Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences

Peptides that mediate dimerization of attached zinc finger DNA-binding doma ins have been evolved in vitro starting from random sequences. We first use d phage display to select dimerization elements from libraries of random 15 -residue polypeptides that were fused to the N terminus of the zinc finger domains. We then reoptimized these peptides by sequentially randomizing fiv e-residue blocks (proceeding across the peptide in three steps) and selecti ng variant peptides that further stabilized the protein-DNA complex. Bioche mical experiments confirmed that the selected peptides promote dimerization of the zinc fingers on an appropriate DNA target site. These results demon strate that dimerization units can be obtained readily from random polypept ide libraries of moderate complexity. Our success reemphasizes the utility of searching random peptide libraries in protein design projects, and the s equences presented here may be useful when designing novel transcription fa ctors.