Stereochemical basis of DNA recognition by Zn fingers

DNA-recognition rules for Zn fingers are discussed in terms of crystal structures. The rules can explain the DNA-binding characteristics of a number of Zn finger proteins for which there are no crystal structures. The rules have two parts: chemical rules, which list the possible pairings between the 4 DNA bases and the 20 amino acid residues, and stereochemical rules, which describe the specific base positions contacted by several amino acid positions in the Zn finger. It is discussed that to maintain the correct binding geometry, in which the N-terminus of the recognition helix is closer to the DNA than the C-terminus, the residues facing the DNA on the helix must be larger near the C-terminus, and that two different types of fingers (A and B) bind to DNA in distinctly different ways and cover different numbers of base pairs.