ArticleBiopolymers2011
Measuring thermodynamic details of DNA hybridization using fluorescence.
Article in Biopolymers, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
37 citing papers in PubMed, 94 citations in OpenAlex.
- A thermodynamically favoured molecular computer.Nature · 2026Article
- Coupling pH-Responsive Dyes to Agarose Hydrogels for Monitoring Metabolic States of Encapsulated Phototrophic Microbial Consortia.ACS applied bio materials · 2025Article
- Fluorescent modifications in aptamer switches-positional, structural, and neighboring pair effects on sensor performance.Nucleic acids research · 2025Article
- Single-Sample Melt-Based Screening for Rifampicin Susceptibility in the Emerging Mutation Hotspot atACS infectious diseases · 2025Article
- High-throughput DNA melt measurements enable improved models of DNA folding thermodynamics.Nature communications · 2025Article
- Counterintuitive DNA destabilization by monovalent salt at high concentrations due to overcharging.Nature communications · 2025Article
- Effects of Molecular Crowding on the Structure, Folding, and Stability of DNA.Sub-cellular biochemistry · 2025Review
- L-DNA-Based Melt Analysis Enables Within-Sample Validation of PCR Products.Analytical chemistry · 2024Article
- Implementing L-DNA analogs as mirrors of PCR reactant hybridization state: theoretical and practical guidelines for PCR cycle control.Analytical methods : advancing methods and applications · 2024Article
- Article
- Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing.Advances in biochemical engineering/biotechnology · 2024Review
- Functional advantages of building nanosystems using multiple molecular components.Nature chemistry · 2023Article
- Thermodynamic Characterization of Nucleic Acid Nanoparticles Hybridization by UV Melting.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.Biochemistry · 2022Article
- Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides.Nucleic acids research · 2022Article
- Best practice for improved accuracy: A critical reassessment of van't Hoff analysis of melt curves.Biophysical journal · 2022Article
- Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments.PLoS computational biology · 2022Article
- Fluorescence-Based Binding Characterization of Small Molecule Ligands Targeting CUG RNA Repeats.International journal of molecular sciences · 2022Article
- Kinetics of heterochiral strand displacement from PNA-DNA heteroduplexes.Nucleic acids research · 2021Article
- DNA hybridisation kinetics using single-molecule fluorescence imaging.Essays in biochemistry · 2021Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Modern real-time PCR systems make it easy to monitor fluorescence while temperature is varied for hundreds of samples in parallel, permitting high-throughput studies. We employed such system to investigate melting transitions of ordered nucleic acid structures into disordered random coils. Fluorescent dye and quencher were attached to oligonucleotides in such a way that changes of fluorescence intensity with temperature indicated progression of denaturation. When fluorescence melting data were compared with traditional ultraviolet optical experiments, commonly used dye/quencher combinations, like fluorescein and tetramethylrhodamine, showed substantial discrepancies. We have therefore screened 22 commercially available fluorophores and quenchers for their ability to reliably report annealing and melting transitions. Dependence of fluorescence on temperature and pH was also investigated. The optimal performance was observed using Texas Red or ROX dyes with Iowa Black RQ or Black Hole quenchers. These labels did not alter two-state nature of duplex melting process and provided accurate melting temperatures, free energies, enthalpies, and entropies. We also suggest a new strategy for determination of DNA duplex thermodynamics where concentration of a dye-labeled strand is kept constant and its complementary strand modified with a quencher is added at increasing excess. These methodological improvements will help build predictive models of nucleic acid hybridization.
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Registered trials
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.