ArticleJournal of the American Chemical Society2012
Expanding the rule set of DNA circuitry with associative toehold activation.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 163 citations in OpenAlex.
- Fuel-Driven Catalytic Molecular Templating.Journal of the American Chemical Society · 2026Article
- Deep convolutional and fully-connected DNA neural networks.Nature communications · 2025Article
- Kinetics and Activation Strategies in Toehold-Mediated and Toehold-Free DNA Strand Displacement.Biosensors · 2025Review
- Information propagation through enzyme-free catalytic templating of DNA dimerization with weak product inhibition.Nature chemistry · 2025Article
- Modular CRISPR/Cas12a synergistic activation platform for detection and logic operations.Nucleic acids research · 2024Article
- Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions.Journal of the American Chemical Society · 2023Article
- A PAM-free CRISPR/Cas12a ultra-specific activation mode based on toehold-mediated strand displacement and branch migration.Nucleic acids research · 2022Article
- DNA Strand Displacement Driven by Host-Guest Interactions.Journal of the American Chemical Society · 2022Article
- A nanopore interface for higher bandwidth DNA computing.Nature communications · 2022Article
- Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems.Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology · 2022Review
- Programmable allosteric DNA regulations for molecular networks and nanomachines.Science advances · 2022Article
- Development of Synthetic DNA Circuit and Networks for Molecular Information Processing.Nanomaterials (Basel, Switzerland) · 2021Review
- A Cooperative DNA Catalyst.Journal of the American Chemical Society · 2021Article
- Cofactor-assisted three-way DNA junction-driven strand displacement.RSC advances · 2021Article
- CRISPR-Mediated Strand Displacement Logic Circuits with Toehold-Free DNA.ACS synthetic biology · 2021Article
- Dynamically elongated associative toehold for tuning DNA circuit kinetics and thermodynamics.Nucleic acids research · 2021Article
- Quasi-robust control of biochemical reaction networks via stochastic morphing.Journal of the Royal Society, Interface · 2021Article
- Morphological Manipulation of DNA Gel Microbeads with Biomolecular Stimuli.Nanomaterials (Basel, Switzerland) · 2021Article
- Feedback regulation of crystal growth by buffering monomer concentration.Nature communications · 2020Article
- De novo-designed translation-repressing riboregulators for multi-input cellular logic.Nature chemical biology · 2019Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Toehold-mediated strand displacement has proven extremely powerful in programming enzyme-free DNA circuits and DNA nanomachines. To achieve multistep, autonomous, and complex behaviors, toeholds must be initially inactivated by hybridizing to inhibitor strands or domains and then relieved from inactivation in a programmed, timed manner. Although powerful and reasonably robust, this strategy has several drawbacks that limit the architecture of DNA circuits. For example, the combination between toeholds and branch migration (BM) domains is 'hard wired' during DNA synthesis thus cannot be created or changed during the execution of DNA circuits. To solve this problem, I propose a strategy called 'associative toehold activation', where the toeholds and BM domains are connected via hybridization of auxiliary domains during the execution of DNA circuits. Bulged thymidines that stabilize DNA three-way junctions substantially accelerate strand displacement reactions in this scheme, allowing fast strand displacement initiated by reversible toehold binding. To demonstrate the versatility of the scheme, I show (1) run-time combination of toeholds and BM domains, (2) run-time recombination of toeholds and BM domains, which results in a novel operation 'toehold switching', and (3) design of a simple conformational self-replicator.
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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.