title: Bulk and single-molecule fluorescence studies of the saturation of the DNA double helix using YOYO-3 intercalator dye.
abstract: We report a thorough photophysical characterization of the interactions between double-stranded DNA (dsDNA) and the trimethine cyanine homodimer dye YOYO-3. The fluorescence emission of this dye is enhanced by intercalation within the DNA double helix. We have explored the saturation of the dsDNA by bound YOYO-3 at the single-molecule level by studying the single-pair Förster resonance energy transfer (FRET) from an energy donor, Alexa Fluor 488, tagged at the 5' end of the double helix and the energy acceptor, YOYO-3, bound to the same DNA molecule. The spontaneous binding of YOYO-3 gives rise to an effective distribution of different FRET efficiencies and, therefore, donor-acceptor (D-A) distances. These distributions reveal the existence of multiple states of YOYO-3. Steady-state and time-resolved fluorescence and circular dichroism confirmed the presence of a DNA-bound aggregate of YOYO-3, conspicuous at high dye/base pair ratios. The spectral features of the aggregate suggest that it may have the structure of a parallel H-aggregate.
authors.affiliation: Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada, Spain.
authors.forename: Sergio G
authors.initials: SG
authors.lastname: Lopez
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Ruedas-Rama
authors.forename: Salvador
authors.initials: S
authors.lastname: Casares
authors.forename: Jose M
authors.initials: JM
authors.lastname: Alvarez-Pez
authors.forename: Angel
authors.initials: A
authors.lastname: Orte
mesh_terms: D004247:DNA / Q000737:chemistry*; D005453:Fluorescence; D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes / Q000737:chemistry*; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D010080:Oxazoles / Q000737:chemistry*
chemical_list: D005456:Fluorescent Dyes; D010080:Oxazoles; C412625:YoYo-3; D004247:DNA