Cooperative Oligomerization Enhances Sequence-Selective DNA Binding by a Short Peptide

Abstract

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 e-amino group was incorporated at the N-terminal position, and β-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 β-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...