Figure 3. Methylation modulates the interaction free energy of two dsDNA molecules by altering the number of bridging Sm⁴⁺.

(a) Typical spatial arrangement of Sm⁴⁺ molecules around a pair of DNA helices. The phosphates groups of DNA and the amine groups of Sm⁴⁺ are shown as red and blue spheres, respectively. ‘Bridging' Sm⁴⁺ molecules reside between the DNA helices. Orange rectangles illustrate the volume used for counting the number of bridging Sm⁴⁺ molecules. (b) The number of bridging amine groups as a function of the inter-DNA distance. The total number of Sm⁴⁺ nitrogen atoms was computed by averaging over the corresponding MD trajectory and the 10 Å (x axis) by 20 Å (y axis) rectangle prism volume (a) centred between the DNA molecules. (c) Schematic representation of the dependence of the interaction free energy of two DNA molecules on their nucleotide sequence. The number and spatial arrangement of nucleotides carrying a methyl group (T or mC) determine the interaction free energy of two dsDNA molecules.