Perturbing the DNA Sequence Selectivity of Metallointercalator−Peptide Conjugates by Single Amino Acid Modification

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Abstract
Metallointercalator−peptide conjugates that provide small molecular mimics to explore peptide−nucleic acid recognition have been prepared. Specifically, a family of peptide conjugates of [Rh(phi)2(phen‘)]3+ [where phi = 9,10-phenanthrenequinone diimine and phen‘ = 5-(amidoglutaryl)-1,10-phenanthroline] has been synthesized and their DNA-binding characteristics examined. Single amino acid modifications were made from the parent metallointercalator−peptide conjugate [Rh(phi)2(phen‘)]3+-AANVAIAAWERAA-CONH2, which targets 5‘-CCA-3‘ site-specifically. Moving the glutamate at position 10 in the sequence of the appended peptide to position 6 {[Rh(phi)2(phen‘)]3+-AANVAEAAWARAA-CONH2} changed the sequence preference of the metallointercalator−peptide conjugate to 5‘-ACA-3‘. Subsequent mutation of the glutamate at position 6 to arginine {[Rh(phi)2(phen‘)]3+-AANVARAAWARAA-CONH2} caused more complex changes in DNA recognition. Thermodynamic dissociation constants were determined for these metallointercalator−peptide conjugates by photoactivated DNA cleavage assays with the rhodium intercalators. At 55 °C in the presence of 5 mM MnCl2, [Rh(phi)2(phen‘)]3+-AANVAIAAWERAA-CONH2 binds to a 5‘-CCA-3‘ site with Kd = 5.7 × 10-8 M, whereas [Rh(phi)2(phen‘)]3+-AANVAEAAWARAA-CONH2 binds to its target 5‘-ACA-3‘ site with Kd = 9.9 × 10-8 M. The dissociation constant for [Rh(phi)2(phen‘)]3+ with random-sequence DNA is 7.0 × 10-7 M. Structural models have been developed and refined to account for the observed sequence specificities. As with much larger DNA-binding proteins, with these metal−peptide conjugate mimics, single amino acid changes can lead to single or multiple base changes in the DNA site targeted.