title: Orientation of the chromophore dipoles in the TOTO-DNA system.
abstract: BACKGROUND
  Flow cytometry has been applied successfully to the sizing of medium to large-sized DNA molecules, thanks to the excellent staining properties of cyanine chromophores such as TOTO (homodimer of thiazole orange) (Petty et al.: Anal Chem 67:1755-1761, 1995). The hydrodynamic flow, used to focus the sample molecules in a small laser-illuminated volume, is also responsible for their alignment, thereby allowing the determination of the TOTO-dipole orientation with respect to the DNA axis (Agronskaia et al.: Appl Opt 38:714-719, 1999).
  
  
  METHODS
  We present model calculations of the fluorescence yield of TOTO-stained DNA measured in a flow-cytometric setup with high numerical aperture. The models consider different orientations of the chromophore dipoles.
  
  
  RESULTS
  Comparison of measurement and calculation suggests that the absorption dipoles of the TOTO molecule make a mean angle of 61 degrees with the helix axis of the DNA molecule. This mean angle can be the consequence of two binding modes.
  
  
  CONCLUSIONS
  Our results indicate that any model with a significant contribution of perpendicularly-oriented chromophores fails to reproduce the experimental results.
authors.affiliation: Department of Applied Physics, Twente University, Enschede, Netherlands. j.m.schins@tn.utwente.nl
authors.forename: J M
authors.initials: JM
authors.lastname: Schins
authors.forename: A
authors.initials: A
authors.lastname: Agronskaia
authors.forename: B G
authors.initials: BG
authors.lastname: de Grooth
authors.forename: J
authors.initials: J
authors.lastname: Greve
mesh_terms: D010582:Bacteriophage lambda / Q000737:chemistry; D002469:Cell Separation; D004269:DNA, Bacterial / Q000032:analysis*; D005434:Flow Cytometry / Q000379:methods; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011806:Quinolinium Compounds / Q000737:chemistry*; D013844:Thiazoles / Q000737:chemistry*
chemical_list: D004269:DNA, Bacterial; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D011806:Quinolinium Compounds; D013844:Thiazoles; C075295:1,1'-(4,4,7,7-tetramethyl-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-thiazole)-2-methylidene)quinolinium