title: Heterogeneous staining: a tool for studies of how fluorescent dyes affect the physical properties of DNA.
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.
authors: Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden and Department for Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
authors: Lena
authors: L
authors: Nyberg
authors: Fredrik
authors: F
authors: Persson
authors: Björn
authors: B
authors: Akerman
authors: Fredrik
authors: F
authors: Westerlund
mesh_terms: D001583:Benzoxazoles / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D011806:Quinolinium Compounds / Q000737:chemistry*; D013194:Staining and Labeling
chemical_list: D001583:Benzoxazoles; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium; D004247:DNA
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