title: The fluorescence properties and binding mechanism of SYTOX green, a bright, low photo-damage DNA intercalating agent.
abstract: DNA intercalators are widely used in cancer therapeutics, to probe protein-DNA interactions and to investigate the statistical-mechanical properties of DNA. Here, we employ single-molecule fluorescence microscopy, magnetic tweezers, and ensemble-binding assays to investigate the fluorescence properties and binding mechanism of SYTOX green, a DNA labeling dye previously used for staining dead cells and becoming of common use for single-molecule methodologies. Specifically, we show that SYTOX green presents several advantages with respect to other dyes: (1) binds DNA rapidly and with high affinity; (2) has a good signal-to-noise ratio even at low concentrations; (3) exhibits a low photobleaching rate; and (4) induces lower light-induced DNA degradation. Finally, we show that SYTOX green is a DNA intercalator that binds DNA cooperatively with a binding site of 3.5 bp, increasing the DNA length upon binding by 43%, while not affecting its mechanical properties.
authors.affiliation: Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090, Montpellier, France.
authors.forename: Shreyasi
authors.initials: S
authors.lastname: Thakur
authors.forename: Diego I
authors.initials: DI
authors.lastname: Cattoni
authors.forename: Marcelo
authors.initials: M
authors.lastname: Nöllmann
mesh_terms: D004247:DNA / Q000737:chemistry / Q000187:drug effects*; D004249:DNA Damage; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry* / Q000494:pharmacology; D009153:Mutagens / Q000737:chemistry* / Q000494:pharmacology; D009930:Organic Chemicals / Q000737:chemistry / Q000494:pharmacology; D014466:Ultraviolet Rays
chemical_list: D005456:Fluorescent Dyes; D009153:Mutagens; D009930:Organic Chemicals; C402795:SYTOX Green; D004247:DNA