title: Nanomechanics of Fluorescent DNA Dyes on DNA Investigated by Magnetic Tweezers.
abstract: Fluorescent DNA dyes are broadly used in many biotechnological applications for detecting and imaging DNA in cells and gels. Their binding alters the structural and nanomechanical properties of DNA and affects the biological processes that are associated with it. Although interaction modes like intercalation and minor groove binding already have been identified, associated mechanic effects like local elongation, unwinding, and softening of the DNA often remain in question. We used magnetic tweezers to quantitatively investigate the impact of three DNA-binding dyes (YOYO-1, DAPI, and DRAQ5) in a concentration-dependent manner. By extending and overwinding individual, torsionally constrained, nick-free dsDNA molecules, we measured the contour lengths and molecular forces that allow estimation of thermodynamic and nanomechanical binding parameters. Whereas for YOYO-1 and DAPI the binding mechanisms could be assigned to bis-intercalation and minor groove binding, respectively, DRAQ5 exhibited both binding modes in a concentration-dependent manner.
authors.affiliation: Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany.
authors.forename: Andy
authors.initials: A
authors.lastname: Sischka
authors.affiliation: Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany.
authors.forename: Volker
authors.initials: V
authors.lastname: Walhorn
authors.affiliation: Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany.
authors.forename: Katja
authors.initials: K
authors.lastname: Tönsing
authors.affiliation: Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany. Electronic address: dario.anselmetti@physik.uni-bielefeld.de.
authors.forename: Dario
authors.initials: D
authors.lastname: Anselmetti
mesh_terms: D001583:Benzoxazoles / Q000737:chemistry*; D001696:Biomechanical Phenomena; D002021:Buffers; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D004548:Elasticity; D005456:Fluorescent Dyes / Q000737:chemistry*; D060328:Magnetic Phenomena; D055595:Mechanical Phenomena; D036103:Nanotechnology; D011806:Quinolinium Compounds / Q000737:chemistry*
chemical_list: D001583:Benzoxazoles; D002021:Buffers; D005456:Fluorescent Dyes; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium; D004247:DNA