Patent ID: 8617807

Claim:
A method for designing a nucleic acid binding protein that binds to a target nucleotide sequence, wherein the binding protein comprises a plurality of zinc fingers of the Cys2-His2 class, wherein the second His in Cys2-His2 is His or Cys, and wherein each zinc finger has an alpha helix and amino acids numbered âˆ’1, 1, 2, 3, 4, 5, 6, 7, 8, and 9 with position 1 being the first amino acid of the alpha helix, further wherein 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 A, then position +6 in the Î±-helix is Glu, Asn or Val; b) if base 4 in the quadruplet is C, then position +6 in the Î±-helix is Ser, Thr, Val, Ala, Glu or Asn.