Sequence-specific DNA binding by covalently constrained peptide dimers of the basic leucine zipper protein GCN4.

DNA binding of covalently bonded peptide dimers was studied by using enantiomeric and C2-symmetric templates as a dimerization module. Amino acid sequence of the peptide is derived from that of DNA contact region of the basic leucine zipper protein GCN4. These peptide dimers were designed to possess different constraints with respect to the orientation of two peptides. The basic region peptides were covalently linked to the enantiomeric template at the C-terminal ends. Two peptides are arranged either in a right-handed or left-handed geometry depending on the chirality of the template. The GCN4 basic region dimers with both right-handed and left-handed geometries show equal affinity to the native GCN4 binding DNA sequences, 5'-ATGACTCAT-3' and 5'-ATGACGTCAT-3', as revealed by the gel mobility shift assay. Specific recognition of the palindromic DNA sequence by the peptide dimers was confirmed by the DNase I footprinting. Circular dichroism spectroscopic study indicates that the basic region peptides bound the target DNA sequence in a helical conformation. The degree to which a chiral constraint effects may depend on the geometry of two DNA binding domains in the parent protein-DNA complex and on a position to apply the chiral constraint.