title: Interference of ATP with the fluorescent probes YOYO-1 andYOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels.
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.
authors.affiliation: Department of Physics, NC State University, Raleigh, NC 27695-8202, USA.
authors.forename: Maedeh
authors.initials: M
authors.lastname: Roushan
authors.affiliation: Department of Physics, NC State University, Raleigh, NC 27695-8202, USA.
authors.forename: Zubair
authors.initials: Z
authors.lastname: Azad
authors.affiliation: Department of Physics, NC State University, Raleigh, NC 27695-8202, USA.
authors.forename: Shuang Fang
authors.initials: SF
authors.lastname: Lim
authors.affiliation: Department of Physics, NC State University, Raleigh, NC 27695-8202, USA.
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Physics, NC State University, Raleigh, NC 27695-8202, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Riehn
keywords: ATP; DAPI; DNA; Intercalating dye; Nanofluidics; YOYO-1