Serine at position 2 in the DNA recognition helix of a Cys2-His2 zinc finger peptide is not, in general, responsible for base recognition.

The roles of certain amino acids within zinc finger peptides of the Cys2His2 type in determining DNA-binding site specificity were investigated. A variety of three domain peptides designed using a consensus sequence framework were prepared with different potential DNA-contacting residues and tested in a recently developed specificity determination assay. Proteins with recognition helix sequence Q-1S1S2N3L4Q5K6 and QSSDLQK prefer binding subsites 5'-GAA-3' and 5'-(G/T)C(A/G)-3', respectively. Changing the Ser residues in position 2 to Ala in these proteins did not significantly affect the DNA binding site preferences, indicating that Ser residues, which occur frequently in position 2 in known zinc finger proteins are not, in general, responsible for determining binding site preferences. Examination of proteins with recognition helices HSSNLQK and ASSNLQK revealed considerable loss of binding site discrimination throughout the binding subsite. These observations provide further evidence for the importance of residues in positions -1 and 3 in determining DNA binding specificity. Moreover, these results illustrate the effects of changes of one residue in the recognition helix on binding site preferences throughout the recognition subsite.