ArticleNucleic acids research2018
Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction.Nucleic acids research · 2023Article
- Generation of DNA oligomers with similar chemical kinetics via in-silico optimization.Communications chemistry · 2023Article
- FRET Imaging of Nonuniformly Distributed DNA SAMs on Gold Reveals the Role Played by the Donor/Acceptor Ratio and the Local Environment in Measuring the Rate of Hybridization.Chemical & biomedical imaging · 2023Article
- The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.Nucleic acids research · 2022Article
- Nearest-neighbour transition-state analysis for nucleic acid kinetics.Nucleic acids research · 2021Article
- An alternative approach to nucleic acid memory.Nature communications · 2021Article
- 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
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Authors and funding
3 authors.
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Abstract
Nucleic acid secondary structure plays an important role in nucleic acid-nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant.
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