Parametrization of direct and soft steric-undulatory forces between DNA double helical polyelectrolytes in solutions of several different anions and cations

Abstract

Directly measured forces between DNA helices in ordered arrays have been reduced to simple force coefficients and mathematical expressions for the interactions between pairs of molecules. The tabulated force parameters and mathematical expressions can be applied to parallel molecules or, by transformation, to skewed molecules of variable separation and mutual angle. This "toolbox" of intermolecular forces is intended for use in modelling molecular interactions, assembly, and conformation. The coefficients characterizing both the exponential hydration and the electrostatic interactions depend strongly on the univalent counterion species in solution, but are only weakly sensitive to anion type and temperature (from 5 to 50 degrees C). Interaction coefficients for the exponentially varying hydration force seen at spacings less than 10 to 15 A between surfaces are extracted directly from pressure versus interaxial distance curves. Electrostatic interactions are only observed at larger spacings and are always coupled with configurational fluctuation forces that result in observed exponential decay lengths that are twice the expected Debye-Huckel length. The extraction of electrostatic force parameters relies on a theoretical expression describing steric forces of molecules "colliding" through soft exponentially varying direct interactions.

Network of hydrogen bonds as a medium for DNA interaction in solvents

“…For another, the value of d 0 is determined by the relative sizes of the elastic constants A and λ. According to [7], [8], [11], the cholesteric phase is observed for the values d ≈ 30Å and l ≈ 500Å, therefore, we may conclude that A could be less than λ at least by an order of magnitude, so that d 0 may be of the same order as l. Thus, Eq. (6) describes the cholesteric twist φ * , within the range of 30Å to 50Å for d. Our discussion is very crude, and qualitative, so that we may only infer from Eq.…”

“…But the region of d is too small to make any asymptotic conclusions, especially that a significant dependence of φ * on the spatial separation d has not been observed, so far. It should be noted, as well, that paper [9] neglects the conclusions of Parsegian et al, [7], [8], that the hydration forces be of primary importance, and does not consider the PEG experiments.…”

“…The size of the silica pore is similar to that of the inter-molecular distance of the DNA dispersions, so that allowing for the difference in the potentials of surface interaction, one may suggest that the water molecules confined in the DNA dispersion may exhibit a similar behaviour. In this respect it is worthwhile to recall papers [7], [8], that claim the importance of what they call hydration forces, which dominate at close separations between the DNA molecules, so that the resultant interaction resemble neither the pure electrostatic nor the steric one.…”

“…The osmotic pressure can be controlled through the variation of the concentration of PEG in the solvent; to a certain extent, it is similar to the classical experiment with a semipermeable piston that exerts a pressure equal to the osmotic pressure of the PEG solution. It is generally considered to be an efficient means for estimating the repulsion interaction between the DNA helices in solution, [7], [8]. The results of paper [11] are illustrated in Fig.1; it appears that there should be a change in the state of the dispersion.…”

“…Therefore, the force generates the principal interaction between DNA molecules, rather than the van der Waals or the electrostatic one (cf. [8]). …”