Heterogeneous staining: a tool for studies of how fluorescent dyes affect the physical properties of DNA
Journal article, 2013

The commonly used fluorescent dye YOYO-1 (YOYO) has, using bulk techniques, been demonstrated to stain DNA heterogeneously at substoichiometric concentrations. We here, using nanofluidic channels and fluorescence microscopy, investigate the heterogeneous staining on the single DNA molecule level and demonstrate that the dye distribution is continuous. The equilibration of YOYO on DNA is extremely slow but can be accelerated by increasing the ionic strength and/or the temperature. Furthermore, we demonstrate how to use the heterogeneous staining as a tool for detailed and time-efficient studies of how fluorescent dyes affect the physical properties of DNA. We show that the relative increase in extension of DNA with increasing amount of YOYO bound is higher at low ionic strengths and also extrapolate the extension of native DNA. Our study reveals important information on how YOYO affects the physical properties of DNA, but it also has broader applications. First, it reveals how cationic intercalators, such as potential DNA drugs, affect DNA under strong confinement. Second, the strategy of using heterogeneous staining is of general use for single molecule studies of DNA interacting with proteins or ligands.

EQUILIBRIUM

INTERCALATION

BINDING

KINETICS

SPECTROSCOPY

OPTICAL TWEEZERS

MAGNETIC TWEEZERS

YOYO-1

DOUBLE-STRANDED DNA

SINGLE-MOLECULE

Author

Lena Nyberg

Chalmers, Chemical and Biological Engineering, Physical Chemistry

Fredrik Persson

Uppsala University

Björn Åkerman

Chalmers, Chemical and Biological Engineering, Physical Chemistry

Fredrik Westerlund

Chalmers, Chemical and Biological Engineering, Physical Chemistry

Nucleic Acids Research

0305-1048 (ISSN) 1362-4962 (eISSN)

Vol. 41 19 articlenr e184-

Areas of Advance

Nanoscience and Nanotechnology (2010-2017)

Life Science Engineering (2010-2018)

Subject Categories

Biochemistry and Molecular Biology

DOI

10.1093/nar/gkt755

More information

Latest update

2/28/2018