif.) · 2025Article
- Language Modelling Techniques for Analysing the Impact of Human Genetic Variation.Bioinformatics and biology insights · 2025Review
- Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.Nucleic acids research · 2024Article
- Sequence modeling and design from molecular to genome scale with Evo.Science (New York, N.Y.) · 2024Article
- Optimization of Exon-Skipping Riboswitches and Their Applications to Control Mammalian Cell Fate.ACS synthetic biology · 2024Article
- Deep generative design of RNA family sequences.Nature methods · 2024Article
- Synthetic Gene Circuits for Regulation of Next-Generation Cell-Based Therapeutics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Small-Molecule Aptamer for Regulating RNA Functions in Mammalian Cells and Animals.Journal of the American Chemical Society · 2023Article
- Article
- Method for Identifying Sequence Motifs in Pre-miRNAs for Small-Molecule Binding.ACS chemical biology · 2022Article
- Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes.Nature communications · 2022Article
- Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors.Pharmaceuticals (Basel, Switzerland) · 2021Review
- A multiplexed, automated evolution pipeline enables scalable discovery and characterization of biosensors.Nature communications · 2021Article
- Phased nucleotide inserts for sequencing low-diversity RNA samples from in vitro selection experiments.RNA (New York, N.Y.) · 2020Article
- High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cells.Nature communications · 2020Article
- Aptamer-based and aptazyme-based riboswitches in mammalian cells.Current opinion in chemical biology · 2019Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
Self-cleaving ribozymes are found in all domains of life and are believed to play important roles in biology. Additionally, self-cleaving ribozymes have been the subject of extensive engineering efforts for applications in synthetic biology. These studies often involve laborious assays of multiple individual variants that are either designed rationally or discovered through selection or screening. However, these assays provide only a limited view of the large sequence space relevant to the ribozyme function. Here, we report a strategy that allows quantitative characterization of greater than 1000 ribozyme variants in a single experiment. We generated a library of predefined ribozyme variants that were converted to DNA and analyzed by high-throughput sequencing. By counting the number of cleaved and uncleaved reads of every variant in the library, we obtained a complete activity profile of the ribozyme pool which was used to both analyze and engineer allosteric ribozymes.
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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.