Appeal No. 2006-0189 Page 4
Application No. 09/825,242
nucleic acid sequence bound by the three zinc fingers in each of the zinc finger
proteins.
Claim 35 requires the further steps of providing a target site for the zinc finger
protein being designed (the target site being of a size that will be bound by three zinc
fingers); identifying three sets of zinc finger proteins in the database, each of which
includes proteins that include a zinc finger that will bind to one-third of the intended
target site; outputting the designations for the proteins and zinc fingers in each of the
three identified sets; and producing a zinc finger protein that includes the zinc fingers
identified as binding to part of the intended target site.
2. Obviousness
The examiner rejected claims 35, 40, 48, 49, and 53 under 35 U.S.C. § 103 as
obvious in view of Choo (PNAS),1 Choo (Nature)2 and Corbi.3 The examiner
characterized Choo (Nature) as
show[ing] a method of designing a zinc finger protein that binds to a BCR-
ABL recombined oncogene target site. . . . [E]ach triplet of the intended
binding site (shown in figure 1) was used to screen a randomized zinc
finger library. . . . Selected zinc fingers that bound a desired triplet were
combined into a set of three finger zinc finger proteins.
Examiner’s Answer, page 4. The examiner acknowledged that Choo (Nature) “does not
show the extent of precharacterization of the zinc finger proteins in the randomized zinc
finger library or a database of the randomized zinc finger library.” Id., page 5.
1 Choo et al., “Toward a code for the interactions of zinc fingers with DNA: Selection of randomized
fingers displayed on phage,” Proc. Natl. Acad. Sci. USA, Vol. 91, pp. 11163-11167 (1994).
2 Choo et al., “In vivo repression by a site-specific DNA-binding protein designed against an oncogenic
sequence,” Nature, Vol. 372, pp. 642-645 (1994).
3 Corbi et al., “Synthesis of a new zinc finger peptide; comparison of its ‘code’ deduced and ‘CASTing’
derived binding sites,” FEBS Letters, Vol. 417, pp. 71-74 (1997).
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