Effective interaction between helical biomolecules

Abstract

The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple model for B-DNA incorporating explicitly its charge pattern as a double-helix structure. The effective force and the effective torque exerted onto the molecules depend on the central distance and on the relative orientation. The contributions of nonlinear screening by monovalent counterions to these forces and torques are analyzed and calculated for different salt concentrations. As a result, we find that the sign of the force depends sensitively on the relative orientation. For intermolecular distances smaller than 6Å it can be both attractive and repulsive. Furthermore we report a nonmonotonic behaviour of the effective force for increasing salt concentration. Both features cannot be described within linear screening theories. For large distances, on the other hand, the results agree with linear screening theories provided the charge of the bio-molecules is suitably renormalized.

Electrostatic interactions in strongly coupled soft matter

“…Several numerical simulations have been reported on charged cylinders [27,40,41,42] and also on more detailed models, which incorporate the charge pattern of DNA [26,36]. Attraction is found in a wide range of Manning parameters (including ξ ≈ 1.0) and for moderate to large coupling parameters.…”

“…The energetic and entropic contributions from counterions enter on the leading order through the second term in Eq. (36). It is important to note that the main qualitative features regarding the binding-unbinding behavior of counterions is reproduced by this term.…”

“…The fact that both the de-condensation process and the repulsive regime for unconfined spheres are consistently captured by the asymptotic strong-coupling free energy indicates that the 1/Ξ-expansion scheme used to obtain the asymptotic contribution for Ξ → ∞ [69] is not only based on energetic considerations, and can also account for entropic effects on the leading order [69,71]. Now let us consider the spheres in a finite confinement volume and investigate the strong-coupling prediction for the interaction free energy (36). For small Manning parameters, the free energy exhibits only a long-range repulsion (Figure 9a), but as Manning parameter exceeds a threshold value of ξ (1) c , a local minimum is developed at small separations indicating a short-range attraction and a meta-stable bound state.…”

“…The main scenarios which are put forward to explain the phenomenon of like-charge attraction have gone beyond the mean-field level by demonstrating that this phenomenon can be reproduced quantitatively by inclusion of electrostatic correlations [19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,…”

“…Counterions form electrostatically-bound clouds in the proximity of macroions and in many cases, predominantly determine the electric properties of charged solutions [3]. In particular, counterions can alter the effective interaction between like-charged macroions, and may generate a dominant electrostatic attraction between them in certain physical conditions [7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,…”