Engineered designer nucleases can be used to efficiently modify genomic sequence in a wide variety of model organisms and cell types. Zinc finger nucleases (ZFNs), consisting of an engineered zinc finger array fused to a non-specific cleavage domain, have been extensively used to modify a broad range of endogenous genes. Protocols for engineering ZFNs targeted to specific gene sequences of interest using the context-dependent assembly (CoDA) method are described in this unit.