ArticleNature communications2020
Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 108 citations in OpenAlex.
- RNA structure modulates Cas13 activity and enables mismatch detection.Nature biotechnology · 2026Article
- Fuel-Driven Catalytic Molecular Templating.Journal of the American Chemical Society · 2026Article
- Enzymatic DNA Reaction Networks for Orchestrating Stimuli-Dependent Temporal Molecular Pulse.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Optimization of SWCNT-FET Biosensors by Aptamer Engineering and Toehold-Mediated Strand Displacement.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Fitting coarse-grained models to macroscopic experimental data via automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- An information ratchet improves selectivity in molecular recognition under non-equilibrium conditions.Nature nanotechnology · 2025Article
- Mismatch-Assisted Toehold Exchange Cascades for Magnetic Nanoparticle-based Nucleic Acid Diagnostics.JACS Au · 2025Article
- Supervised learning in DNA neural networks.Nature · 2025Article
- Mismatch-Induced Toehold-Free Strand Displacement Used to Control a DNA Nanodevice.ACS synthetic biology · 2025Article
- Controlling DNA-RNA strand displacement kinetics with base distribution.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Predicting DNA Reactions with a Quantum Chemistry-Based Deep Learning Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Understanding the relationship between sequences and kinetics of DNA strand displacements.Nucleic acids research · 2024Article
- Single-molecule force spectroscopy of toehold-mediated strand displacement.Nature communications · 2024Article
- Kinetic Proofreading Can Enhance Specificity in a Nonenzymatic DNA Strand Displacement Network.Journal of the American Chemical Society · 2024Article
- Article
- The motive forces in DNA-enabled nanomachinery.iScience · 2024Review
- Transient states during the annealing of mismatched and bulged oligonucleotides.Nucleic acids research · 2024Article
- RNA structure modulates Cas13 activity and enables mismatch detection.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a mechanism for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing forward reaction rates: the introduction of mismatches within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of non-equilibrium systems that rely on catalytic control and must be robust to leak reactions.
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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.