A bacterial two-hybrid selection system for studying protein–DNA and protein–protein interactions

We have developed a bacterial “two-hybrid” system that readily allows selection from libraries larger than 10(8) in size. Our bacterial system may be used to study either protein–DNA or protein—protein interactions, and it offers a number of potentially significant advantages over existing yeast-based one-hybrid and two-hybrid methods. We tested our system by selecting zinc finger variants (from a large randomized library) that bind tightly and specifically to desired DNA target sites. Our method allows sequence-specific zinc fingers to be isolated in a single selection step, and thus it should be more rapid than phage display strategies that typically require multiple enrichment/amplification cycles. Given the large library sizes our bacterial-based selection system can handle, this method should provide a powerful tool for identifying and optimizing protein–DNA and protein–protein interactions.