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

Abstract

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.

Light scattering study of natural DNAs over a wide range of molecular weights: Evidence for compaction of the large molecules

“…Evidences for the effect of the salt concentration on DNA hydrodynamic radius were produced by Newman et al [34] and Liu et al [35] but only for DNA fragments shorter than 2300 bp and, in this case, the observed variation of hydrodynamic radius is much less pronounced than in the coil-globule transition case and in our case too. At present no systematic studies have been carried out to understand the effect of ionic strength for DNA molecules longer than few thousand bp.…”

DNA and surfactants in bulk and at interfaces

“…While there has been a number of DLS reports on the properties of DNA solutions (see, for example Refs. [71][72][73][74]), studies involving interactions between DNA and cationic amphiphiles are in a very limited number [18,24,75].…”

Monodisperse DNA restriction fragments

“…Stiff rodlike particles experience a considerably larger Stokes drag. Earlier sedimentation [9,17] as well as translational diffusion [10,11] measurements on monodisperse DNA fragments of up to 2311 bp have shown that the Stokes drag is predicted correctly by the Yamakawa-Fujii [18] theory for smooth wormlike cylinders without excluded volume and neglecting endeffects. The orientationally averaged friction coefficient of a wormlike Brownian cylinder of contour length L c , diameter D, and persistence length q resembles the friction factor for a sphere but contains an additional term, F (D, L c , q), that is affected by the actual shape [18]:…”

“…Several studies have addressed static properties of DNA solutions, including the molecular conformation and intermolecular interactions [2][3][4][5] and mesophase formation [6][7][8]. Transport properties investigated include mutual diffusion [3][4][5][9][10][11], self-diffusion [12], rotational diffusion [13][14][15], rheology [5,16], and sedimentation [9,17]. A systematic study of the length and concentration dependence of the transport properties of DNA molecules and a comparison with theoretical models for semiflexible polymers is, however, still lacking.…”

“…We study aqueous saline solutions of DNA containing 100 mM Na + , so the electrostatic contribution to the persistence length q is negligible and the total persistence length q is ca. 50 nm [11,23].…”