Counterion accumulation effects on a suspension of DNA molecules: Equation of state and pressure-driven denaturation

Abstract

The study of the effects associated with the electrostatic properties of DNA is of fundamental importance to understand both its molecular properties at the single molecule level, like the rigidity of the chain, and its interaction with other charged bio-molecules, including other DNA molecules; such interactions are crucial to maintain the thermodynamic stability of the intra-cellular medium. In the present work, we combine the Poisson-Boltzmann mean-field theory with an irreversible thermodynamic approximation to analyze the effects of counterion accumulation inside DNA on both the denaturation profile of the chain and the equation of state of the suspension. To this end, we model the DNA molecule as a porous charged cylinder immersed in an aqueous solution. These thermo-electrostatic effects are explicitly studied in the particular case of some genes for which damage in their sequence is associated with diffuse large B-cell lymphoma.

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

“…While theories of DNA interactions abound (see SI), based mostly on an increasingly more sophisticated description of the electrostatic interactions 18 , spanning the regime of simple electrolyte screening and then all the way to the counterion correlation-driven attractions in a multivalent ion-DNA system 19 , the nature of the interaction-induced ordering was much less prone to theoretical scrutiny 20 . The continuum modeling 19–22 and coarse grained simulation approaches 23–31 , which mostly underpin these theoretical endeavors, certainly led to important insights, especially in elucidating the significance of the counterion valency for the emergence of correlations, reversing the sign of the electrostatic interactions between charged helices, that in its turn leads to DNA condensation and precipitation. However, the difficulties connected with the full implementation of molecular details of the DNA solution exposed surface, the granularity of the molecular solvent, and the interactions between both and the mobile charges in solution, together with the extraordinary demands they make on available computer resources, hamper the ambitions to understand all the relevant molecular details”.…”

Probing and evaluating the electric potential of a polyelectrolyte with dielectric spectroscopy

“…We took the most simple potential but there are also other suggested polyelectrolyte potentials. 11,53 Only exact mathematical formulation of the average dipole moment would discriminate the one which best agrees to experimental data. Now the question remains about interpretation of L in solutions with added salt on which both theoretical and experimental work is needed.…”

Colloidal Soft Matter Physics

“…In particular, theoretical frameworks, such as the integral equations theory [45], and molecular simulation-based models [46] have been developed during the last few years to account for the structure, dynamics, effective interactions and the phase behavior (in and out of equilibrium) of colloids. Furthermore, mean-field approximations have been proposed to study the denaturation processes of bio-colloids [47,48], i.e., structural changes in macromolecules caused by extreme thermodynamic conditions.…”