DYNAMICS OF LOW-MOLECULAR-WEIGHT DNA FRAGMENTS IN DILUTE AND SEMIDILUTE SOLUTIONS

The scattered light intensity autocorrelation functions of dilute and semidilute solutions of sonicated calf thymus DNA fragments in the presence of 0.2 M NaCl were measured. In addition, the weight-average molecular weight and the second virial coefficient of this system were determined by low-angle laser light scattering (LALLS). The weight-average molecular weight was found to be (1.56 +/- 0.05) x 10(5), corresponding to a fragment size of 236 +/- 8 base pairs, and the second virial coefficient was (2.7 +/- 0.2) x 10(-7) (mol L g-2). The scattered light intensity correlation functions were analyzed by three different methods of data analysis: CONTIN, the method of cumulants, and a double-exponential fitting procedure. CONTIN gave evidence of the existence of a single relaxation process at low DNA concentrations and an additional slower process at DNA concentrations higher than approximately 2 g L-1. The rates of the fast and slow processes were shown to vary linearly with the square of the length of the scattering vector q. The fast mode was interpreted as the translational diffusion process of the DNA fragments. The measured mutual diffusion coefficient was found to increase linearly with the DNA concentration. The infinitely dilute solution value of the mutual diffusion coefficient was determined by extrapolation and is in excellent agreement with the theoretical value for a perfectly rigid rod, calculated according to the Tirado and Garcia de la Torre theory. The second virial coefficient is in reasonable agreement with theory if charge effects, as proposed by Stigter, are taken into account. The molecular origin of the slow mode is still unknown, although its behavior is consistent with the formation of aggregates at high DNA concentrations. The aggregates are probably highly polydisperse. The amplitude and diffusion coefficient of the slow process appeared to decrease with increasing DNA concentration. The results are in poor agreement with the predictions of the Doi, Shimada, and Okano theory for semidilute and concentrated solutions of hard, rigid rods as well as that for such systems near the spinodal.