A detailed study of the substrate specificity of a chimeric restriction enzyme

Abstract

Recently, the crystal structure of the designed zinc finger protein, ΔQNK, bound to a preferred DNA sequence was reported. We have converted ΔQNK into a novel site-specific endonuclease by linking it to the FokI cleavage domain (F_N). The substrate specificity and DNA cleavage properties of the resulting chimeric restriction enzyme (ΔQNK-F_N) were investigated, and the binding affinities of ΔQNK and ΔQNK-F_N for various DNA substrates were determined. Substrates that are bound by ΔQNK with high affinity are the same as those that are cleaved efficiently by ΔQNK-FN. Substrates bound by ΔQNK with lower affinity are cleaved with very low efficiency or not at all by ΔQNK-F_N. The binding of ΔQNK-F_N to each substrate was ∼2-fold weaker than that for ΔQNK. Thus, the fusion of the FokI cleavage domain to the zinc finger motif does not change the DNA sequence specificity of the zinc finger protein and does not change its binding affinity significantly.