Appeal No. 2006-0189 Page 3
Application No. 09/825,242
Claim 35 is representative and reads as follows:
35. A method of producing a zinc finger protein or a nucleic acid
encoding the same, comprising:
(a) providing a database comprising designations for a plurality of
precharacterized zinc finger proteins, each protein comprising at least first, second and
third fingers, and subdesignations for each of the three fingers of each of the zinc finger
proteins, wherein at least one protein in the database has a third finger that is different
from the third finger of at least one other protein in the database; a corresponding
nucleic acid sequence for each zinc finger protein, each sequence comprising at least
first, second and third triplets specifically bound by the at least first, second and third
fingers respectively in each zinc finger protein, the first, second and third triplets being
arranged in the nucleic acid sequence (3’-5’) in the same respective order as the first,
second and third fingers are arranged in the zinc finger protein (N-terminal to C-
terminal);
(b) providing a preselected target site for design of a zinc finger protein,
the target site comprising contiguous first, second and third triplets in a 3’-5’ order,
(c) for the first, second and third triplet in the target site, identifying first,
second and third sets of zinc finger protein(s) in the database, the first set comprising
zinc finger protein(s) comprising a finger specifically binding to the first triplet in the
target site, the second set comprising zinc finger protein(s) comprising a finger
specifically binding to the second triplet in the target site, the third set comprising zinc
finger protein(s) comprising a finger specifically binding to the third triplet in the target
site;
(d) outputting designations and subdesignations of the zinc finger proteins
in the first, second, and third sets identified in step (c); and
(e) producing (i) a zinc finger protein that binds to the target site
comprising a first finger from a zinc finger protein from the first set, a second finger from
a zinc finger protein from the second set, and a third finger from a zinc finger protein
from the third set, or (ii) a nucleic acid encoding the zinc finger protein.
Thus, claim 35 is directed to a method of making a zinc finger protein that has
been designed to bind to a specific target site. The method comprises providing a
database that includes designations for zinc finger proteins that each comprise at least
three zinc fingers. The claim requires that the database also include subdesignations
for each of the three zinc fingers in each protein, as well as the complete (9-nucleotide)
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