Docking of DB1255 to d[(5′-CCATGATCT-3′)(5′-AGATCATGG-3′)]
by using Autodock version 4.02. Two thiophene S atoms (yellow) form
bifurcated hydrogen bonds with the G-NH in the minor groove (shown
with a yellow dashed line). The lower amidine group forms H-bonds
with the thymine (T) carbonyl of T4, which is at the 5′ side
of G on the opposite strand), and to a deoxyribose oxygen of the DNA
backbone (yellow dashed lines) on the same strand as G. The top amidine
group is adjacent to the flanking 3′-T in cATGAt and forms
an H-bond with the DNA backbone (yellow dashed line). The DNA backbone
is shown as a stick model, colored by atom type (gray for carbon,
red for oxygen, blue for nitrogen, and orange for phosphorus). The
G5 base is displayed as a ball and stick and colored by atom type
(cyan for carbon, white for hydrogen, and blue for nitrogen), and
the ligand is displayed as a ball and stick also and colored by atom
type (magenta for carbon, white for hydrogen, and blue for nitrogen).