FIGURE 17.

Schematic representation of the locations of counterions binding sites in the minor groove of simulated structures obtained with: (A) AMBER, (B) BMS, (C) CHARMM27. The positions of sodium ions (Na⁺) are indicated by lines annotated with the coordination distance to N3 of purines and O2 of pyrimidines. The position of the magnesium binding (Mg²⁺) site found in the x-ray structure is indicated for comparison. The presence of high counterion density spots around the phosphate groups are pointed out by a purple P atom. A red dashed line joins the cross-strand phosphate groups when their distance is lower than the standard value for a regular B-DNA helix (narrowing of the minor groove).