title: Binding mechanism of PicoGreen to DNA characterized by magnetic tweezers and fluorescence spectroscopy.
abstract: Fluorescent dyes are broadly used in many biotechnological applications to detect and visualize DNA molecules. However, their binding to DNA alters the structural and nanomechanical properties of DNA and, thus, interferes with associated biological processes. In this work we employed magnetic tweezers and fluorescence spectroscopy to investigate the binding of PicoGreen to DNA at room temperature in a concentration-dependent manner. PicoGreen is an ultrasensitive quinolinium nucleic acid stain exhibiting hardly any background signal from unbound dye molecules. By means of stretching and overwinding single, torsionally constrained, nick-free double-stranded DNA molecules, we acquired force-extension and supercoiling curves which allow quantifying DNA contour length, persistence length and other thermodynamical binding parameters, respectively. The results of our magnetic tweezers single-molecule binding study were well supported through analyzing the fluorescent spectra of stained DNA. On the basis of our work, we could identify a concentration-dependent bimodal binding behavior, where, apparently, PicoGreen associates to DNA as an intercalator and minor-groove binder simultaneously.
authors.affiliation: Experimental Biophysics and Applied Nanoscience, Physics Department, Physics Faculty, Bielefeld Institute for Nanoscience (BINAS), Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Experimental Biophysics and Applied Nanoscience, Physics Department, Physics Faculty, Bielefeld Institute for Nanoscience (BINAS), Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany.
authors.forename: Helene
authors.initials: H
authors.lastname: Schellenberg
authors.affiliation: Experimental Biophysics and Applied Nanoscience, Physics Department, Physics Faculty, Bielefeld Institute for Nanoscience (BINAS), Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany.
authors.forename: Volker
authors.initials: V
authors.lastname: Walhorn
authors.affiliation: Experimental Biophysics and Applied Nanoscience, Physics Department, Physics Faculty, Bielefeld Institute for Nanoscience (BINAS), Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany.
authors.forename: Katja
authors.initials: K
authors.lastname: Toensing
authors.affiliation: Experimental Biophysics and Applied Nanoscience, Physics Department, Physics Faculty, Bielefeld Institute for Nanoscience (BINAS), Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany. dario.anselmetti@physik.uni-bielefeld.de.
authors.forename: Dario
authors.identifier: http://orcid.org/0000-0002-8720-4369
authors.initials: D
authors.lastname: Anselmetti
mesh_terms: D004247:DNA / Q000737:chemistry*; D060328:Magnetic Phenomena; D055595:Mechanical Phenomena; D009930:Organic Chemicals / Q000737:chemistry; D013050:Spectrometry, Fluorescence
chemical_list: D009930:Organic Chemicals; C099476:PicoGreen; D004247:DNA
keywords: DNA; Intercalator; Magnetic tweezers; Minor-groove binder; PicoGreen