ArticlePLoS computational biology2009
Design principles for riboswitch function.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 129 citations in OpenAlex.
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- Enhanced RNA secondary structure prediction through integrative deep learning and structural context analysis.Nucleic acids research · 2025Article
- Review
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- RNA cis-regulators are important for Streptococcus pneumoniae in vivo success.PLoS genetics · 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
- Riboswitches, from cognition to transformation.Synthetic and systems biotechnology · 2023Review
- RNA secondary structure packages evaluated and improved by high-throughput experiments.Nature methods · 2022Article
- Discovering adaptation-capable biological network structures using control-theoretic approaches.PLoS computational biology · 2022Article
- Using sliding mode observers to estimateIET systems biology · 2020Article
- Pesticide Aptasensors-State of the Art and Perspectives.Sensors (Basel, Switzerland) · 2020Review
- Modeling a synthetic aptamer-based riboswitch biosensor sensitive to low hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) concentrations.PloS one · 2020Article
- Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy.Frontiers in bioengineering and biotechnology · 2020Article
- Evaluating riboswitch optimality.Methods in enzymology · 2019Article
- RNA-based dynamic genetic controllers: development strategies and applications.Current opinion in biotechnology · 2018Review
- Dynamic metabolic control: towards precision engineering of metabolism.Journal of industrial microbiology & biotechnology · 2018Article
- Comprehensive profiling of the ligand binding landscapes of duplexed aptamer families reveals widespread induced fit.Nature communications · 2018Article
- Synthetic Botany.Cold Spring Harbor perspectives in biology · 2017Review
- Ribo-attenuators: novel elements for reliable and modular riboswitch engineering.Scientific reports · 2017Article
- Design of nucleic acid strands with long low-barrier folding pathways.Natural computing · 2017Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems. RNA provides a promising building block for the construction of tunable regulatory components based on its rich regulatory capacity and our current understanding of the sequence-function relationship. One prominent example of RNA-based regulatory components is riboswitches, genetic elements that mediate ligand control of gene expression through diverse regulatory mechanisms. While characterization of natural and synthetic riboswitches has revealed that riboswitch function can be modulated through sequence alteration, no quantitative frameworks exist to investigate or guide riboswitch tuning. Here, we combined mathematical modeling and experimental approaches to investigate the relationship between riboswitch function and performance. Model results demonstrated that the competition between reversible and irreversible rate constants dictates performance for different regulatory mechanisms. We also found that practical system restrictions, such as an upper limit on ligand concentration, can significantly alter the requirements for riboswitch performance, necessitating alternative tuning strategies. Previous experimental data for natural and synthetic riboswitches as well as experiments conducted in this work support model predictions. From our results, we developed a set of general design principles for synthetic riboswitches. Our results also provide a foundation from which to investigate how natural riboswitches are tuned to meet systems-level regulatory demands.
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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.