ArticleNucleic acids research2016
Automated physics-based design of synthetic riboswitches from diverse RNA aptamers.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 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
69 citing papers in PubMed, 277 citations in OpenAlex.
- Design and discovery of 'tug-of-war' riboswitches.bioRxiv : the preprint server for biology · 2026Article
- The Fragmented Nature of Biosensor Development: Challenges and Paths to Mitigation.Biosensors · 2026Review
- High-throughput engineering of ligand-activated splicing ribozyme through domain insertion.bioRxiv : the preprint server for biology · 2026Article
- Engineering high-titer lentiviral vectors for robust expression of RNA-based gene circuits.bioRxiv : the preprint server for biology · 2026Article
- Engineering ligands for theophylline riboswitches expands its regulatory dynamic range in prokaryotic and eukaryotic systems.Nature communications · 2026Article
- Programming Next-Generation Synthetic Biosensors by Genetic Circuit Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- RNA elements and their biotechnological applications in plants.The New phytologist · 2025Review
- RNA folding kinetics control riboswitch sensitivity in vivo.Nature communications · 2025Article
- Riboswitch Design Using MODENA.Methods in molecular biology (Clifton, N.J.) · 2025Article
- An autonomous microbial sensor enables long-term detection of TNT explosive in natural soil.Nature communications · 2024Article
- RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models.Bioinformatics (Oxford, England) · 2024Article
- RNA folding kinetics control riboswitch sensitivity in vivo.bioRxiv : the preprint server for biology · 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
- Recent Advancements of Aptamers in Cancer Therapy.ACS omega · 2023Review
- Engineering cellular communication between light-activated synthetic cells and bacteria.Nature chemical biology · 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
- Article
- Automated design of protein-binding riboswitches for sensing human biomarkers in a cell-free expression system.Nature communications · 2023Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. However, it remains unclear how their sequence controls the physics of riboswitch switching and activation, particularly when changing the ligand-binding aptamer domain. We report the development of a statistical thermodynamic model that predicts the sequence-structure-function relationship for translation-regulating riboswitches that activate gene expression, characterized inside cells and within cell-free transcription-translation assays. Using the model, we carried out automated computational design of 62 synthetic riboswitches that used six different RNA aptamers to sense diverse chemicals (theophylline, tetramethylrosamine, fluoride, dopamine, thyroxine, 2,4-dinitrotoluene) and activated gene expression by up to 383-fold. The model explains how aptamer structure, ligand affinity, switching free energy and macromolecular crowding collectively control riboswitch activation. Our model-based approach for engineering riboswitches quantitatively confirms several physical mechanisms governing ligand-induced RNA shape-change and enables the development of cell-free and bacterial sensors for diverse applications.
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.