Structure based design of protein linkers for zinc finger nuclease

Abstract

Zinc finger nucleases are a promising tool to edit DNA in many biological applications, in particular for gene knockout. Despite many efforts the number of genes that can be effectively targeted with ZFNs remains severely limited, as available constructs cannot address arbitrary gene sequences. Here, we develop a novel concept to significantly enhance the number of DNA sequences that can be targeted by ZFN. Using an efficient computational model, we provide an extensive library of possible linker molecules between individual zinc finger motifs in the construct that can skip up to 10 base pairs between adjacent zinc finger recognition sites in the DNA sequence, which increases the number of genes that can be efficiently targeted by more than an order of magnitude.

Keywords: CRISPR; Gene therapy; Krüppel type linker; Linker design; MOE; TALENs; ZFM; ZFN; ZFP; Zif268; Zinc finger nuclease; base pairs; bp; clustered regularly interspaced short palindromic repeats; molecular operating environment; transcription activator-like effector nucleases; zinc finger nucleases; zinc finger proteins; zinc-finger motifs.