Internal dynamics of linear and superhelical DNA as studied by photon correlation spectroscopy

Photon correlation spectroscopy has been used to study the translational (D0) and internal dynamics of monodisperse linear and polydisperse superhelical plasmid-DNAs. Scattering vector dependent correlation functions were measured and analyzed with the inverse Laplace transform CONTIN written by S. Provencher. For scattering vectors (q) lower than 1.3 X 10(5) cm-1, D0 can be separated from internal dynamics. Using the measured D0 value, the q dependence of internal modes was determined. Extrapolation of the internal relaxation times for q----0 yields the longest internal relaxation time t1. This time can be connected to the persistence length in terms of the Berg-Soda model, which describes the molecule as a semiflexible circular polymer with hydrodynamic interactions. The calculated length of 76 nm for DNA, I = 0.15 mol/L, is a little higher than the one obtained from static light scattering data without excluded volume corrections. A comparison of experimental and simulated correlation functions for the Berg-Soda model shows that the model gives a fairly good description of the dynamics of the linear molecule, whereas large discrepancies between model and experimental functions are observed for the superhelical DNA. Small differences between model and experimental functions are mainly attributed to the neglect of the torsional modes that may be coupled to bending and flexing modes. For the superhelical DNA the agreement is improved if the calculation is carried out with a linear molecule, with shorter contour length and increased diameter. Both quantities can be derived from the known superhelix tilt angle.