Synthesis of a new zinc finger peptide; comparison of its `code' deduced and `CASTing' derived binding sites

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Abstract
Using two synthetic oligonucleotides, we have constructed a new gene containing three zinc finger motifs of the Cys2‐His2 type. We named this artificial gene `Mago'. The Mago nucleotide triplets encoding the amino acid positions, described to be crucial for DNA binding specificity, have been chosen on the basis of the proposed recognition `code' that relates the zinc finger's primary structure to the DNA binding target. Here we demonstrate that Mago protein specifically binds the `code' DNA target, with a dissociation constant (K d) comparable to the K d of the well known Zif268 protein with its binding site. Moreover, we show that the deduced Mago `code' and the `experimental' selected DNA binding sites are almost identical, differing only in two nucleotides at the side positions.