Coarse Grained Molecular Simulations of DNA Condensation in the Presence of Cobalt Hexamine

We present a coarse grained model able to reproduce the interactions between nucleic acids and small external molecules. We propose expanding the oxDNA2 model for DNA to include interactions with an all atoms representation of the cobalt (III) hexamine molecule. To do so, the cross-interactions between the nucleic acids and the CoHex³⁺ molecule are defined via a Lennard-Jones potential, accounting for the Van der Waals interaction, in tandem with Debye-Huckel interactions, accounting for the electrostatics. We will first parameterize the proposed coarse grained model by finding the optimal parameters that produce interaction energies between the nucleotide and the CoHex³⁺ molecule closest to those found in the all atoms approach. We will then perform molecular dynamics simulations of systems composed of DNA segments in the presence of CoHex³⁺. We hope these results help to better understand how CoHex³⁺ affects DNA condensation and toroid formation