DNA recognition by metal-peptide complexes containing the recognition helix of the phage 434 repressor

Short oligopeptides (14 residues) derived from the DNA recognition helix of the phage 434 repressor (434R) have been tethered onto the metallointercalating [Rh(phi)(2)(phen')](3+), and the DNA recognition characteristics of the resultant metal-peptide complexes have been examined. DNA sequence selectivities for the family of metal-peptide complexes, determined in photoactivated DNA cleavage experiments, reproduce features of operator recognition by the native 434R. Binding to the DNA duplex depends both on the appended peptide and upon the metallointercalating unit, as determined through variations in the peptide sequence and in the diastereomeric configuration of the metal-peptide. The complexes preferentially target 5'-ACAA-3' operator sites and single-base variants, bind at 50 nM concentrations, and, as determined by chemical footprinting, protect 7-10 bp of DNA around the target sites. Comparative cleavage studies on synthetic oligonucleotides containing variations in operator sequence, furthermore, reveal a hierarchy in sequence preference which resembles the native protein, but highest affinity for the metal-peptides, unlike 434R, is found for 5'-ACGA-3'. These studies illustrate a new route to the rational design of small, artificial repressors through the construction of metal-peptide complexes.