Figure 2: Molecular mechanism of polyamine-mediated DNA sequence recognition.

(a–c) Representative configurations of Sm⁴⁺ molecules at the DNA–DNA distance of 28 Å for the (AT)₁₀–(AT)₁₀ (a), (GC)₁₀–(GC)₁₀ (b) and (GmC)₁₀–(GmC)₁₀ (c) DNA pairs. The backbone and bases of DNA are shown as ribbon and molecular bond, respectively; Sm⁴⁺ molecules are shown as molecular bonds. Spheres indicate the location of the N7 atoms and the methyl groups. (d–f) The average distributions of cations for the three sequence pairs featured in a–c. Top: density of Sm⁴⁺ nitrogen atoms (d=28 Å) averaged over the corresponding MD trajectory and the z axis. White circles (20 Å in diameter) indicate the location of the DNA helices. Bottom: the average density of Sm⁴⁺ nitrogen (blue), DNA phosphate (black) and sodium (red) atoms projected onto the DNA–DNA distance axis (x axis). The plot was obtained by averaging the corresponding heat map data over y=[−10, 10] Å. See Supplementary Figs 4 and 5 for the cation distributions at d=30, 32, 34 and 36 Å.