The reactions of metallointercalator-peptide conjugates and DNA

A family of metallointercalator-peptide conjugates for reaction with DNA has been constructed. In these chimeras, the metallointercalator provides binding affinity for DNA and the peptide contributes reactivity. With the goal of creating an artificial nuclease, we have tethered metal-binding peptides to a sequence neutral intercalator, [Rh(phi)2bpy' ]3+ (phi = phenanthrenequinone diimine, bpy ' = 4-butyric acid-4'-methyl-2,2 '-bipyridine). This is a general strategy, and we have observed Zn2+-promoted cleavage of plasmid DNA with widely different peptides: a designed helical peptide with histidine residues, and a hairpin peptide modeled after the active site of the BamHI endonuclease. To optimize the peptide composition of our artificial nuclease we created a library of 16,000 conjugates, but no new active conjugates were identified with this combinatorial strategy. To achieve oxidative cleavage of the DNA backbone we have also used our intercalator-peptide conjugates to deliver copper to DNA. Tethered peptides containing histidine residues promote oxidative strand scission in DNA restriction fragments and oligonucleotides in the presence of Cu2+ and a reducing agent. Importantly, by comparing the photocleavage pattern of the rhodium intercalator with the copper cleavage pattern of the metal-binding peptide, the interactions of the conjugate with DNA could be dissected. Finally, short peptides were tethered to [Ru(phen)(bpy ')(dppz)]2+ (phen = 1,10-phenanthroline, dppz = dipyridophenazine) to create fluorescent DNA crosslinking agents. Through a flash-quench reaction, the ruthenium intercalator generates guanine radicals in a DNA duplex. These guanine radicals can react with water or oxygen, but also with tethered peptides to produce permanent DNA-peptide crosslinks. The DNA-peptide crosslinks were detected by gel electrophoresis and absorbance measurements, and characterized by mass spectrometry. Although they have low affinity for DNA, untethered peptides could also be crosslinked to DNA using the ruthenium chemistry. The peptide composition influences conjugate binding and the extent and pattern of crosslinking; indeed, positively charged residues were essential for effective crosslinking. Although the flexibility of our tethered peptides is an obstacle to the rational design of reactive conjugates, we have demonstrated that peptides can mediate a variety of reactions if delivered to DNA by metallointercalators.