ArticleNucleic acids research2013
De novo design of a synthetic riboswitch that regulates transcription termination.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed, 196 citations in OpenAlex.
- Exploiting conformational changes in a caffeine aptamer to engineer synthetic RNA devices.Nucleic acids research · 2026Article
- Development of a tetracycline-inducible programmed ribosomal frameshifting platform for sensitive regulation of mammalian gene expression.Nucleic acids research · 2026Article
- SUPER: Upcycling Genetic Parts for Precise Gene Expression Control, Leakage Minimization, and Genetic Circuit Stability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Structural basis for ligand recognition in the tobramycin riboswitch.Nucleic acids research · 2025Article
- Reconfigurable Nucleic Acid Nanoparticles with Therapeutic RNAi Responses to Intracellular Disease Markers.Advanced functional materials · 2025Article
- Temperature-responsive regulation of the polycyclic aromatic hydrocarbon-degrading mesophilic bacteriumApplied and environmental microbiology · 2025Article
- Autonomous Nucleic Acid and Protein Nanocomputing Agents Engineered to Operate in Living Cells.ACS nano · 2025Review
- Article
- Machine Learning for RNA Design: LEARNA.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Riboswitch Design Using MODENA.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Partial RNA design.Bioinformatics (Oxford, England) · 2024Article
- T7 phage-assisted evolution of riboswitches using error-prone replication and dual selection.Scientific reports · 2024Article
- Assessing the Quality of Cotranscriptional Folding Simulations.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Rational design of eukaryotic riboswitches that up-regulate IRES-mediated translation initiation with high switching efficiency through a kinetic trapping mechanism in vitro.RNA (New York, N.Y.) · 2023Article
- Riboswitches, from cognition to transformation.Synthetic and systems biotechnology · 2023Review
- A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria.Nature communications · 2023Article
- Application of Metabolite-Responsive Biosensors for Plant Natural Products Biosynthesis.Biosensors · 2023Review
- Fitness functions for RNA structure design.Nucleic acids research · 2023Article
- Design of artificial small regulatorySynthetic and systems biotechnology · 2023Article
- A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria.bioRxiv : the preprint server for biology · 2023Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are regulatory RNA elements typically located in the 5'-untranslated region of certain mRNAs and control gene expression at the level of transcription or translation. These elements consist of a sensor and an adjacent actuator domain. The sensor usually is an aptamer that specifically interacts with a ligand. The actuator contains an intrinsic terminator or a ribosomal binding site for transcriptional or translational regulation, respectively. Ligand binding leads to structural rearrangements of the riboswitch and to presentation or masking of these regulatory elements. Based on this modular organization, riboswitches are an ideal target for constructing synthetic regulatory systems for gene expression. Although riboswitches for translational control have been designed successfully, attempts to construct synthetic elements regulating transcription have failed so far. Here, we present an in silico pipeline for the rational design of synthetic riboswitches that regulate gene expression at the transcriptional level. Using the well-characterized theophylline aptamer as sensor, we designed the actuator part as RNA sequences that can fold into functional intrinsic terminator structures. In the biochemical characterization, several of the designed constructs show ligand-dependent control of gene expression in Escherichia coli, demonstrating that it is possible to engineer riboswitches not only for translational but also for transcriptional regulation.
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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.