Recognition of Selective DNA Sequences by Cooperative Binding Peptides

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Sequence-specific DNA binding proteins generally consist of more than two DNA contacting regions to ensure the selectivity of recognition. The multiple DNA binding modules are connected either through the covalent linker or through the noncovalent dimerization domain, We have compared the DNA binding of peptide dimers with covalent and noncovalent dimerization domains to explore the potential advantage of each linkage on the sequence-specific DNA binding. Three sets of head-to-tail peptide dimers were synthesized by using the same basic region peptide to target the same DNA sequence : one dimer was assembled with a bridged biphenyl derivative as a covalent dimerization domain and other two dimers with the cyclodextrin-guest noncovalent dimerization domains. One of the noncovalent dimers was a heterodimer consisted of cyclodextrin- and guest-peptides, while the other was a homodimer consisted of peptides bearing both cyclodextrin and the guest molecule within the same chain. Both noncov … More alent dimers formed the specific DNA complexes within narrower ranges of peptide concentrations and showed higher sequence selectivity than the covalent dimer did. Among the three dimers, the noncovalent homodimer that can form an intramolecular inclusion complex showed the highest sequence-selectivity. Because the noncovalent homodimer with the higher stability of the circular intramolecular inclusion complex revealed the higher sequence-selectivity, it was concluded that an equilibrium involving a conformational transition of a monomeric peptide effectively reduced the stability of its non-specific binding complex hence increasing the efficacy of cooperative dimer formation at the specific DNA sequence. The basic region peptides with five different guest molecules were synthesized and their equilibrium dissociation constants with a peptide possessing b-cyclodextrin were determined. These values, ranging from 1.3 to 15 muM, were used to estimate the stability of the complexes between the dimers with various guest/cyclodextrin dimerization domains and GCN4 target sequences. An efficient cooperative formation of the dimer complexes at the GCN4 binding sequence was observed when the adamantyl group was replaced with the norbornyl or noradamantyl group, but not with the cyclohexyl group that formed a b-cyclodextrin complex with an order of magnitude lower stability than the adamantyl group. Thus, cooperative formation of the stable dimer-DNA complex appeared to be effected by the stability of dimerization domain. Less