Position dependent recognition of GNN nucleotide triplets by zinc fingers

A polynucleotide encoding a zinc finger protein that binds to a target site in a gene in a position-specific fashion, the target site comprising, in a 3′ to 5′ direction, first (S1), second (S2) and third (S3) target subsites, each target subsite having the nucleotide sequence GNN, the zinc finger protein comprising:

• (a) a non-naturally-occurring zinc finger protein that has been engineered to bind the target site;
• and
• (b) first (F1), second (F2) and third (F3) zinc fingers ordered F1, F2, F3 from N-terminus to C-terminus that bind to S1, S2 and S3, wherein:
• if S1 comprises GGA, F1 comprises the amino acid sequence QSGHLAR (SEQ ID NO:413);
• if S2 comprises GGT, F2 comprises the amino acid sequence TSGHLSR (SEQ ID NO:1201);
• if S2 comprises GCA, F2 comprises QSGDLTR (SEQ ID NO:220);
• if S2 comprises GCC, F2 comprises the amino acid sequence DRSDLTR (SEQ ID NO:417);
• if S3 comprises GAT, F3 comprises the amino acid sequence TSANLSR (SEQ ID NO:377);
• if S3 comprises GCA, F3 comprises QSGDLTR (SEQ ID NO:220);
• if S3 comprises GCC, F3 comprises the amino acid sequence DRSDLTR (SEQ ID NO:417);
• if S3 comprises GCT, F3 comprises the amino acid sequence QSSDLQR (SEQ ID NO:132);
• and further wherein the zinc finger protein binds to the target site, thereby modulating expression of the gene.