The most common DNA-binding motif found in humans and multicellular organism is the cysteine-histidine (Cys2-His2) zinc finger.
As reported in the literature, the complementing structures of ZFPs and their corresponding DNA binding domains make these systems highly conducive for designing artificial DNA binding proteins .
Such experiments typically show a two to ten-fold increase in the K value for each single base-pair change in the binding site, with mutations near the centre of the binding site usually having larger effects than mutations near the periphery.
These side directed mutational studies may aid computational analysis of the binding affinity altered by mutations of choice in the protein template.
Although there is no simple, general code for zinc finger protein–DNA recognition, selection strategies have been developed that allow these proteins to be designed to target almost any desired site on double-stranded DNA.
The Cys2His2 zinc finger proteins, and more often, Zif-268, offers a stable and versatile framework for the design of such proteins .
Here, we present an ab-initio method that is based on mutation of the key α-helical residues of individual fingers of the parent template for Zif-268 and its consensus sequence (PDB ID: 1AAY).
In an attempt to elucidate the mechanism of zinc finger protein-DNA interactions, we evaluated and compared three approaches, differing in the amino acid mutations introduced in the Zif-268 parent template, and the mode of binding they try to mimic, i.e., modular and synergistic mode of binding.
Comparative evaluation of the three strategies reveals that the synergistic mode of binding appears to mimic the ideal mechanism of DNA-zinc finger protein binding.
The recognition site for a ZFP motif is primarily composed of a three-nucleotide sequence triplet within the DNA substrate and the recognition specificity is strongly dependent on the amino acids located at positions −1, 1, 2, 3, 4, 5 and 6, relative to the start position of the alpha helix.
While the remaining residues form a conserved backbone of the ZFP, any changes in the variable residues, specifically, at the positions −1, 2, 3 and 6 are expected to have a much more pronounced impact on the binding specificity of the ZFP, as compared to any changes in the residues forming the conserved backbone.