ArticleNucleic acids research2022
The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.
Article in Nucleic acids research, 2022. 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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14 citing papers in PubMed.
- Clocked stepping of an artificial protein walker along a DNA track.Nature nanotechnology · 2026Article
- Accurate prediction of oligonucleotide probe hybridization efficiency via a transformer-based model.BMC genomics · 2026Article
- High-speed multiplexed DNA-PAINT imaging of nuclear organization using an expanded sequence repertoire.Nature communications · 2026Article
- Non-enzymatic error correction in self-replicators without extraneous energy supply.Scientific reports · 2026Article
- Rapid Forensic DNA Profiling via Real-Time Recombinase Polymerase Amplification of InDel Markers.Biosensors · 2026Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins.Nature communications · 2025Article
- Predicting DNA Reactions with a Quantum Chemistry-Based Deep Learning Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Transient states during the annealing of mismatched and bulged oligonucleotides.Nucleic acids research · 2024Article
- Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics.Biophysical journal · 2024Article
- A Theoretical Framework for Implementable Nucleic Acids Feedback Systems.Bioengineering (Basel, Switzerland) · 2023Article
- Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes.Analytical chemistry · 2022Article
- Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides.Nucleic acids research · 2022Article
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6 authors.
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Abstract
The kinetics of DNA hybridization are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridize at different rates are not well understood. Secondary structure is one predictable factor that influences hybridization rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. In this context, we measured hybridization rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify our observations. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters. Our results indicate that greater repetition of Watson-Crick pairs increases the number of initial states able to proceed to full hybridization, with the stability of those pairings dictating the likelihood of such progression, thus providing new insight into the physical factors underpinning DNA hybridization rates.
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