Figure 4.

Cation RDF of AA-TT (blue) and AT-TA (red) in 60 mM MgCl₂ salt solution at inter-helical spacing of 29 Å. Panels A–E shows the RDF. (A) Minor groove (B) phosphate groups and (C) major groove. Further analysis of atoms at the major groove shows that the favorable binding is mainly due to two electronegative groups: (D) N7 atom that resides at adenine, and (E) N6 atoms at adenine. A more intricate picture of the role of these atoms in sequence specificity can be gleaned by looking at their spatial positioning on the DNA surface. (F) Illustrates how these two atoms are located at the surface of one turn of the DNA major groove in AA-TT (left), AT-TA (right). The two negatively charged atoms are colored orange (N7) and blue (N6). Hexa-hydrated Mg^{2 +} ions are represented with ball and stick.