ArticleBiophysical journal2009
Interaction of oxazole yellow dyes with DNA studied with hybrid optical tweezers and fluorescence microscopy.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 94 citations in OpenAlex.
- Azure A Dye Interaction with Double-Stranded DNA Can Be Modulated by the Ionic Strength: Choosing the Binding Mode.ACS omega · 2026Article
- Effects of MgBiochemistry and biophysics reports · 2025Article
- TMPyP binding evokes a complex, tunable nanomechanical response in DNA.Nucleic acids research · 2024Article
- Measuring the Adsorption Cross Section of YOYO-1 to Immobilized DNA Molecules.The journal of physical chemistry. B · 2024Article
- Studying the Effects and Competitive Mechanisms of YOYO-1 on the Binding Characteristics of DOX and DNA Molecules Based on Surface-Enhanced Raman Spectroscopy and Molecular Docking Techniques.International journal of molecular sciences · 2024Article
- 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
- Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA.Nature communications · 2022Article
- Optical tweezer and TIRF microscopy for single molecule manipulation of RNA/DNA nanostructures including their rubbery property and single molecule counting.Biophysics reports · 2021Article
- Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA.Molecules (Basel, Switzerland) · 2021Article
- DNA Manipulation and Single-Molecule Imaging.Molecules (Basel, Switzerland) · 2021Review
- Progress and challenges in the use of fluorescence-based flow cytometric assays for anti-malarial drug susceptibility tests.Malaria journal · 2021Review
- Stretching DNA to twice the normal length with single-molecule hydrodynamic trapping.Lab on a chip · 2020Article
- Binding mechanism of anti-cancer chemotherapeutic drug mitoxantrone to DNA characterized by magnetic tweezers.Journal of nanobiotechnology · 2018Article
- DNA intercalation optimized by two-step molecular lock mechanism.Scientific reports · 2016Article
- Nanomechanics of Fluorescent DNA Dyes on DNA Investigated by Magnetic Tweezers.Biophysical journal · 2016Article
- Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy.Nucleic acids research · 2016Article
- A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps.Nucleic acids research · 2015Article
- The fluorescence properties and binding mechanism of SYTOX green, a bright, low photo-damage DNA intercalating agent.European biophysics journal : EBJ · 2015Article
- The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics.Nature communications · 2015Article
- Interference of ATP with the fluorescent probes YOYO-1 andYOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels.Mikrochimica acta · 2015Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have integrated single molecule fluorescence microscopy imaging into an optical tweezers set-up and studied the force extension behavior of individual DNA molecules in the presence of various YOYO-1 and YO-PRO-1 concentrations. The fluorescence modality was used to record fluorescent images during the stretching and relaxation cycle. Force extension curves recorded in the presence of either dye did not show the overstretching transition that is characteristic for bare DNA. Using the modified wormlike chain model to curve-fit the force extension data revealed a contour length increase of 6% and 30%, respectively, in the presence of YO-PRO-1 and YOYO-1 at 100 nM. The fluorescence images recorded simultaneously showed that the number of bound dye molecules increased as the DNA molecule was stretched and decreased again as the force on the complex was lowered. The binding constants and binding site sizes for YO-PRO-1 and YOYO-1 were determined as a function of the force. The rate of YO-PRO-1 binding and unbinding was found to be 2 orders of magnitude larger than that for YOYO-1. A kinetic model is proposed to explain this observation.
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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.