Zinc Finger Nuclease DNA Cleavage

Zinc finger nucleases cut DNA only when two independently-binding halves come together: a pair of engineered zinc finger arrays, each fused to a FokI nuclease domain, must land on two flanking half-sites in the correct orientation before their tethered FokI domains can dimerize and cleave. This simulator renders a real 3D DNA double helix and animates that whole cycle — one-dimensional facilitated diffusion as each monomer slides along the strand searching for its half-site, binding, FokI dimerization gated by how well the spacer length matches FokI's dimer geometry, and the resulting double-strand break. A spacer-length control and a wild-type-vs-obligate-heterodimer FokI toggle let you see directly why spacer geometry and nuclease engineering both matter for on-target cleavage and for suppressing off-target homodimer cuts.