ArticleNucleic acids research2019
Next-level riboswitch development-implementation of Capture-SELEX facilitates identification of a new synthetic riboswitch.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Mammalian therapeutic riboswitches: Engineering and custom ligands.Molecular therapy. Nucleic acids · 2026Review
- Mechanism underlying the high regulatory performance of the doxycycline riboswitch G12.Nature communications · 2026Article
- Exploiting conformational changes in a caffeine aptamer to engineer synthetic RNA devices.Nucleic acids research · 2026Article
- The interaction between the RNA aptamer Dap1 and DasR mirrors DNA operator site recognition in GntR repressors.Nucleic acids research · 2026Article
- Engineering ligands for theophylline riboswitches expands its regulatory dynamic range in prokaryotic and eukaryotic systems.Nature communications · 2026Article
- Designing molecular RNA switches with Restricted Boltzmann machines.Nature communications · 2025Article
- Beyond the niche - unlocking the full potential of synthetic riboswitches.Nature communications · 2025Review
- Aptamer-Based Biosensors for Rapid Detection and Early Warning of Food Contaminants: From Selection to Field Applications.Molecules (Basel, Switzerland) · 2025Review
- Structural basis for ligand recognition in the tobramycin riboswitch.Nucleic acids research · 2025Article
- Robotic-Assisted Capture-Systematic Evolution of Ligands by Exponential Enrichment of RNA Aptamers Binding to Small Molecules.Chembiochem : a European journal of chemical biology · 2025Article
- Advancements and Prospects in DNA-Based Bioanalytical Technology for Environmental Toxicant Detection.JACS Au · 2025Review
- Improving Aptamer Affinity and Determining Sequence-Activity Relationships via Motif-SELEX.Journal of the American Chemical Society · 2025Article
- Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation.Journal of microbiology (Seoul, Korea) · 2025Review
- Engineering oxypurinol-responsive riboswitches based on bacterial xanthine aptamers for gene expression control in mammalian cell culture.Nucleic acids research · 2025Article
- Synthetic Dual-Input Hybrid Riboswitches─Optimized Genetic Regulators in Yeast.ACS synthetic biology · 2025Article
- Article
- Examining the Relationship between Aptamer Complexity and Molecular Discrimination of a Low-Epitope Target.ACS central science · 2024Article
- Microbial biosensors for diagnostics, surveillance and epidemiology: Today's achievements and tomorrow's prospects.Microbial biotechnology · 2024Review
- Synthetic gene circuit evolution: Insights and opportunities at the mid-scale.Cell chemical biology · 2024Review
- Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives.Biosensors · 2024Review
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9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The development of synthetic riboswitches has always been a challenge. Although a number of interesting proof-of-concept studies have been published, almost all of these were performed with the theophylline aptamer. There is no shortage of small molecule-binding aptamers; however, only a small fraction of them are suitable for RNA engineering since a classical SELEX protocol selects only for high-affinity binding but not for conformational switching. We now implemented RNA Capture-SELEX in our riboswitch developmental pipeline to integrate the required selection for high-affinity binding with the equally necessary RNA conformational switching. Thus, we successfully developed a new paromomycin-binding synthetic riboswitch. It binds paromomycin with a KD of 20 nM and can discriminate between closely related molecules both in vitro and in vivo. A detailed structure-function analysis confirmed the predicted secondary structure and identified nucleotides involved in ligand binding. The riboswitch was further engineered in combination with the neomycin riboswitch for the assembly of an orthogonal Boolean NOR logic gate. In sum, our work not only broadens the spectrum of existing RNA regulators, but also signifies a breakthrough in riboswitch development, as the effort required for the design of sensor domains for RNA-based devices will in many cases be much reduced.
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