Determination of DNA binding specificities of mutated zinc finger domains

By substituting non conserved amino acids present in the postulated alpha-helical region of zinc finger domains, we demonstrated that Cys2/His2 type zinc finger domains could be targeted to new DNA binding sites. The putative alpha-helical region of the second SP1 zinc finger (RSDELQRH) was replaced by amino acids (KSSALISH) occurring in analogous zinc finger positions of human zinc finger protein Kox 29. The DNA binding specificity of the FPLC purified chimaeric protein (SP1-Kox 29) was determined by use of the target detection assay (TDA). Chimaeric protein SP1-Kox 29 was subjected to randomized oligonucleotides (GGG NNNN GGC) that were designed on the basis that each SP1 zinc finger interacts with 3-4 nucleotides concerning its cognate target site GGG GCGG GGC. By this analysis the DNA binding specificity of SP1-Kox 29 was shown to have switched from the cognate SP1 binding site to GGG GGTG GGC. Structure-function analysis of this type should facilitate the determination of DNA binding specificities for any individual zinc finger of interest.