Effect of electrostatic interactions on the structure and dynamics of a model polyelectrolyte. II. Intermolecular correlations

Abstract

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.

Denaturation and aggregation of hen egg lysozyme in aqueous ethanol solution studied by dynamic light scattering

“…We consider that any large aggregates cannot be formed in the low ethanol solution because of the strong repulsion between the lysozyme molecules. A similar slow mode was often observed when dynamic light scattering was used for a salt-free polyelectrolyte solution, [17][18][19][20] where strong repulsion exists between polyelectrolytes. The origin of the slow mode in these cases is thought to be "temporary clusters," proposed recently 19,20 to form via strong repulsion between polyelectrolytes.…”

Unusual salt-induced behaviour of guanine-rich natural DNA evidenced by dynamic light scattering

“…For example, it could be associated with the translation of slowed down single molecules inside some sort of dominium of entangled molecules interacting each other or to the movement of the entire dominium, which, however, cannot be interpreted as a single massive particle. Such an interpretation could be rather satisfactory for long DNA chains (Skibinska et al 1999), and perhaps it is valid, in our case, for the 20,000-bp calf thymus DNA.…”

“…Other experimental evidence, obtained by direct observation of Brownian motion, have shown, at low sodium salt concentration, one order of magnitude reduction in the translational diffusion coefficient at a DNA concentration of 1 mg/ml for 6-kbp long chains and at a DNA concentration of 0.3 mg/ml for 45-kbp long chains, respectively (Skibinska et al 1999).…”

“…However, a recent observation of Brownian motion of entangled linear and circular DNA molecules up to 45 kbp long has evidenced a reduction of the translational diffusion coefficient that, in specific salt concentration and DNA conditions, may become even three orders of magnitude lower than the one of the single molecule (Skibinska et al 1999). This reduction has been correlated with the formation of large domains of entangled DNA chains, and the decreased mobility has been attributed both to slow motion of the entire domain itself and to the reduced mobility of the single molecule inside the domain.…”

Inverse Monte Carlo procedure for conformation determination of macromolecules

“…Examples include the pH-dependent helix-coil transition of some polypeptides 3 and the salt-concentration conformational dependence of charged biopolymers such as DNA and anionic glycosaminoglycans. 4,5 Solution structure studies are therefore particularly important for flexible macromolecules, because X-ray crystallography typically results in a single conformation that may not be relevant to the biologically active conformer(s). 6,7 NMR and X-ray or neutron scattering are the predominant experimental approaches to structure determination in solution.…”