ArticleNucleic acids research2013
Heterogeneous staining: a tool for studies of how fluorescent dyes affect the physical properties of DNA.
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 29 papers.
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Who cites it
29 citing papers in PubMed.
- Effects of MgBiochemistry and biophysics reports · 2025Article
- Biological Amyloids Chemically Damage DNA.ACS chemical neuroscience · 2025Article
- Design and in vitro anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease.Nucleic acids research · 2025Article
- Effect of Flow Rate and Ionic Strength on the Stabilities of YOYO-1 and YO-PRO-1 Intercalated in DNA Molecules.The journal of physical chemistry. B · 2023Article
- High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays.Micromachines · 2022Article
- A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids.Micromachines · 2021Article
- The HIV-1 nucleocapsid chaperone protein forms locally compacted globules on long double-stranded DNA.Nucleic acids research · 2021Article
- Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale.Essays in biochemistry · 2021Article
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- Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital.The Journal of antimicrobial chemotherapy · 2020Article
- Phosphorylated CtIP bridges DNA to promote annealing of broken ends.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Enzyme-free optical DNA mapping of the human genome using competitive binding.Nucleic acids research · 2019Article
- Article
- Alpha-Synuclein Modulates the Physical Properties of DNA.Chemistry (Weinheim an der Bergstrasse, Germany) · 2018Article
- Evaluation of Blob Theory for the Diffusion of DNA in Nanochannels.Macromolecules · 2018Article
- Entropic trap purification of long DNA.Lab on a chip · 2018Article
- A Label-Free Fluorescent Array Sensor Utilizing Liposome Encapsulating Calcein for Discriminating Target Proteins by Principal Component Analysis.Sensors (Basel, Switzerland) · 2017Article
- Halogen-containing thiazole orange analogues - new fluorogenic DNA stains.Beilstein journal of organic chemistry · 2017Article
- DNA compaction by the bacteriophage protein Cox studied on the single DNA molecule level using nanofluidic channels.Nucleic acids research · 2016Article
- Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The commonly used fluorescent dye YOYO-1 (YOYO) has, using bulk techniques, been demonstrated to stain DNA heterogeneously at substoichiometric concentrations. We here, using nanofluidic channels and fluorescence microscopy, investigate the heterogeneous staining on the single DNA molecule level and demonstrate that the dye distribution is continuous. The equilibration of YOYO on DNA is extremely slow but can be accelerated by increasing the ionic strength and/or the temperature. Furthermore, we demonstrate how to use the heterogeneous staining as a tool for detailed and time-efficient studies of how fluorescent dyes affect the physical properties of DNA. We show that the relative increase in extension of DNA with increasing amount of YOYO bound is higher at low ionic strengths and also extrapolate the extension of native DNA. Our study reveals important information on how YOYO affects the physical properties of DNA, but it also has broader applications. First, it reveals how cationic intercalators, such as potential DNA drugs, affect DNA under strong confinement. Second, the strategy of using heterogeneous staining is of general use for single molecule studies of DNA interacting with proteins or ligands.
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