ArticleRNA biology2015
Design criteria for synthetic riboswitches acting on transcription.
Article in RNA biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 51 citations in OpenAlex.
- Prediction of Circular RNA Secondary Structures and Their Targets.Advances in experimental medicine and biology · 2025Review
- Intelligent guide RNA: dual toehold switches for modulating luciferase in the presence of trigger RNA.Communications biology · 2024Article
- Infrared: a declarative tree decomposition-powered framework for bioinformatics.Algorithms for molecular biology : AMB · 2024Article
- RNA Secondary Structure Thermodynamics.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Riboswitches, from cognition to transformation.Synthetic and systems biotechnology · 2023Review
- Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes.RNA (New York, N.Y.) · 2022Article
- Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing.Nature communications · 2022Article
- Cell-free riboswitches.RSC chemical biology · 2021Review
- What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials.Nucleic acids research · 2021Article
- Beyond Plug and Pray: Context Sensitivity andRNA biology · 2021Article
- Using sliding mode observers to estimateIET systems biology · 2020Article
- Developments of Riboswitches and Toehold Switches for Molecular Detection-Biosensing and Molecular Diagnostics.International journal of molecular sciences · 2020Review
- Rapid generation of sequence-diverse terminator libraries and their parameterization using quantitative Term-Seq.Synthetic biology (Oxford, England) · 2019Article
- Synthetic Biology of Small RNAs and Riboswitches.Microbiology spectrum · 2018Review
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
- Computational design of small transcription activating RNAs for versatile and dynamic gene regulation.Nature communications · 2017Article
- Design of Artificial Riboswitches as Biosensors.Sensors (Basel, Switzerland) · 2017Review
- Applicability of a computational design approach for synthetic riboswitches.Nucleic acids research · 2017Article
- Modular arrangement of regulatory RNA elements.RNA biology · 2017Review
- incaRNAfbinv: a web server for the fragment-based design of RNA sequences.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell.
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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.