Adsorption of mono- and multivalent cat- and anions on DNA molecules

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure

Electrostatic interactions in biological DNA-related systems

In this perspective article, we focus on recent developments in the theory of charge effects in biological DNA-related systems. The electrostatic effects on different levels of DNA organization are considered, including the DNA-DNA interactions, DNA complexation with cationic lipid membranes, DNA condensates and DNA-dense cholesteric phases, protein-DNA recognition, DNA wrapping in nucleosomes, and inter-nucleosomal interactions. For these systems, we develop a theoretical framework to describe the physical-chemical mechanisms of structure formation and anticipate some biological consequences. General biophysical principles of DNA compaction in chromatin fibers and DNA spooling inside viral capsids are discussed in the end, with emphasis on electrostatic aspects

Polyelectrolyte adsorption onto oppositely charged interfaces: unified approach for plane, cylinder, and sphere

A universal description is presented for weak adsorption of flexible polyelectrolyte chains onto oppositely charged planar and curved surfaces. It is based on the WKB (Wentzel-Kramers-Brillouin) quantum mechanical method for the Green function equation in the ground state dominance limit. The approach provides a unified picture for the scaling behavior of the critical characteristics of polyelectrolyte adsorption and the thickness of the adsorbed polymer layer formed adjacent to the interface. We find, particularly at low-salt conditions, that curved convex surfaces necessitate much larger surface charge densities to trigger polyelectrolyte adsorption, as compared to a planar interface in the same solution. In addition, we demonstrate that the different surface geometries yield very distinct scaling laws for the critical surface charge density required to initiate chain adsorption. Namely, in the low-salt limit, the surface charge density scales cubical with the inverse Debye screening length for a plane, quadratic for an adsorbing cylinder, and linear for a sphere. As the radius of surface curvature grows, the parameter of critical chain adsorption onto a rod and a sphere turns asymptotically into that of a planar interface. The transition occurs when the radius of surface curvature becomes comparable to the Debye screening length. The general scaling trends derived appear to be consistent with the complex-formation experiments of polyelectrolyte chains with oppositely charged spherical and cylindrical micelles. Finally, the WKB results are compared with the existing theories of polyelectrolyte adsorption and future perspectives are outlined

DNA Cyclization: Suppression or Enhancement by Electrostatic Repulsions?

First, we develop a model of counterion condensation on highly charged polyelectrolyte rings. Using the known analytical results for the electrostatic energy of ring formation, a stronger counterion adsorption is anticipated onto a cyclized polyelectrolyte, as compared to the Manning prediction for a straight rod-like polyelectrolyte. This fact ensures a lower energetic cost of polyelectrolyte bending into a ring. In the main part of the work, we investigate the impact of charges on cyclization of short DNA fragments, both theoretically and by computer simulations. An approximate expression for the electrostatically renormalized DNA cyclization probability is proposed that incorporates the electrostatic energies of polyelectrolyte cyclization and dimerization reactions. Depending on concentration of simple salt and chain length, the probability of formation of ideal polyelectrolyte rings can be either electrostatically inhibited or enhanced. The latter effect is quite counterintuitive. Afterward, simple computer simulations are performed to enumerate the effects of DNA thermal fluctuations onto the electrostatic energies of cyclized and dimerized DNA fragments in solution. Their outcomes support the possibility of electrostatically enhanced polyelectrolyte ring formation reaction in solution. In the end, we discuss some implications of the results obtained for the future DNA cyclization experiments and provide a short analysis of possible DNA-related features neglected in the modeling

DNA-DNA sequence homology recognition: physical mechanisms and open questions

First, we summarize recent experimental facts on homologous DNA pairing in vitro and discuss possible mechanisms of DNA-DNA sequence recognition. Then, we overview the mechanism of DNA-DNA recognition based on complementarity of DNA charge patterns. The theory predicts the recognition energy up to 10 k(B) T for close parallel homologous DNA fragments of gene-relevant lengths. We argue why this estimate cannot be directly applied to pairing of homologous DNA loci in experiments on yeast chromosomes. Namely, DNA-DNA distances assessed from experiments are much larger than those typically used in theory. Finally, we suggest some experiments that could help to judge whether short-range electrostatic forces indeed govern DNA pairing. This viewpoint paper introduces recently developed theoretical concepts to molecular biologists, with a hope to generate a junction between theory and future experiments on DNA recognition

Critical Polyelectrolyte Adsorption under Confinement: Planar Slit, Cylindrical Pore, and Spherical Cavity

We explore the properties of adsorption of flexible polyelectrolyte chains in confined spaces between the oppositely charged surfaces in three basic geometries. A method of approximate uniformly valid solutions for the Green function equation for the eigenfunctions of polymer density distributions is developed to rationalize the critical adsorption conditions. The same approach was implemented in our recent study for the "inverse" problem of polyelectrolyte adsorption onto a planar surface, and on the outer surface of rod-like and spherical obstacles. For the three adsorption geometries investigated, the theory yields simple scaling relations for the minimal surface charge density that triggers the chain adsorption, as a function of the Debye screening length and surface curvature. The encapsulation of polyelectrolytes is governed by interplay of the electrostatic attraction energy toward the adsorbing surface and entropic repulsion of the chain squeezed into a thin slit or small cavities. Under the conditions of surface-mediated confinement, substantially larger polymer linear charge densities are required to adsorb a polyelectrolyte inside a charged spherical cavity, relative to a cylindrical pore and to a planar slit (at the same interfacial surface charge density). Possible biological implications are discussed briefly in the end

Polyelectrolyte Adsorption onto Oppositely Charged Interaces: Image-Charge Repulsion and Surface Curvature

We analyze theoretically the influence of low-dielectric boundaries on the adsorption of flexible polyelectrolytes onto planar and spherical oppositely charged surfaces in electrolyte solutions. We rationalize to what extent polymer chains are depleted from adsorbing interfaces by repulsive image forces. We employ the WKB (Wentzel-Kramers-Brillouin) quantum mechanical method for the Green function of the Edwards equation to determine the adsorption equilibrium. Scaling relations are determined for the critical adsorption strength required to initiate polymer adsorption onto these low-dielectric supports. Image-force repulsion shifts the equilibrium toward the desorbed state, demanding larger surface charge densities and polyelectrolyte linear charge densities for the adsorption to take place. The effect is particularly pronounced for a planar interface in a low-salt regime, where a dramatic change in the scaling behavior for the adsorption-desorption transition is predicted. For the adsorbed state, polymers with higher charge densities are displaced further from the interface by image-charge repulsions. We discuss relevant experimental evidence and argue about possible biological applications of the results