Ionic distribution around simple DNA models. I. Cylindrically averaged properties

Abstract

Properties depending on the radial ionic concentration profiles are calculated by Monte Carlo simulation for several simple B-DNA models in the presence of added ͑monovalent͒ salt up to 2.5 M concentration. The models include both homogeneously and discretely charged polyions. Besides, the effect of hard and soft repulsive forces is considered. A novel model which represents the DNA grooved structure in a simplified manner is introduced. From a methodological point of view, special attention is paid to the treatment of long-range forces along the axial direction. Exact formulas for discretely charged polyelectrolytes are used. Regarding the density profile results, it is concluded that the main effect is not due to the discreteness of the positions of the charges, i.e., homogeneously charged models lead to properties not significantly different from discretely charged ones. A similar statement holds for the comparison between hard and soft models. Nevertheless, the inclusion of the grooved shape of DNA modifies this behavior. A double hump in the concentration profile function is brought about by the coupling between repulsive and coulombic forces in the grooved model. It is shown that not only this but also other properties of full atomic models of DNA are adequately predicted by our simplified grooved model. Finally, at high concentrations of added salt, it is seen that the condensed ionic cloud overneutralizes the polyelectrolyte charge. This charge reversal phenomenon, which is observed in all the models studied, has not been previously observed due to the high salt concentration required.

A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

“…Here, the following values of the hard radii were used: R(K . These values are typical for hydrated ion radii used in a number of models and well reproduce thermodynamic properties and the features of ion distributions compared to all-atom simulations [12,65,66,82,85]. They also fit well the radius of the repulsive core region of the effective potentials derived within the IMC procedure, which is reflected in the corresponding RDFs in Figure S2 of the Supporting Material.…”

“…The equilibrium geometry of the beads corresponds closely to the B-form of DNA and the whole structure forms a helical DNA with two clearly distinguishable strands of phosphate groups and minor and major grooves between them ( Figure 1B). The overall DNA structure thus resembles space-filling grooved DNA models used previously to model the ionic environment of DNA [12,[64][65][66]. Table 1.…”

Effective interaction between helical biomolecules

“…The groove structure of DNA is expected to be of increasing significance as one approaches its surface [87]. We incorporate this in our model by increasing the phosphate diameter towards d p = 2Å (run B) and d p = 6Å (run C).…”

Molecular Simulations of DNA Counterion Distributions

“…[12] More elaborate DNA models may include specific details of its structure. One example is the so-called ''grooved'' model of DNA, [13] in which the charged groups of DNA are located outside the cylindrical hard core, on the sites corresponding to the phosphate groups of DNA. In addition, full-atomic molecular models of DNA or other polyelectrolytes in continuum solvent have been considered.…”

“…Such behavior was typically observed for divalent or higher-valence counterions under certain thermodynamic conditions, [25] but it may happen even for monovalent ions if the salt concentration is high enough. [13] The charge reversal cannot be obtained in the PB theory. There is no clear experimental evidence of the charge reversal, except perhaps for a rather old work by Strauss et al, [28] who observed a cationic polyion (poly-4-vinilpyridine) moving against the electric field at high salt concentration.…”