DNA Recognition by Peptide Complexes of Rhodium(III): Example of a Glutamate Switch

Abstract

A family of metal-peptide complexes has been synthesized by coupling short oligopeptides (13 residues) onto the metallointercalating [Rh(phi)_2(phen’)]^(3+) (phi = 9,10-phenanthrenequinone diimine; phen’ = 5-(amidoglutaryl)-1,10-phenanthroline). These complexes were prepared to explore whether the side-chain functionalities of small peptides may be used to augment metal complex recognition. The metal-peptide complexes bind and, with photoactivation, cleave DNA. The DNA site-specificity is seen to depend on the peptide side-chain functional groups. In particular, a single glutamate at position 10 is found to be essential in directing DNA site-recognition to the sequence 5’-CCA-3’. Methylation of the glutamate side chain or direct substitution of glutamine for glutamate abolishes the 5’-CCA-3’ selectivity, while substitutions at other likely DNA-binding residues show no appreciable change in selectivity. Significantly, the 5’-CCA-3’ selectivity is even sensitive to a highly conservative E10D substitution. DNA photocleavage of oligonucleotides by the metal-peptide complexes and HPLC analysis of DNA products provide evidence for major groove chemistry. Circular dichroism indicates significant α-helical content in the peptide, which depends upon the presence of the glutamate. A model for the glutamate-dependent site-selectivity is presented using shape-selective intercalation of the metal complex and base-specific contacts of the ancillary peptide. These monomeric metal-peptide complexes appear to serve as particularly useful mimics for larger site-specific DNA-binding proteins and may provide a basis for the design of an array of small, sequence-specific DNA-binding metal complexes.