Perturbing the DNA sequence selectivity of metallointercalator - Peptide conjugates by single amino acid modification

Metallointercalator-peptide conjugates that provide small molecular mimics to explore peptide-nucleic acid recognition have been prepared. Specificall y, a family of peptide conjugates of [Rh(phi)(2)-(phen')](3+) [where phi = 9,10-phenanthrenequinone diimine and phen' = 5-(amidoglutaryl)-1,10-phenant hroline] has been synthesized and their DNA-binding characteristics examine d. Single amino acid modifications were made from the parent metallointerca lator-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 metallointerc alator-peptide conjugate to 5'-ACA-3'. Subsequent mutation of the glutamate at position 6 to arginine {[Rh(phi)(2)(phen')](3+)-AANVARAAWARAA-CONH2} ca used more complex changes in DNA recognition. Thermodynamic dissociation co nstants were determined for these metallointercalator-peptide conjugates by photoactivated DNA cleavage assays with the rhodium intercalators. At 55 d egrees C in the presence of 5 mM MnCl2, [Rh(phi)(2)(phen')](3+)-AANVAIAAWER AA-CONH2 binds to a 5'-CCA-3' site with K-d = 5.7 x 10(-8) M, whereas [Rh(p hi)(2)(phen')](3+) AANVAEAAWARAA-CONH2 binds to its target 5'-ACA-3' site w ith K-d = 9.9 x 10(-8) M. The dissociation constant for [Rh(phi)2(phen')](3 +) with random-sequence DNA is 7.0 x 10(-7) M. Structural models have been developed and refined to account for the observed sequence specificities. A s with much larger DNA-binding proteins, with these metal-peptide conjugate mimics, single amino acid changes can lead to single or multiple base chan ges in the DNA site targeted.