Selection of a high-affinity DNA pool for a bZip protein with an out-of-phase alignment of the basic region relative to the leucine zipper Original Research Article

bZip transcription factors contain two regions that are required for DNA binding: a leucine zipper dimerization domain and a highly charged basic region that directly contacts DNA. The spacing between these subdomains is strictly conserved, and changes in this spacing result in a loss of function. Using an in vitro selection strategy, we have investigated the ability of a bZip protein with incorrect spacing between these two regions to bind specifically to DNA. Surprisingly, we find that although such a protein does not bind to its predicted site, it is possible to isolate a pool of DNAs that bind with very similar affinity to that of GCN4 for its optimum DNA site.