DNA-RECOGNITION CODE TABLES FOR TRANSCRIPTION FACTORS IN THE C4 ZINC-BINDING AND C2H2 ZINC-FINGER FAMILIES

A simple way of understanding the structure of the DNA recognition code of transcription factors is shown taking two DNA binding motifs as examples (the C4 class zinc binding proteins and the C2H2 zinc fingers). Interaction between DNA and factors of the motifs can be understood as that between two lines, a line connecting residue positions op the surface of a recognition helix and a line connecting base positions in the DNA major groove. The base-residue pairing along the two lines are summarised in the stereochemical charts. The DNA recognition table for each of the two motifs, which can be used for prediction and design of recognition helix-DNA interactions, can be created by choosing residue-base partners from the chemical code table according to the stereochemical chart