Quantitative super-resolution localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe

Dominika Żurek-Biesiada; Aleksander T Szczurek; Kirti Prakash; Gerrit Best; Giriram K Mohana; Hyun-Keun Lee; Jean-Yves Roignant; Jurek W Dobrucki; Christoph Cremer; Udo Birk

doi:10.1016/j.dib.2016.01.041

Quantitative super-resolution localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe

Data Brief. 2016 Jan 29:7:157-71. doi: 10.1016/j.dib.2016.01.041. eCollection 2016 Jun.

Affiliations

¹ Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
² Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany.
³ Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
⁴ Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany.
⁵ Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany.
⁶ Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany.
⁷ Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany.

Abstract

Single Molecule Localization Microscopy (SMLM) is a recently emerged optical imaging method that was shown to achieve a resolution in the order of tens of nanometers in intact cells. Novel high resolution imaging methods might be crucial for understanding of how the chromatin, a complex of DNA and proteins, is arranged in the eukaryotic cell nucleus. Such an approach utilizing switching of a fluorescent, DNA-binding dye Vybrant® DyeCycle™ Violet has been previously demonstrated by us (Żurek-Biesiada et al., 2015) [1]. Here we provide quantitative information on the influence of the chemical environment on the behavior of the dye, discuss the variability in the DNA-associated signal density, and demonstrate direct proof of enhanced structural resolution. Furthermore, we compare different visualization approaches. Finally, we describe various opportunities of multicolor DNA/SMLM imaging in eukaryotic cell nuclei.

Keywords: Chromatin; DNA; DNA dye; Fluorescence; Localization microscopy; Nucleus; Single molecules; Super-Resolution; Vybrant violet; dSTORM.