Amino Acid Switch Turns Protein From Binder To Cleaver

By replacing a single naturally occurring amino acid with an unnatural amino acid, chemists at Scripps Research Institute have turned a protein that only binds to DNA into one that also cleaves the DNA specifically at the site next to the unnatural amino acid (J. Am. Chem. Soc., DOI: 10.1021/ja804653f). Changing the location of the unnatural amino acid causes DNA cleavage at different spots. The technique could be used to map interactions between proteins and their DNA partners. Peter G. Schultz and Hyun Soo Lee perform this binder-to-cleaver transformation on Escherichia coli catabolite activator protein (CAP), a homodimer that binds to a 22-base-pair site. They insert bipyridinyl alanine (Bpy-Ala) in place of a lysine that lies at the protein-DNA interface near both ends of the binding site in the dimeric protein. The bipyridinyl group chelates transition-metal ions, which Schultz and Lee expected would induce oxidative cleavage of the DNA backbone next to the unnatural amino acid. When the researchers incubate the modified protein with metal ions, a reducing agent, and DNA containing the binding sequence, they do indeed see cleavage of the DNA backbone in the expected locations.