ArticleNucleic acids research2013
On the biophysics and kinetics of toehold-mediated DNA strand displacement.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 171 papers.
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Who cites it
171 citing papers in PubMed.
- RNA structure modulates Cas13 activity and enables mismatch detection.Nature biotechnology · 2026Article
- DNA-Based Boolean Logic Gates for Molecular Computation and Biosensing: A Critical Review.Molecular biotechnology · 2026Review
- Enzymatic DNA Reaction Networks for Orchestrating Stimuli-Dependent Temporal Molecular Pulse.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Visualizing and Quantifying microRNA-Induced DNA Origami Separation at the Nanoscale.Angewandte Chemie (International ed. in English) · 2026Article
- How do RNA molecules distinguish self from non-self?Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Decoupling Dynamics and Crosslink Stability in Supramolecular Hydrogels Using Associative Exchange.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Programming DNA machines to move.Nature reviews. Chemistry · 2026Review
- Anionic Liposomes as Optimal Membrane Fusion Carriers Enabling in Situ Multiplexed Detection of Extracellular Vesicle MicroRNAs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
- Engineering and Assay of Enzymes for Expanded Genetic Alphabet Replication.Biochemistry · 2025Article
- Kinetics and Activation Strategies in Toehold-Mediated and Toehold-Free DNA Strand Displacement.Biosensors · 2025Review
- Article
- Mismatch-Assisted Toehold Exchange Cascades for Magnetic Nanoparticle-based Nucleic Acid Diagnostics.JACS Au · 2025Article
- Overcoming the Speed Limit of Four-Way DNA Branch Migration with Bulges in Toeholds.Nano letters · 2025Article
- Reconfigurable Nucleic Acid Nanoparticles with Therapeutic RNAi Responses to Intracellular Disease Markers.Advanced functional materials · 2025Article
- Design of mismatch closure for enhanced specificity in DNA strand displacement reactions.Nucleic acids research · 2025Article
- Controlling DNA-RNA strand displacement kinetics with base distribution.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Review
- How We Simulate DNA Origami.Small methods · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
111 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.
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