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

Lena Nyberg (Institutionen för kemi- och bioteknik, Fysikalisk kemi) ; Fredrik Persson ; Björn Åkerman (Institutionen för kemi- och bioteknik, Fysikalisk kemi) ; Fredrik Westerlund (Institutionen för kemi- och bioteknik, Fysikalisk kemi)
Nucleic Acids Research (0305-1048). Vol. 41 (2013), 19, p. articlenr e184.
[Artikel, refereegranskad vetenskaplig]

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.

Nyckelord: DOUBLE-STRANDED DNA, SINGLE-MOLECULE, MAGNETIC TWEEZERS, OPTICAL TWEEZERS, BINDING, SPECTROSCOPY, YOYO-1, INTERCALATION, EQUILIBRIUM, KINETICS



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Denna post skapades 2013-11-28. Senast ändrad 2015-07-28.
CPL Pubid: 187602

 

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Institutioner (Chalmers)

Institutionen för kemi- och bioteknik, Fysikalisk kemi (2005-2014)

Ämnesområden

Livsvetenskaper
Nanovetenskap och nanoteknik
Biokemi och molekylärbiologi

Chalmers infrastruktur