Effect of electrostatic interactions on the dynamics of semiflexible monodisperse DNA fragments

The dynamics of three monodisperse linear duplex DNA fragments-a 2311 base pair restriction fragment and 1500 and 1100 base pair polymerase chain reaction fragments-in dilute solution are studied as functions of added salt (NaCl) concentration by dynamic light scattering-photon correlation spectroscopy. Translational diffusion coefficients and intramolecular relaxation times are extracted from the measured light scattering intensity time autocorrelation functions as the added salt concentration is reduced from 100 mM to approximately 0.1 mM. The relaxation times of the first intramolecular mode increase as the added salt concentration is lowered. The dependence of the translational diffusion coefficient D on the added salt concentration is not very large, although it exhibits a maximum for all three fragments. The maximum is interpreted as the consequence of two opposing effects-the stiffening of the molecule that produces an increase of the size (decrease of D) as the added salt concentration is lowered, and the coupling of the diffusion of the DNA through the electrostatic forces to the motion of the small and other polyions in the solution that results in an increase of its mobility (increase of D). The increase of the slowest intramolecular relaxation times as the salt concentration is lowered is interpreted in terms of a theory relating this time to the mean-squared radius of gyration of the molecule. (C) 2000 American Institute of Physics. [S0021-9606(00)50638-2].