ArticleNucleic acids research2017
Elasticity of the transition state for oligonucleotide hybridization.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Quantitative Super-Resolution Imaging of Molecular Tension.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- DNA calorimetric force spectroscopy at single base pair resolution.Nature communications · 2025Article
- Stacking correlation length in single-stranded DNA.Nucleic acids research · 2024Article
- Engineering tunable catch bonds with DNA.Nature communications · 2024Article
- Transient states during the annealing of mismatched and bulged oligonucleotides.Nucleic acids research · 2024Article
- Force-Induced Site-Specific Enzymatic Cleavage Probes Reveal That Serial Mechanical Engagement Boosts T Cell Activation.Journal of the American Chemical Society · 2024Article
- Weak tension accelerates hybridization and dehybridization of short oligonucleotides.Nucleic acids research · 2023Article
- High-throughput single-molecule quantification of individual base stacking energies in nucleic acids.Nature communications · 2023Article
- Low cost and massively parallel force spectroscopy with fluid loading on a chip.Nature communications · 2022Article
- The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.Nucleic acids research · 2022Article
- Backbone Hydrocarbon-Constrained Nucleic Acids Modulate Hybridization Kinetics for RNA.Journal of the American Chemical Society · 2022Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- DNA hybridisation kinetics using single-molecule fluorescence imaging.Essays in biochemistry · 2021Review
- DNA Tension Probes to Map the Transient Piconewton Receptor Forces by Immune Cells.Journal of visualized experiments : JoVE · 2021Article
- Parallel, linear, and subnanometric 3D tracking of microparticles with Stereo Darkfield Interferometry.Science advances · 2021Article
- Optical tweezers in single-molecule biophysics.Nature reviews. Methods primers · 2021Article
- Live-cell super-resolved PAINT imaging of piconewton cellular traction forces.Nature methods · 2020Article
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
- Multimodal Measurements of Single-Molecule Dynamics Using FluoRBT.Biophysical journal · 2018Article
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Authors and funding
3 authors.
Funding
Abstract
Despite its fundamental importance in cellular processes and abundant use in biotechnology, we lack a detailed understanding of the kinetics of nucleic acid hybridization. In particular, the identity of the transition state, which determines the kinetics of the two-state reaction, remains poorly characterized. Here, we used optical tweezers with single-molecule fluorescence to observe directly the binding and unbinding of short oligonucleotides (7-12 nt) to a complementary strand held under constant force. Binding and unbinding rate constants measured across a wide range of forces (1.5-20 pN) deviate from the exponential force dependence expected from Bell's equation. Using a generalized force dependence model, we determined the elastic behavior of the transition state, which we find to be similar to that of the pure single-stranded state. Our results indicate that the transition state for hybridization is visited before the strands form any significant amount of native base pairs. Such a transition state supports a model in which the rate-limiting step of the hybridization reaction is the alignment of the two strands prior to base pairing.
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