The Influence of Ionic Environment on Nucleosome–Mica Interactions Revealed via Molecular Dynamics Simulations

Nucleosomes are the fundamental units of DNA compaction, playing a key role in modulating gene expression. As such, they are widely studied through both experimental and computational methods. While atomic force microscopy (AFM) is a powerful tool for visualizing and characterizing both canonical and modified nucleosomes, it relies on nucleosome interactions with mica surfaces. These interactions occur through cations adsorbed on the negatively charged mica, but the specific influences of monovalent and divalent cations on nucleosome adsorption remain unclear. In this study, we used molecular dynamics simulations to investigate how monovalent potassium ions and divalent magnesium ions affect nucleosome binding to mica surfaces. We also explored the impact of pretreated mica surfaces on nucleosome binding and structure. Our findings reveal that nucleosome-mica interactions depend on the type of cations present, which leads to distinct effects on nucleosome structure. Notably, nucleosomes bind effectively to mica surfaces in the presence of potassium ions with minimal structural perturbations.