Sequence-specific DNA recognition by peptide heterodimers.

The DNA binding motif rich in basic amino acid residues is used by a variety of DNA binding proteins to recognize specific DNA sequences. We report here a sequence-specific DNA recognition by peptide heterodimers derived from the basic leucine zipper proteins. Specific hetero-dimerization is controlled by an artificial dimerization module consisting of a host-guest inclusion complex. Efficiency of the sequence discrimination by the peptide dimers depends on a stability of the half-matched binding complex. However, structures of the matched and half-matched binding complexes differ from one another.