Flow dichroism, flow polarized fluorescence and viscosity of the DNA acridine complexes

The strong binding of various acridine dyes to DNA has been studied by the measurements of flow dichroism, flow polarized fluorescence and viscosity. Negative flow dichroism and percentage change in polarized fluorescence intensity show that intercalated dye molecules are oriented rather perpendicularly to the main axis of the DNA helix, like base pairs. On the other hand, viscosity measurements show that the increase of the contour length of DNA depends on the dye structure, being much smaller in the case of dyes with bulky substituents compared to that of the other dyes. This may be attributed to the formation of the outside bound complex. Further, the introduction of bulk substituents to the acridine ring leads to a little smaller values of the reduced dichroism and intensity change of polarized fluorescence. The results may be qualitatively understood if we assume that the outside bound dye lies in the groove of the DNA helix and the plane of the dye tilts from the perpendicular direction relative to the main axis of the helix.