Polarization and angle dependence of fluorescence from dye-labeled DNA molecules adsorbed and aligned on surfaces

Abstract

The absorption and emission of fluorescence radiation from oriented molecules are polarization and angular dependent, determined by the adsorption and emission dipole axes' alignment relative to the incident excitation direction and to the emission direction. In this study, DNA molecules are aligned on polymethylmethacrylate (PMMA)-coated silicon surfaces and their fluorescence behavior is studied for different dye molecules (SyBr Gold, Acridine Orange and YOYO)for both double-stranded and single-stranded DNA(dsDNA and ssDNA). The polarization dependence for different angles of incidence and orientations of the DNA molecules was measured and used to infer the binding modes of the dye molecules. The dsDNA molecules, as expected, were found to have the dye molecules intercalated between the bases. However, surprisingly, in the case of ssDNA, the dye molecules were also found to bind with their absorption axes' parallel to the bases protruding from the single strand backbone. This is in contrast to conjectured binding modes of dyes aligned along the backbone of ssDNA.