Figure 4.

Superimposition of the DDD (PDB entry BDL084) (black) and DDD^Z10 (gray) duplexes. The view is into the (A) minor groove and (B) major groove, with respect to the central base pairs. Mg²⁺ and a partial spermine molecule in the structure of the native DDD are shown in a ball-and-stick representation. The helix axes are based on the central hexamer duplexes and are coincident (straight gray and black lines for DDD^Z10 and DDD, respectively). In both duplexes, the helix axes defined by base pairs G¹⁰ · C¹⁵, C¹¹ · G¹⁴, and G¹² · C¹³ at one end are parallel with those of the central hexamers. Conversely, the helix axis defined by base pairs C¹ · G²⁴, G² · C²³, and C³ · G²² at the other end is inclined more in the native DDD than in DDD^Z10 relative to the respective helix axis.