T. Morii et al., COOPERATIVE OLIGOMERIZATION ENHANCES SEQUENCE-SELECTIVE DNA-BINDING BY A SHORT PEPTIDE, Journal of the American Chemical Society, 118(42), 1996, pp. 10011-10017
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.