Figure 11.

Molecular Dynamics (MD) model of DB2528 bound to a two G·C bps containing sequence AAAGAAACTTT site. A space filling model with DNA tan color is shown on the left where the compound DB2528 (magenta) covers a full helical turn of 10 bps in the minor groove. On the right side, the DNA bases are represented in tan-white-red-blue-orange (C−H−O−N−P) color scheme and DB2528 is magenta-white-blue-yellow (C−H−N−S) color scheme. The detailed important interactions, H-bonds and other interactions described in the text, between the symmetrical bis amidine-phenyl-N-methyl-BI-thiophene of DB2258 with DNA bases are shown with yellow color circle and arrows; arrow 1: Am-N-H---O-H₂, arrow 2: H₂-O---N3-dA, arrow 3: Am-NH---O=dT, arrow 4: BI-N---H-dG.