Abstract
Intercalating fluorescent probes are widely used to visualize DNA in studies on DNA-protein interactions. Some require the presence of adenosine triphosphate (ATP). We have investigated the mechanical properties of DNA stained with the fluorescent intercalating dyes YOYO-1 and YOYO-3 as a function of ATP concentrations (up to 2 mM) by stretching single molecules in nanofluidic channels with a channel cross-section as small as roughly 100 × 100 nm2. The presence of ATP reduces the length of the DNA by up to 11 %. On the other hand, negligible effects are found if DNA is visualized with the minor groove-binding probe 4′,6-diamidino-2-phenylindole. The apparent drop in extension under nanoconfinement is attributed to an interaction of the dye and ATP, and the resulting expulsion of YOYO-1 from the double helix.
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We acknowledge support from the National Institutes of Health (R01GM107559), and thank Keith Weninger for fruitful discussions.
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Roushan, M., Azad, Z., Lim, S.F. et al. Interference of ATP with the fluorescent probes YOYO-1 and YOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels. Microchim Acta 182, 1561–1565 (2015). https://doi.org/10.1007/s00604-015-1495-7
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DOI: https://doi.org/10.1007/s00604-015-1495-7