ArticleNature communications2024
Single-molecule force spectroscopy of toehold-mediated strand displacement.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Mechanism underlying the high regulatory performance of the doxycycline riboswitch G12.Nature communications · 2026Article
- Massively parallel bead-free force spectroscopy with fluorescence.Science advances · 2026Article
- Engineered CRISPR/Cas12a2 Nanoprobe Imaging in Living Cells for Precise Tumor Diagnosis.Small methods · 2026Article
- Operating CRISPR/Cas12a in a complex nucleic acid sequence background.Nucleic acids research · 2026Article
- Visualizing and Quantifying microRNA-Induced DNA Origami Separation at the Nanoscale.Angewandte Chemie (International ed. in English) · 2026Article
- Amplification-Free Dual-Blocking Autocatalytic CRISPR-Cascade for Atto-Molar DNA Detection with Low Nonspecific Signal.bioRxiv : the preprint server for biology · 2025Article
- Functions and applications of enzymes in nucleic acid nanotechnology.Journal of nanobiotechnology · 2025Review
- Beyond the niche - unlocking the full potential of synthetic riboswitches.Nature communications · 2025Review
- Kinetics and Activation Strategies in Toehold-Mediated and Toehold-Free DNA Strand Displacement.Biosensors · 2025Review
- Mismatch-Assisted Toehold Exchange Cascades for Magnetic Nanoparticle-based Nucleic Acid Diagnostics.JACS Au · 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
- Roquin exhibits opposing effects on RNA stem-loop stability through its two ROQ domain binding sites.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation.Journal of microbiology (Seoul, Korea) · 2025Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Toehold-mediated strand displacement (TMSD) is extensively utilized in dynamic DNA nanotechnology and for a wide range of DNA or RNA-based reaction circuits. Investigation of TMSD kinetics typically relies on bulk fluorescence measurements providing effective, bulk-averaged reaction rates. Information on individual molecules or even base pairs is scarce. In this work, we explore the dynamics of strand displacement processes at the single-molecule level using single-molecule force spectroscopy with a microfluidics-enhanced optical trap supported by state-of-the-art coarse-grained simulations. By applying force, we can trigger and observe TMSD in real-time with microsecond and nanometer resolution. We find TMSD proceeds very rapidly under load with single step times of 1 µs. Tuning invasion efficiency by introducing mismatches allows studying thousands of forward/backward invasion events on a single molecule and analyze the kinetics of the invasion process. Extrapolation to zero force reveals single step times for DNA invading DNA four times faster than for RNA invading RNA. We also study the kinetics of DNA invading RNA, a process that in the absence of force would rarely occur. Our results reveal the importance of sequence effects for the TMSD process and have relevance for a wide range of applications in nucleic acid nanotechnology and synthetic biology.
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Registered trials
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