ArticleNucleic acids research2015
DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- 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
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides.Nucleic acids research · 2022Article
- The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.Nucleic acids research · 2022Article
- OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures.Nucleic acids research · 2021Article
- Understanding DNA interactions in crowded environments with a coarse-grained model.Nucleic acids research · 2020Article
- A review on nonlinear DNA physics.Royal Society open science · 2020Review
- Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation.Nucleic acids research · 2020Article
- Free energy landscape of salt-actuated reconfigurable DNA nanodevices.Nucleic acids research · 2020Article
- Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size.Nucleic acids research · 2018Article
- Rolling circle amplification shows a sinusoidal template length-dependent amplification bias.Nucleic acids research · 2018Article
- Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics.Nucleic acids research · 2018Article
- Comprehensive profiling of the ligand binding landscapes of duplexed aptamer families reveals widespread induced fit.Nature communications · 2018Article
- Predicting DNA hybridization kinetics from sequence.Nature chemistry · 2018Article
- The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics.Natural computing · 2018Article
- Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification.Nature communications · 2017Article
- Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage.Nucleic acids research · 2015Article
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7 authors.
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Abstract
The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how hairpins influence the rate and reaction pathways of DNA hybridzation. We compare to experimental systems studied by Gao et al. (1) and find that 3-base pair hairpins reduce the hybridization rate by a factor of 2, and 4-base pair hairpins by a factor of 10, compared to DNA with limited secondary structure, which is in good agreement with experiments. By contrast, melting rates are accelerated by factors of ∼100 and ∼2000. This surprisingly large speed-up occurs because hairpins form during the melting process, and significantly lower the free energy barrier for dissociation. These results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands.
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