Patent ID: 7241574

Claim:
A method for binding a nucleic acid binding protein to a target nucleotide sequence, wherein the binding protein comprises a plurality of zinc fingers, and further wherein at least two adjacent zinc fingers bind synergistically to overlapping quadruplet target subsites, wherein the method comprises: i) selecting a quadruplet within the target nucleotide sequence; ii) designing the binding protein such that binding of a zinc finger to the quadruplet is obtained by choosing the sequence of particular residues of the zinc finger depending on the nucleotide sequence of the quadruplet, as follows: a) if base 4 in the quadruplet is G, then position +6 in the α-helix is Arg; or position +6 is Ser or Thr and position ++2 is Asp; b) if base 4 in the quadruplet is A, then position +6 in the α-helix is Gln and position ++2 is not Asp; c) if base 4 in the quadruplet is T, then position +6 in the α-helix is Ser or Thr and position ++2 is Asp; d) if base 4 in the quadruplet is C, then position +6 in the α-helix may be any amino acid, provided that position ++2 in the α-helix is not Asp; e) if base 3 in the quadruplet is G, then position +3 in the α-helix is His: f) if base 3 in the quadruplet is A, then position +3 in the α-helix is Asn; g) if base 3 in the quadruplet is T, then position +3 in the α-helix is Ala, Ser or Val; provided that if it is Ala, then the residues at −1 or +6 are small residues; h) if base 3 in the quadruplet is C, then position +3 in the α-helix is Ser, Asp, Glu, Leu, Thr or Val; i) if base 2 in the quadruplet is G, then position −1 in the α-helix is Arg; j) if base 2 in the quadruplet is A, then position −1 in the α-helix is Gln; k) if base 2 in the quadruplet is T, then position −1 in the α-helix is Asn or Gln; l) if base 2 in the quadruplet is C, then position −1 in the α-helix is asp; m) if base 1 in the quadruplet is G, then position +2 is Asp; n) if base 1 in the quadruplet is A, then position +2 is not Asp; o) if base 1 in the quadruplet is C, then position +2 is not Asp; p) if base 1 in the quadruplet is T, then position +2 is Ser or Thr; (iii) preparing a nucleic acid encoding the binding protein of (ii); and (iv) introducing the nucleic acid of (iii) into a cell, whereby the encoded nucleic acid binding protein is expressed and binds to the target sequence.