Distinguishing binding modes of a new phosphonium dye with DNA by surface-enhanced Raman spectroscopy

To understand the disruption of the cell processes induced by small molecule binding to DNA, numerous structural studies of DNA complexes have been done, whereby a variety of methods has been applied. The use of various techniques is required, not only for the unique information on the structure provided by each of the methods, but also for limitations that arise during the sample preparation or measurement procedures. Here, surface-enhanced Raman scattering (SERS) spectroscopy has been employed to study binding of a new mitochondria-specific dye with ds-DNA polynucleotides. Concentration dependent differences in the SERS spectra of the dye were attributed to concentration induced changes in position of the dye molecules on the enhancing metal surface and assigned to aggregated molecules formed due to pi-stacking interactions at higher dye concentration (5.0 x 10(-5) mol L-1) and to single molecules at lower dye concentration (5.0 x 10(-6) mol L-1). The characteristic SERS spectra were further on correlated with the spectra of the dye/DNA complexes, implying binding of the monomeric dye molecules at the excess of the adenine-thymine polynucleotide, [dye]/[AT] - 1/10, and in form of the stacked dye molecules at the higher [dye]/[AT] ratio of 1/2. In addition, the distinctive SERS spectra of the complexes with the AT alternating and homo-polymer indicated different placement of the dye molecules within the minor groove, affected by the polynucleotide groove width. Beside well-known quantitative, this study emphasized structural sensitivity of SERS, able to distinguish various molecular forms of the small molecules in the complex structures such as those formed with biomacromolecules.