Zinc-finger nucleases (ZFNs) are a fusions of ‘Zinc Finger Proteins’ and ‘Nuclease Domains’.
Zinc fingers proteins can be coded by the user to recognise specific DNA sequences enabling targeting of the protein complex to specific regions of any genome.
The most commonly used nuclease domain is the DNA cleavage domain from the restriction endonuclease FokI.
Since FokI is active as a dimer, a pair of ZFN proteins are usually delivered each designed to recognised 9-21 base-pairs either side of the desired cut site.
Two ZFN target a specific DNA sequence and create a double strand break. The break can be repaired by the endogenous mechanisms of non-homologous end-joining and homologous recombination. Carroll, D. Genome engineering with zinc-finger nucleases. Genetics Society of America, 2011, 188(4), pp 773-782. This image is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.
Several on-line tools exist for designing ZFNs:
ZFNtools (Barbas lab)
ZiFIT (Zinc Finger Consortium)
ZFN Genome (Dobbs Laboratory)
ZFN algorithm (Wolfe Lawson Assembly)