ArticleNucleic acids research2022
Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides.
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 19 papers.
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Who cites it
19 citing papers in PubMed.
- Beyond the genetic code: orchestrating epigenetic and immune landscapes with multivalent mRNA-exosome vaccines.Precision clinical medicine · 2026Review
- Periodic Temperature Fluctuations as an Energy Source for RNA Evolution.Life (Basel, Switzerland) · 2026Article
- How do RNA molecules distinguish self from non-self?Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Non-enzymatic error correction in self-replicators without extraneous energy supply.Scientific reports · 2026Article
- Kinetics and Activation Strategies in Toehold-Mediated and Toehold-Free DNA Strand Displacement.Biosensors · 2025Review
- TrueProbes: Quantitative Single-Molecule RNA-FISH Probe Design Improves RNA Detection.bioRxiv : the preprint server for biology · 2025Article
- Stereoselectivity of Aminoacyl-RNA Loop-Closing Ligation.Journal of the American Chemical Society · 2025Article
- Conserved long-range interactions are required for stable folding of orthoflaviviral genomic RNA.Nucleic acids research · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Autocatalytic assembly of a chimeric aminoacyl-RNA synthetase ribozyme.Science advances · 2025Article
- Single-molecule force spectroscopy of toehold-mediated strand displacement.Nature communications · 2024Article
- Did the exposure of coacervate droplets to rain make them the first stable protocells?Science advances · 2024Article
- RNA Complexes with Nicks and Gaps: Thermodynamic and Kinetic Effects of Coaxial Stacking and Dangling Ends.Journal of the American Chemical Society · 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
- Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.Biophysical journal · 2023Article
- Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis.Biochemistry · 2023Article
- Experimental Tests of the Virtual Circular Genome Model for Nonenzymatic RNA Replication.Journal of the American Chemical Society · 2023Article
- Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes.Analytical chemistry · 2022Article
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2 authors.
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Abstract
Hybridization and strand displacement kinetics determine the evolution of the base paired configurations of mixtures of oligonucleotides over time. Although much attention has been focused on the thermodynamics of DNA and RNA base pairing in the scientific literature, much less work has been done on the time dependence of interactions involving multiple strands, especially in RNA. Here we provide a study of oligoribonucleotide interaction kinetics and show that it is possible to calculate the association, dissociation and strand displacement rates displayed by short oligonucleotides (5nt-12nt) that exhibit no expected secondary structure as simple functions of oligonucleotide length, CG content, ΔG of hybridization and ΔG of toehold binding. We then show that the resultant calculated kinetic parameters are consistent with the experimentally observed time dependent changes in concentrations of the different species present in mixtures of multiple competing RNA strands. We show that by changing the mixture composition, it is possible to create and tune kinetic traps that extend by orders of magnitude the typical sub-second hybridization timescale of two complementary oligonucleotides. We suggest that the slow equilibration of complex oligonucleotide mixtures may have facilitated the nonenzymatic replication of RNA during the origin of life.
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