Schematic representation of the helical coordinates system.

<p>A) The helical coordinate system establishes the position of the ligand center of mass with respect to the DNA’s axis. The DNA axis was aligned to the z-axis. The helical coordinate system is defined in terms of coordinates (<i>ρ</i>, <i>ϕ</i>, <i>ξ</i>) (in yellow). Coordinates (<i>r</i>, <i>θ</i>, <i>z</i>) (in red) correspond to a cylindrical coordinate system. <i>p</i> is the pitch of the helix and <i>α</i> the pitch angle. B) The components of a vector <b>V</b> in a surface of constant <i>ρ</i> in both helical (yellow) and cylindrical coordinates (red). C) Snapshot of the initial DNA methyl-guanidinium complex.