DNA recognition and superstructure formation by helix-turn-helix proteins.

The way helix-turn-helix proteins recognize DNA is analysed by comparing their sequences, structures, and binding specificities. Individual recognition helices in these proteins bind to four DNA base pairs with the same geometry. However, pairs of recognition helices in the protein dimers can have different separations and orientations. These differences are used for discriminating between DNAs which have different superstructures, in particular, different numbers of base pairs between sets of the four base pairs.

[1]  T. Steitz,et al.  Structural studies of protein–nucleic acid interaction: the sources of sequence-specific binding , 1990, Quarterly Reviews of Biophysics.

[2]  C. Branden,et al.  Introduction to protein structure , 1991 .

[3]  E. Westhof,et al.  Nucleic Acids and Molecular Biology , 1988, Nucleic Acids and Molecular Biology.

[4]  B. Matthews,et al.  Structural studies of protein-nucleic acid interactions. , 1983, Annual review of biophysics and bioengineering.