ArticleNucleic acids research2023
Tuning strand displacement kinetics enables programmable ZTP riboswitch dynamic range in vivo.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Design and discovery of 'tug-of-war' riboswitches.bioRxiv : the preprint server for biology · 2026Article
- High-throughput engineering of ligand-activated splicing ribozyme through domain insertion.bioRxiv : the preprint server for biology · 2026Article
- U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism.Nucleic acids research · 2026Article
- Engineering plasmids with synthetic origins of replication.Nature communications · 2026Article
- Beyond the niche - unlocking the full potential of synthetic riboswitches.Nature communications · 2025Review
- RNA folding kinetics control riboswitch sensitivity in vivo.Nature communications · 2025Article
- Beyond ligand binding: Single molecule observation reveals how riboswitches integrate multiple signals to balance bacterial gene regulation.Current opinion in structural biology · 2024Review
- Opportunities for Riboswitch Inhibition by Targeting Co-Transcriptional RNA Folding Events.International journal of molecular sciences · 2024Review
- A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration.Nature communications · 2024Article
- The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch.Nucleic acids research · 2024Article
- RNA folding kinetics control riboswitch sensitivity in vivo.bioRxiv : the preprint server for biology · 2024Article
- A transient intermediate RNA structure underlies the regulatory function of theRNA (New York, N.Y.) · 2023Article
- Dynamic RNA synthetic biology: new principles, practices and potential.RNA biology · 2023Review
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2 authors.
Funding
Abstract
A large body of work has shown that transcriptional riboswitches function through internal strand displacement mechanisms that guide the formation of alternative structures which drive regulatory outcomes. Here, we sought to investigate this phenomenon using the Clostridium beijerinckii pfl ZTP riboswitch as a model system. Using functional mutagenesis with Escherichia coli gene expression assays, we show that mutations designed to slow strand displacement of the expression platform enable precise tuning of riboswitch dynamic range (2.4-34-fold), depending on the type of kinetic barrier introduced, and the position of the barrier relative to the strand displacement nucleation site. We also show that expression platforms from a range of different Clostridium ZTP riboswitches contain sequences that impose these barriers to affect dynamic range in these different contexts. Finally, we use sequence design to flip the regulatory logic of the riboswitch to create a transcriptional OFF-switch, and show that the same barriers to strand displacement tune dynamic range in this synthetic context. Together, our findings further elucidate how strand displacement can be manipulated to alter the riboswitch decision landscape, suggesting that this could be a mechanism by which evolution tunes riboswitch sequence, and providing an approach to optimize synthetic riboswitches for biotechnology applications.
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