Binding to distorted DNA structures

The basis of the preference of the A domain, relative to the B domain, of HMGBl for binding to distorted DNA structures has become apparent from numerous structural and biophysical studies. In contrast to the B domain, the A domain has only the secondary potentially intercalating residue, namely Phe at position Y (Table 1 and Fig. 2). This presumably accounts for the smaller bend angle in the A domain/cisplatin-modified DNA eomplex (61°) than in the B domain complex (80-95°) [34,43]. As yet, there is no strueture of a complex between the A domain and linear DNA. However, in the erystal structure of the A domain complexed with cisplatin-modified DNA the domain binds to one side of the cA-platinum adduet. 

Red HMG boxes from sequence-specific single HMG box proteins black HMG boxes from abundant single box yeast and Drosophila HMG box proteins blue A box from HMGBl green B box from HMGBl. Adapted from Ref [13] with permission. 

---