Cooperative oligomerization enhances sequence-selective DNA binding by a short peptide

A series of short peptides derived from the basic region of the basic leucine zipper protein GCN4 were synthesized to study the cooperative DNA binding to direct repeat sequences. A modified lysine residue bearing an adamantyl group at the epsilon-amino group was incorporated at the N-terminal position, and beta-cyclodextrin was attached at the C-terminal cysteine residue of the parent basic region peptide, The resulting peptide G2AdCd possesses both host and guest molecules in the same peptide chain. DNA binding of the G2AdCd peptides to the single-, double-, and triple-direct-repeat sequences of the CRE half-site was compared by titration of the gel shift. The G2AdCd peptide did not bind the single CRE half-site, although a peptide lacking the beta-cyclodextrin group formed a specific monomer-half-site complex. G2AdCd bound the double-direct-repeat sequence as a dimer in a cooperative manner. Moreover, cooperative formation of a 3:1 G2AdCd-DNA complex was observed for a triple-direct-repeat sequence, No monomer-DNA complex of G2AdCd was observed for the double- or triple-direct-repeat sequence. In the absence of DNA, G2AdCd forms an intramolecular host-guest complex. Formation of this cyclic peptide reduces the affinity of monomeric G2AdCd. The highly selective binding of G2AdCd observed here was accomplished by (i) its cooperative nature of DNA binding and (ii) destabilization of its nonspecific DNA binding complex.