Journal
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
Volume 44, Issue 5, Pages 337-348Publisher
SPRINGER
DOI: 10.1007/s00249-015-1027-8
Keywords
DNA intercalator; DNA staining; Single molecule; Intercalators binding mechanism; Fluorescence microscopy
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Funding
- Plate-forme Integree de Biologie Structurale (IBISA)
- France-BioImaging infrastructure - French National Research Agency [ANR-10-INSB-04]
- Agence Nationale de la Recherche [ANR-2010-BLAN-1525-01, ANR-2010-BLAN-1221-01]
- Human Frontiers Science Program through a Career Development Award
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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.
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