Characterizing the counterionic cloud of DNA-functionalized nanoparticles with molecular dynamics simulations

DNA-functionalization of proteins allows for cell penetration and self-assembly of protein systems that have the potential for applications in therapeutics and other fields. However, the impacts of the resulting electrostatic interactions associated with the DNA shell and counterionic cloud are still being explored. Here, we use molecular dynamics simulations to examine the stability of a protein’s DNA shell in the presences of DNAse, as it relates to the composition of this counterionic cloud. We use molecular dynamics simulations and a simple thermodynamic model in tandem with SAXS measurements to understand the composition of this cloud under varying salt conditions and protein shapes. This work builds on previous efforts to calculate this composition of this cloud using DFT calculations; detailed molecular dynamics simulations have been used to incorporate multiple species of ion as well as excluded volume effects and correlations.