Effect of sodium and potassium ions on conformation of linker parts of nucleosomes

The chromatin structure and DNA accessibility to proteins depend on the structure of linker DNA entering and exiting the nucleosome. Since DNA is a negatively charged polymer, the conformation of linker DNA, in turn, depends on the ionic microenvironment. In the present work, the effect of Na⁺ and K⁺ ions on the structure of mono nucleosome linker DNA was studiedby fluorescence microscopy of single complexes. It was revealed that nucleosomes adopt one of two conformational states, whose occupancy is significantly changed after the substitution of K⁺ ions by Na⁺. These changes are likely caused by different interaction of Na⁺ and K⁺ with DNA in the regions of DNA entry and exit of the nucleosome. Cation-dependent changes in the conformation of linker DNA may affect topological barriers in the nucleosome, structure of polynucleosome chromatin, and interactions with different protein factors.