ArticleNucleic acids research2007
Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 121 citations in OpenAlex.
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- Mimetic nucleic probes to study the thermodynamics of aptamer-based pH switches.Analytical and bioanalytical chemistry · 2026Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- DNA Hybridization Kinetics Observed at the Single-Molecule Level Using Graphene Near-Field Effects.The journal of physical chemistry. A · 2024Article
- Generation of DNA oligomers with similar chemical kinetics via in-silico optimization.Communications chemistry · 2023Article
- Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme.International journal of molecular sciences · 2023Article
- Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.Biophysical journal · 2023Article
- Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs.bioRxiv : the preprint server for biology · 2023Article
- Beneficial and detrimental effects of non-specific binding during DNA hybridization.Biophysical journal · 2023Article
- Improved PCR by the Use of Disruptors, a New Class of Oligonucleotide Reagents.Methods in molecular biology (Clifton, N.J.) · 2023Article
- An Advanced Detection System forActa histochemica et cytochemica · 2022Article
- The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.Nucleic acids research · 2022Article
- Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.Journal of the American Chemical Society · 2021Article
- Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics.Angewandte Chemie (International ed. in English) · 2021Article
- Nearest-neighbour transition-state analysis for nucleic acid kinetics.Nucleic acids research · 2021Article
- DNA hybridisation kinetics using single-molecule fluorescence imaging.Essays in biochemistry · 2021Review
- Temperature-Jump 2D IR Spectroscopy with Intensity-Modulated CW Optical Heating.The journal of physical chemistry. B · 2020Article
- 5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex.The journal of physical chemistry. B · 2020Article
- Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics.Nucleic acids research · 2018Article
- Single-Molecule Photoactivation FRET: A General and Easy-To-Implement Approach To Break the Concentration Barrier.Angewandte Chemie (International ed. in English) · 2017Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hybridization of nucleic acids with secondary structure is involved in many biological processes and technological applications. To gain more insight into its mechanism, we have investigated the kinetics of DNA hybridization/denaturation via fluorescence resonance energy transfer (FRET) on perfectly matched and single-base-mismatched DNA strands. DNA hybridization shows non-Arrhenius behavior. At high temperature, the apparent activation energies of DNA hybridization are negative and independent of secondary structure. In contrast, when temperature decreases, the apparent activation energies of DNA hybridization change to positive and become structure dependent. The large unfavorable enthalpy of secondary structure melting is compensated for by concomitant duplex formation. Based on our results, we propose a reaction mechanism about how the melting of secondary structure influences the hybridization process. A significant point in the mechanism is that the rate-limiting step switches along with temperature variation in the hybridization process of structured DNA, because the free energy profile of hybridization in structured DNA varies with the variation in temperature.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.