ArticleEuropean biophysics journal : EBJ2015
Characterizing the interaction between DNA and GelRed fluorescent stain.
Article in European biophysics journal : EBJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 56 citations in OpenAlex.
- Molecular structure and DNA binding mode of unsymmetric cyanine dyes RiboGreen and OliGreen.Nucleic acids research · 2026Article
- Versatile DNA-Functionalized Biohybrid Hydrogel Platforms for Electrothermally Activated On-Demand Payload Release.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Microglia-Targeted Biomimetic Tetrahedral Framework Nucleic Acid Nanovesicles for Synergistic Treatment of Sepsis-Associated Encephalopathy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Azure A Dye Interaction with Double-Stranded DNA Can Be Modulated by the Ionic Strength: Choosing the Binding Mode.ACS omega · 2026Article
- Fluorescent Dyes for Differential Scanning Fluorimetry of RNA.Chembiochem : a European journal of chemical biology · 2025Article
- Freezing induced incorporation of betaine in lipid nanoparticles enhances mRNA delivery.Nature communications · 2025Article
- Comparative Analysis of Methods for Assessing On-Target Gene Editing Efficiencies.Methods and protocols · 2025Article
- DNA binding to small anionic ligands: the case of Orange G dye.European biophysics journal : EBJ · 2025Article
- A Novel Fluorescent DNA Sensor for Acrylamide Detection in Food Samples Based on Single-Stranded DNA and GelRed.Journal of fluorescence · 2024Article
- On the interactions involving serine proteases obtained from Monacrosporium thaumasium (Ascomycota: Orbiliomycetes) and deoxyribonucleic acid (DNA): biological macromolecules in action.Archives of microbiology · 2023Article
- Relative Nuclease Resistance of a DNA Aptamer Covalently Conjugated to a Target Protein.International journal of molecular sciences · 2022Article
- Article
- Immunoassay-aptasensor for the determination of tumor-derived exosomes based on the combination of magnetic nanoparticles and hybridization chain reaction.RSC advances · 2021Article
- A polymeric approach toward resistance-resistant antimicrobial agent with dual-selective mechanisms of action.Science advances · 2021Article
- Cryopreservation of human cerebral microvascular endothelial cells and astrocytes in suspension and monolayers.PloS one · 2021Article
- Functionalized DNA nanostructures as scaffolds for guided mineralization.Chemical science · 2019Article
- Cellular microRNA detection with miRacles: microRNA- activated conditional looping of engineered switches.Science advances · 2019Article
- Identification of Novel Nuclear Factor of Activated T Cell (NFAT)-associated Proteins in T Cells.The Journal of biological chemistry · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have performed single-molecule stretching and dynamic light-scattering (DLS) experiments to characterize the interaction between the DNA molecule and the fluorescent stain GelRed. The results from single-molecule stretching show that the persistence length of DNA-GelRed complexes increases as the ligand concentration increases up to a critical concentration, then decreases for higher concentrations. The contour length of the complexes, on the other hand, increases monotonically as a function of GelRed concentration, suggesting that intercalation is the main binding mechanism. To characterize the physical chemistry of the interaction, we used the McGhee-von Hippel binding isotherm to extract physicochemical data for the interaction from the contour length data. Such analysis enabled us to conclude that the GelRed stain is, in fact, a bis-intercalator. In addition, DLS experiments were performed to study the changes of the effective size of the DNA-GelRed complexes, measured as the hydrodynamic radius, as a function of ligand concentration. We observed qualitative agreement between the results obtained from the two techniques by comparing the behavior of the hydrodynamics radius and the radius of gyration, because the latter quantity can be expressed as a function of mechanical properties determined from the stretching experiments.
Indexed as
Identifiers
What OpenQuestion holds
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.