ArticleBiophysical journal2016
The Effect of Basepair Mismatch on DNA Strand Displacement.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 39 citations in OpenAlex.
- Structural and Physicochemical Optimization of Next-Generation Antisense Oligonucleotide with BROTHERS for Mitigating Off-Target Effects.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Engineering and Assay of Enzymes for Expanded Genetic Alphabet Replication.Biochemistry · 2025Article
- Mismatch-Assisted Toehold Exchange Cascades for Magnetic Nanoparticle-based Nucleic Acid Diagnostics.JACS Au · 2025Article
- Mismatch-Induced Toehold-Free Strand Displacement Used to Control a DNA Nanodevice.ACS synthetic biology · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Twinkle-Catalyzed Toehold-Mediated DNA Strand Displacement Reaction.Journal of the American Chemical Society · 2023Article
- Controlling Dynamic DNA Reactions at the Surface of Single-Walled Carbon Nanotube Electrodes to Design Hybridization Platforms with a Specific Amperometric Readout.Analytical chemistry · 2022Article
- A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity.Nature communications · 2022Article
- Kinetics of heterochiral strand displacement from PNA-DNA heteroduplexes.Nucleic acids research · 2021Article
- Getting swept off your toe(hold)s: Single-molecule DNA fission analysis offers glimpse into kinetics of branch migration.Biophysical journal · 2021Article
- First passage time study of DNA strand displacement.Biophysical journal · 2021Article
- Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP.Nature communications · 2020Article
- ERASE: a novel surface reconditioning strategy for single-molecule experiments.Nucleic acids research · 2019Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single basepair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term the concurrent displacement model, and used the first passage time approach to quantitatively explain the salient features of the observed relationship. We also introduce the concept of splitting probabilities to justify that the concurrent model can be simplified into a three-step sequential model in the presence of an invader mismatch. We expect our model to become a powerful tool to design DNA-based reaction schemes with broad functionality.
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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.