Structure-based design of a dimeric zinc finger protein

Designing DNA-binding proteins with novel sequence specificities may provide valuable tools for biological research and gene therapy. Computer modeling was used to design a dimeric zinc finger protein, ZFGD1, containing zinc fingers 1 and 2 from Zif268 and a portion of the dimerization domain of GAL4. ZFGD1 binds with high affinity and specificity to the predicted binding site, which contains two 6 base-pair symmetry-related zinc finger subsites separated by a 13 base-pair spacer. The DNA-binding specificity of this fusion protein is determined primarily by the zinc fingers and can be systematically altered through the substitution of the zinc fingers with variants selected by phage display. This zinc finger-GAL4 fusion may serve as a prototype for designed DNA-binding proteins that could exploit advantages of homo- and heterodimer formation, and the adaptability of the Cys₂His₂ zinc finger motif, to target virtually any site in the genome.