ArticleNucleic acids research2013
DNA hybridization kinetics: zippering, internal displacement and sequence dependence.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
- Comparative kinetic analysis of PNA and γ-miniPEG-PNA hybridization with RNA by surface plasmon resonance.Organic & biomolecular chemistry · 2026Article
- DNA 'Breathing' Recombination Cloning: A Mismatch-Tolerant, Temperature-Dependent Homologous Recombination Cloning Method.International journal of molecular sciences · 2026Article
- Non-enzymatic error correction in self-replicators without extraneous energy supply.Scientific reports · 2026Article
- DNA Origami and Its Applications in Synthetic Biology.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Accelerated Ostwald Ripening by Chemical Activity.Journal of the American Chemical Society · 2025Article
- A Modular T7 RNA Polymerase Toolbox Linking Selective miRNA Detection to Signal Amplification and Protein Expression.Journal of the American Chemical Society · 2025Article
- Kinetics and Activation Strategies in Toehold-Mediated and Toehold-Free DNA Strand Displacement.Biosensors · 2025Review
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- Temperature-dependent funnel-like DNA folding landscapes.Nucleic acids research · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment.Applied and environmental microbiology · 2025Article
- Massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS).Nature communications · 2025Article
- All-in-one Biocomputing Nanoagents with Multilayered Transformable Architecture based on DNA Interfaces.Theranostics · 2025Article
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- Fluidic Interface for Surface-based DNA Origami Studies.ACS applied materials & interfaces · 2024Article
- Weak-cooperative binding of a long single-stranded DNA chain on a surface.Nucleic acids research · 2024Article
- DNA as a perfect quantum computer based on the quantum physics principles.Scientific reports · 2024Article
- A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower.Nature nanotechnology · 2024Article
- Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics.Biophysical journal · 2024Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although the thermodynamics of DNA hybridization is generally well established, the kinetics of this classic transition is less well understood. Providing such understanding has new urgency because DNA nanotechnology often depends critically on binding rates. Here, we explore DNA oligomer hybridization kinetics using a coarse-grained model. Strand association proceeds through a complex set of intermediate states, with successful binding events initiated by a few metastable base-pairing interactions, followed by zippering of the remaining bonds. But despite reasonably strong interstrand interactions, initial contacts frequently dissociate because typical configurations in which they form differ from typical states of similar enthalpy in the double-stranded equilibrium ensemble. Initial contacts must be stabilized by two or three base pairs before full zippering is likely, resulting in negative effective activation enthalpies. Non-Arrhenius behavior arises because the number of base pairs required for nucleation increases with temperature. In addition, we observe two alternative pathways-pseudoknot and inchworm internal displacement-through which misaligned duplexes can rearrange to form duplexes. These pathways accelerate hybridization. Our results explain why experimentally observed association rates of GC-rich oligomers are higher than rates of AT- rich equivalents, and more generally demonstrate how association rates can be modulated by sequence choice.
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