Nucleosome binding to the mica surface under different ionic environments.

Abstract

Atomic force microscopy (AFM) is a particularly useful experimental technique for studying nucleosome structures and dynamics. In AFM experiments, multivalent ions immobilize nucleosomes to the negatively charged mica surface to facilitate imaging experiments. Although it is presumed that the structure and dynamics of nucleosomes in solution and at the mica surface are similar, specifics of the nucleosome binding mechanisms to the mica surface, how this process may alter nucleosome structures and dynamics, and how they are influenced by different ions, is not fully understood. Here, we have performed all-atom molecular dynamics simulations of nucleosomes interacting with mica surfaces in varied ionic environments, both in solution and at the surface. Different iconic environments were studied to determine the mechanisms by which they modulate nucleosome binding mechanisms and energetics. Our simulations indicate that nucleosomes have stronger binding to mica surfaces when the surface is pre-treated with magnesium ions and potassium ions are in solution. Simulations also show that DNA/nucleosome binding is dependent on the solution's ion composition, with increased DNA opening observed when magnesium is present. Moreover, a higher number of DNA-histone tail contacts were observed when potassium ions were present in solution. Overall, our simulations highlight that nucleosome binding energies and dynamics, as well as DNA and histone interactions with the mica surface, can be fine-tuned by the solution's ion composition.