ArticleNucleic acids research2014
Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed.
- Engineering and Assay of Enzymes for Expanded Genetic Alphabet Replication.Biochemistry · 2025Article
- Controlling DNA-RNA strand displacement kinetics with base distribution.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A cell-free biosensor signal amplification circuit with polymerase strand recycling.Nature chemical biology · 2025Article
- Article
- Plug-and-play protein biosensors using aptamer-regulated in vitro transcription.Nature communications · 2024Article
- Engineering a cell-free biosensor signal amplification circuit with polymerase strand recycling.bioRxiv : the preprint server for biology · 2024Article
- Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions.Journal of the American Chemical Society · 2023Article
- A Combinational Approach for More Efficient miRNA Biosensing.Current genomics · 2022Review
- Programming cell-free biosensors with DNA strand displacement circuits.Nature chemical biology · 2022Article
- Cotranscriptionally encoded RNA strand displacement circuits.Science advances · 2022Article
- Developing predictive hybridization models for phosphorothioate oligonucleotides using high-resolution melting.PloS one · 2022Article
- Quasi-robust control of biochemical reaction networks via stochastic morphing.Journal of the Royal Society, Interface · 2021Article
- Constructing Controllable Logic Circuits Based on DNAzyme Activity.Molecules (Basel, Switzerland) · 2019Article
- Self-powered RNA nanomachine driven by metastable structure.Nucleic acids research · 2019Article
- "Second-generation" fluorogenic RNA-based sensors.Methods (San Diego, Calif.) · 2019Review
- Entropy-driven DNA logic circuits regulated by DNAzyme.Nucleic acids research · 2018Article
- Genetically Encoded Catalytic Hairpin Assembly for Sensitive RNA Imaging in Live Cells.Journal of the American Chemical Society · 2018Article
- Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines.Nature communications · 2018Article
- Establishment of a universal and rational gene detection strategy through three-way junction-based remote transduction.Chemical science · 2018Article
- Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications.International journal of molecular sciences · 2017Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Nucleic acid circuits are finding increasing real-life applications in diagnostics and synthetic biology. Although DNA has been the main operator in most nucleic acid circuits, transcriptionally produced RNA circuits could provide powerful alternatives for reagent production and their use in cells. Towards these goals, we have implemented a particular nucleic acid circuit, catalytic hairpin assembly, using RNA for both information storage and processing. Our results demonstrated that the design principles developed for DNA circuits could be readily translated to engineering RNA circuits that operated with similar kinetics and sensitivities of detection. Not only could purified RNA hairpins perform amplification reactions but RNA hairpins transcribed in vitro also mediated amplification, even without purification. Moreover, we could read the results of the non-enzymatic amplification reactions using a fluorescent RNA aptamer 'Spinach' that was engineered to undergo sequence-specific conformational changes. These advances were applied to the end-point and real-time detection of the isothermal strand displacement amplification reaction that produces single-stranded DNAs as part of its amplification cycle. We were also able to readily engineer gate structures with RNA similar to those that have previously formed the basis of DNA circuit computations. Taken together, these results validate an entirely new chemistry for the implementation of nucleic acid circuits.
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Registered trials
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