Possible role of ions in DNA–protein interactions in the nucleosomes

The interactions of the PO 4 - groups of DNA and the positive parts of lysine/arginine were calculated in the nucleosomes using the ONIOM method. For the model system ( 3 H 2 O, K + ion, PO 4 - group, positive side chains of lysine, arginine, resp., Cl - ) a triple- ζ basis set with polarization functions was applied both at the HF and MP2 levels. For the real system two dezoxyriboses and two guanines were added, the calculations were performed with a double- ζ basis set at the HF level. The direct PO 4 - ⋯ Lys + / Arg + bonds are ∼5 eV strong. These decrease by ∼4 eV due to the Cl - ions. The water-mediated PO 4 - ⋯ H 2 O ⋯ Lys + / Arg + bonds are ∼1 eV strong and the Cl - -s hardly change their strength.