Heterogeneous staining: a tool for studies of how fluorescent dyes affect the physical properties of DNA
Artikel i vetenskaplig tidskrift, 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

Författare

Lena Nyberg

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Fredrik Persson

Uppsala universitet

Björn Åkerman

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Fredrik Westerlund

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Nucleic Acids Research

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

Vol. 41 19 articlenr e184-

Styrkeområden

Nanovetenskap och nanoteknik

Livsvetenskaper och teknik

Ämneskategorier

Biokemi och molekylärbiologi

DOI

10.1093/nar/gkt755

Mer information

Senast uppdaterat

2018-02-28