ArticleNucleic acids research2021
What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- 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
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.Nucleic acids research · 2026Article
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.bioRxiv : the preprint server for biology · 2025Article
- RNA folding kinetics control riboswitch sensitivity in vivo.Nature communications · 2025Article
- Regulatory RNAs inSynthetic and systems biotechnology · 2024Review
- RNA folding kinetics control riboswitch sensitivity in vivo.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Among the many in vitro-selected aptamers derived from SELEX protocols, only a small fraction has the potential to be applied for synthetic riboswitch engineering. Here, we present a comparative study of the binding properties of three different aptamers that bind to ciprofloxacin with similar KD values, yet only two of them can be applied as riboswitches. We used the inherent ligand fluorescence that is quenched upon binding as the reporter signal in fluorescence titration and in time-resolved stopped-flow experiments. Thus, we were able to demonstrate differences in the binding kinetics of regulating and non-regulating aptamers. All aptamers studied underwent a two-step binding mechanism that suggests an initial association step followed by a reorganization of the aptamer to accommodate the ligand. We show that increasing regulatory potential is correlated with a decreasing back-reaction rate of the second binding step, thus resulting in a virtually irreversible last binding step of regulating aptamers. We suggest that a highly favoured structural adaption of the RNA to the ligand during the final binding step is essential for turning an aptamer into a riboswitch. In addition, our results provide an explanation for the fact that so few aptamers with regulating capacity have been found to date. Based on our data, we propose an adjustment of the selection protocol for efficient riboswitch detection.
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