The importance of charge regulation for DNA-like polymer layers in a physiological intranuclear environment: effect of mono- and multivalent cations

The highly negative charge of DNA is not fully neutralized when it packages into chromatin in the nucleus. Thus, the physicochemical environment, including intracellular cations, pH, and DNA density, is expected to have a large influence on chromatin packing. Here, we use a molecular theoretical approach to determine how the packing and charge of DNA-like tethered polyelectrolytes change in response to changing environmental conditions. Overall, we found that Mg²⁺, the most prevalent multivalent cation in the cell, has a large effect on the density distribution as well as the effective charge of the polyelectrolyte, whereas monovalent cations have lesser effects on both the structure and charge of the DNA-like system. This larger effect of Mg²⁺ ions is caused by the possibility of Mg²⁺ forming an ion bridge with two negatively charged DNA phosphates, which results in charge neutralization/reduction, polymer collapse, and increased polymer density.