The dynamics of a 20 base pair oligonucleotide is studied by dynamic light scattering-photon correlation spectroscopy and depolarized Fabry-Perot interferometry. The 20 base pair oligonucleotide is a well-defined, albeit short, rigid rod molecule that serves as a model for polyelectrolyte solution dynamics. The effects of added salt on the solution rotational and translational dynamics are examined in detail as functions of the 20-mer concentration. Coupled mode theory together with counterion condensation theory gives good predictions for the effects of salt on the translational diffusion of the 20-mer at the relatively low oligonucleotide concentrations studied. Comparison of the experimental results with these theories shows that the effective charge density of the polyion in solution is approximately equal to the reciprocal of the product of the Bjerrum length and the counterion charge, eff Х1/N B. Calculation shows that the numerical solution of the coupled mode theory matrix gives a better fit of our measured polyion diffusion coefficients than the approximate equation derived by Lin, Lee, and Schurr. Simple approximations for the effective rod length, L eff ϭLϩ Ϫ1 , and effective rod diameter, d eff ϭdϩ Ϫ1 , are used to model the thermodynamic-hydrodynamic interactions for charged rodlike molecules and to make predictions for the diffusion second virial coefficient as a function of added salt concentration. This alternative to the coupled mode theory also gives good agreement with experiment. The rotational diffusion constants of the oligonucleotide measured by depolarized Fabry-Perot interferometry show a slowing down of the rotation at low added salt concentrations as the oligonucleotide concentration is increased.

The peak in the small angle x-ray scattering and the dynamic light-scattering slow mode for a 20 base-pair duplex oligonucleotide (“B-DNA”) are studied as functions of oligonucleotide and added-salt (NaCl) concentrations. Both the x-ray peak intensity and the relative intensity of the slow mode decrease as the added-salt concentration is increased. The hydrodynamic radius of the slow mode increases as the added-salt concentration is decreased. The x-ray peak gradually disappears with increasing salt while the slow mode decreases in intensity, but still has some residual intensity at the highest added-salt concentration studied. There is no abrupt change in either the peak or the slow mode with increasing salt. The existence and behavior of both the x-ray peak and the slow mode indicate local ordering in the solution due to electrostatic forces. The x-ray peak position for the oligonucleotide is correlated with the static light-scattering peak seen by other workers for dilute solutions of larger polyions. A simple model shows that the reduced electrostatic potential at the average distance between neighboring polyions is approximately the same for these polyelectrolytes. The slow mode has a hydrodynamic radius that increases with decreasing q at low added-salt concentrations, indicating a large correlation volume. The x-ray peak is a more local indicator of nearest-neighbor correlations among the polyions.

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.