The Influence of\nIonic Environment on Nucleosome–Mica\nInteractions Revealed via Molecular Dynamics Simulations

Nucleosomes are the fundamental units\nof DNA compaction,\nplaying\na key role in modulating gene expression. As such, they are widely\nstudied through both experimental and computational methods. While\natomic force microscopy (AFM) is a powerful tool for visualizing and\ncharacterizing both canonical and modified nucleosomes, it relies\non nucleosome interactions with mica surfaces. These interactions\noccur through cations adsorbed on the negatively charged mica, but\nthe specific influences of monovalent and divalent cations on nucleosome\nadsorption remain unclear. In this study, we used molecular dynamics\nsimulations to investigate how monovalent potassium ions and divalent\nmagnesium ions affect nucleosome binding to mica surfaces. We also\nexplored the impact of pretreated mica surfaces on nucleosome binding\nand structure. Our findings reveal that nucleosome–mica interactions\ndepend on the type of cations present, which leads to distinct effects\non nucleosome structure. Notably, nucleosomes bind effectively to\nmica surfaces in the presence of potassium ions with minimal structural\nperturbations.