Position dependent recognition of GNN nucleotide triplets by zinc fingers

A method for designing a zinc finger protein comprising a first (F1), a second (F2), and a third (F3) zinc finger, ordered F1, F2, F3 from N-terminus to C-terminus that binds to a target site comprising, in 3′ to 5′ direction, a first (S 1), a second (S2), and a third (S3) target subsite, each target subsite having the nucleotide sequence GNN, the method comprising the steps of

• selecting the F1 zinc finger such that it binds to the S1 target subsite, wherein if S1 comprises GAA, F1 comprises the amino acid sequence QRSNLVR;
• if S1 comprises GAG, F1 comprises the amino acid sequence RSDNLAR;
• if S1 comprises GAC, F1 comprises the amino acid sequence DRSNLTR;
• if S1 comprises GAT, F1 comprises the amino acid sequence QSSNLAR;
• if S1 comprises GGA, F1 comprises the amino acid sequence QSGHL AR;
• if S1 comprises GGG, F1 comprises the amino acid sequence RSDHLAR;
• if S1 comprises GGC, F1 comprises the amino acid sequence DRSHLRT;
• if S1 comprises GGT, F1 comprises the amino acid sequence QSSHLTR;
• if S1 comprises GCA, F1 comprises QSGSLTR;
• if S1 comprises GCG, F1 comprises RSDDLTR;
• if S2 comprises GCG, F2 comprises RSDDLQR;
• if S1 comprises GCC, F1 comprises ERGTLAR;
• if S1 comprises GCT, F1 comprises the amino acid sequence QSSDLTR;
• if S1 comprises GTA, F1 comprises the amino acid sequence QSGALTR;
• if S1 comprises GTG, F 1 comprises the amino acid sequence RSDALTR;
• if S1 comprises GTC, F 1 comprises the amino acid sequence DRSALAR;
• selecting the F2 zinc finger such that it binds to the S2 target subsite, wherein S2 comprises GAA, F2 comprises the amino acid sequence QSGNLAR;
• if S2 comprises GAG, F2 comprises the amino acid sequence RSDNLAR;
• if S2 comprises GAC, F2 comprises the amino acid sequence DRSNLTR;
• if S2 comprises GAT, F2 comprises the amino acid sequence TSGNLVR;
• if S2 comprises GGA, F2 comprises the amino acid sequence QSGHLQR;
• if S2 comprises GGG, F2 comprises the amino acid sequence RSDHLSR;
• if S2 comprises GGC, F2 comprises the amino acid sequence DRSHLAR;
• if S2 comprises GGT, F2 comprises the amino acid sequence TSGHLSR;
• if S2 comprises GCA, F2 comprises the amino acid sequence QSGDLTR;
• if S2 comprises GCC, F2 comprises the amino acid sequence DRSDLTR;
• if S2 comprises GCT, F2 comprises the amino acid sequence QSSDLTR;
• if S2 comprises GTA, F2 comprises the amino acid sequence QSGALAR;
• if S2 comprises GTG, F2 comprises the amino acid sequence RSDALSR;
• if S2 comprises GTC, F2 comprises the amino acid sequence DRSALAR;
• and
• selecting the F3 zinc finger such that it binds to the S3 target subsite, wherein if S3 comprises GAA, F3 comprises the amino acid sequence QSGNLAR;
• if S3 comprises GAG, F3 comprises the amino acid sequence RSDNLTR;
• if S3 comprises GAC, F3 comprises the amino acid sequence DRSNLTR;
• if S3 comprises GAT, F3 comprises the amino acid sequence TSANLSR;
• if S3 comprises GGA, F3 comprises the amino acid sequence QSGHLQR;
• if S3 comprises GGG, F3 comprises RSDHLSR;
• if S3 comprises GGT, F3 comprises the amino acid sequence TSGHLVR;
• if S3 comprises GCA, F3 comprises the amino acid sequence QSGDLTR;
• if S3 comprises GCG, F3 comprises the amino acid sequence RSDDLTR;
• if S3 comprises GCC, F3 comprises the amino acid sequence DRSDLTR;
• if S3 comprises GCT, F3 comprises the amino acid sequence QSSDLQR;
• if S3 comprises GTG, F3 comprises RSDALTR;
• and if S3 comprises GTC, F3 comprises the amino acid sequence DRSALAR;
• thereby designing a zinc finger protein that binds to a target site.