Figure 3.

(A) Structure of the human SRY/DNA complex (7). Isoleucine 13 (green spheres) is partially intercalated at the A8pA9 step. DNA is colored according to sequence (A = red, T = orange, G = blue, C = green). (B) DNA sequence used for the MD simulations with the binding site delimited by a horizontal black line. The ‘Watson’ strand of the oligomer is numbered 1–14 in the 5′-3′ sense and the ‘Crick’ strand is numbered 1′-14′ in the 3′-5′ sense. Salt bridges, hydrogen bonds and important apolar interactions observed during the MD simulations are indicated by black dots, red dots and green rectangles respectively.