Local dynamics in DNA by temperature-dependent stokes shifts of an intercalated dye

For the first time, the static and dynamic properties of the interior of DNA have been measured through their effects on the Stokes shift of an intercalated dye. Fluorescence excitation and emission spectra of acridine orange (AO) intercalated in DNA have been measured from 100 to 320 K in a 3:1 glycerol-aqueous-buffer mixture. The solvent dependence of the excitation spectrum shows that AO is sensitive to the polarizability of its local environment but is insensitive to the local polarity. The interior of DNA provides a highly polarizable environment, similar to simple aromatic solvents. The Stokes shift of AO results from movements of neighboring groups that change the effective cavity size of the dye. A large portion of the Stokes shift in DNA can be frozen out at low temperature, as it can be in solution. This result shows that the interior of DNA has the diffusive and viscous dynamics characteristic of a fluid, rather than the purely vibrational dynamics of a crystal. At high viscosity, the rate of these dynamics is linked to that of the bulk solvent. We argue that the dye is sensing the movement of the DNA, and we propose that, at high viscosity, the rate of DNA motion is limited by the rate of solvent motion. The potential for extending these measurements to low solvent viscosities with ultrafast spectroscopy is very good.