Hereby we report the design and solid-phase synthesis of de novo 26-residue linear and cyclic peptides with the beta-strand-turn-beta-strand motif for DNA sequence recognition; the only difference was the cyclic counterpart being conformationally restricted by a sulfhydryl bridge. Another product was a 28-residue peptide with N-terminal copper-chelating Gly-Gly-His, a potential DNA-cleaving agent. Binding of these peptides to natural DNAs, an endonuclease restriction fragment, and synthetic polydeoxyribonucleotides was examined by CD spectroscopy, fluorescence assays, and DNase I footprinting. The CD data showed the 26-residue linear and cyclic peptides to be in largely random and partly beta-conformation in water-or 20% trifluroethanol, but to assume a partly alpha-helical conformation in 50% TFE. Both the linear and the cyclic peptides were shown to bind to DNA, with saturation at one peptide per 3-4 bp. The antibiotic distamycin A, binding at the DNA minor groove, was found to compete with the peptides for the binding sites on poly(dA). poly(dT). The CD analysis revealed conformational alterations in the peptides upon binding to DNA, while the DNA structure underwent no appreciable changes. The CD difference spectra of the DNA-peptide mixture minus free DNA were distinct from those of the free peptide, and their shape was consistent with the random-to-beta-like conformational transition in the peptides upon binding to DNA. The DNase footprints showed that the linear and cyclic peptides specifically protected nucleotide sequences at the periphery of operators O(R)1, O(R)2, O(R)3 and pseudooperators in the phage 434 cro gene.
