DNA curvature and deformation in protein-DNA complexes: a step in the right direction.

The sequence target of E2 has the general form ACCGNNNNCGGT, where N4 is variable and does not contact the protein. Binding of the protein yields bends toward the major grooves at the dyad-symmetric ACCG/CGGT elements (4, 5). The bends result primarily from roll, which measures rotation of a base pair plane about its long axis. This motion creates an angle, narrowing toward the major groove for positive roll, between two otherwise parallel adjacent base pairs. Because the centers of the two ACCG/CGGT sequences are less than a full helical turn apart, a writhed curve rather than a planar bend of the DNA axis results.