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 bear ing an adamantyl group at the epsilon-amino group was incorporated at the N-terminal position, and beta-cyclodextrin was attached at the C-t erminal cysteine residue of the parent basic region peptide, The resul ting peptide G2AdCd possesses both host and guest molecules in the sam e peptide chain. DNA binding of the G2AdCd peptides to the single-, do uble-, and triple-direct-repeat sequences of the CRE half-site was com pared by titration of the gel shift. The G2AdCd peptide did not bind t he single CRE half-site, although a peptide lacking the beta-cyclodext rin group formed a specific monomer-half-site complex. G2AdCd bound th e double-direct-repeat sequence as a dimer in a cooperative manner. Mo reover, 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. Fo rmation of this cyclic peptide reduces the affinity of monomeric G2AdC d. The highly selective binding of G2AdCd observed here was accomplish ed by (i) its cooperative nature of DNA binding and (ii) destabilizati on of its nonspecific DNA binding complex.