Journal of Physical Chemistry B, Vol.113, No.7, 2160-2169, 2009
Mediating Role of Multivalent Cations in DNA Electrostatics: An Epsilon-Modified Poisson-Boltzmann Study of B-DNA-B-DNA Interactions in Mixture of NaCl and MgCl2 Solutions
Potentials of mean force acting between two ions in SPC/E water have been determined via molecular dynamics simulations using the spherical cavity approach (J. Phys. Chem. B 2006, 110, 10878). The potentials were obtained for Me2+-Me+ pairs, where Me2+ means cations Mg2+ and Ca2+ and Me+ denotes monovalent ions Li+, Na+, and K+. The hard-core interaction distance for effective Me2+-Me+ potentials appears to be of about 5 A that looks like a sum of the effective radii of a Me-2+ ion (3 angstrom) and of an alkali metal ion Me+ (about 2 angstrom). These ion-ion interaction parameters were used in the epsilon-Modified Poisson-Boltzmann (epsilon-MPB) calculations (J. Phys. Chem. B 2007, 111, 5264) of ionic distributions around DNA generalized for the arbitrary mixture of different ion species. Ionic distributions around an all-atom geometry model of B-DNA in solution of a mixture of NaCl and MgCl2 were obtained. It was found that even a small fraction of ions Mg2+ led to sharp condensation of Mg2+ near the phosphate groups of DNA due to polarization deficiency of cluster [Mg(H2O)(6)](2+) in an external field. The epsilon-MPB calculations of the B-DNA-B-DNA interaction energies suggest that adding 1 MM of Mg2+ to 50 mM solution of NaCl notably affects the force acting between the two macromolecules. Being compared to Poisson-Boltzmann results and to MPB calculations for the primitive model of ions, the epsilon-MPB results also indicate an important contribution of dielectric saturation effects to the mediating role of divalent cations in the DNA-DNA interaction energies.