Re-programming DNA-binding specificity in zinc finger proteins for targeting unique address in a genome

Abstract

Recent studies provide a glimpse of future potential therapeutic applications of custom-designed zinc finger proteins in achieving highly specific genomic manipulation. Custom-design of zinc finger proteins with tailor-made specificity is currently limited by the availability of information on recognition helices for all possible DNA targets. However, recent advances suggest that a combination of design and selection method is best suited to identify custom zinc finger DNA-binding proteins for known genome target sites. Design of functionally self-contained zinc finger proteins can be achieved by (a) modular protein engineering and (b) computational prediction. Here, we explore the novel functionality obtained by engineered zinc finger proteins and the computational approaches for prediction of recognition helices of zinc finger proteins that can raise our ability to re-program zinc finger proteins with desired novel DNA-binding specificities.

Keywords: Genome targeting; Zinc finger proteins.

Fig. 1

Representation of a zinc finger protein and its specific target DNA site. a ββα—three zinc finger domain protein (Zif268) wrapping around the target DNA; the zinc finger amino acid side chains at the alpha helical positions −1, 3 and 6 makes sequence-specific hydrogen bond interactions with the nucleotides on the top DNA strand; a cross-strand interaction to the complementary DNA strand is also depicted (amino acid side chain at position 2 makes the cross-strand interaction)