DETAILED ACTION
Status of the Claims
Claims 1-14 are currently pending.
Claims 12-14 are amended in the set of claims from October 28, 2022.
Claims 1-14 are the subject of this Office Action.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Objections
Claims 1, 5 and 8 are objected to because of the following informalities: claim 1 recites the identical phrase in steps ii) and iii) of “expressing the plurality of zinc fingers in a series of in vivo assays within cells that comprise the DNA substrates”, which appears to be a typo. Claim 5 recites “The method claim 4”, which appears to be a typo for “The method of claim 4”. Claim 8 recites the term “a helices”, which appears to be a typo for either “helices” or “a helix”, and also recites the term “zinc figure”, which appears to be a typo for “zinc finger”. Appropriate correction is required.
Claim Rejections – 35 U.S.C. 103(a)
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Persikov et al. and Choo et al.
Claims 1-14 are rejected under 35 U.S.C. 103 as being unpatentable over Persikov et al. (Nucleic Acids Research, 2015, 43(3):1965-1984) in view of Choo et al. (U.S. PGPub 2007/0009948 A1, cited in IDS of 10/28/2022).
Regarding claim 1(in part), Persikov discloses a method of determining amino acid sequences from a plurality of zinc fingers that bind to specific DNA substrates in a DNA sequence dependent manner, wherein the binding of at least some of the zinc fingers in the plurality is determined by expression of a selectable marker and optionally a detectable marker (e.g., as per the Abstract), the method comprising:
i) providing DNA substrates that are operably linked to expression of the selectable marker (e.g., HIS3 as per Fig. 1B), wherein each DNA substrate includes a segment comprising a DNA sequence configured to detect binding of a contiguous polypeptide comprising three distinct zinc fingers that are F1, F2, and F3, respectively, and wherein the F1, the F2 and the F3 are optionally in an N-terminal to C-terminal orientation (e.g., as per Fig. 1);
iii) expressing the plurality of zinc fingers in a series of in vivo assays within cells that comprise the DNA substrates (e.g., bacterial one-hybrid system as per Fig.1 and the Overview of experimental approach on pp. 1967-1968), wherein:
a) in each assay the F1 comprises the same amino acid sequence (e.g., amino acids are invariant for F1 in all assays as per Fig. 1);
b) F1 and F2 comprise a functional pair in each assay (e.g., as per Fig. 1A – F3 selections); and
c) in each assay one or more of positions -1, 1, 2, 3, 5 and 6 of each F3 α-helix are randomized (e.g., “libraries allowed each of the 20 possible amino acids in the -1, 1, 2, 3, 5 and 6 positions in regard to the alpha-helix of either the middle (F2) or C-terminal (F3) positions of a model Zif268-based system” as per the Overview of experimental approach on pp. 1967-1968 and as depicted in Fig. 1A – F3 selections);
iv) selecting zinc fingers that promote expression of the selectable marker (e.g., “[o]nly a positive interaction between the test finger and the site of interest will lead to an omega-guided recruitment of RNA polymerase and activate the transcription of a necessary HIS3 reporter gene” and as shown in Figure 1B); and
v) determining the sequence of the zinc fingers that promote expression of the selectable marker to identify amino acids that promote said expression (e.g., “[t]o recover these positive protein–DNA interactions, cells from each selection were pooled, DNA harvested and their C2H2-ZF constructs sequenced” as per the paragraph bridging pp. 1967-1968), wherein the identified amino acids that promote said expression are included in at least the F3 (e.g., as per the Systematic screens uncover hundreds to thousands of C2H2-ZFs binding each 3bp target section on p. 1971).
Regarding claim 2, Persikov discloses the above method, wherein all of positions -1, +1, +2, +3, +5 and +6 of each F3 α-helix are randomized (e.g., Fig. 1A – F3 selections).
Regarding claim 4, Persikov discloses the above method, wherein each assay in the series of assays comprises at least 64 million distinct F3 α-helices (e.g., 6 positions each with 20 alternatives as per the Overview of experimental approach section on pp. 1967-1968 produces a library of size 206 = 64 million).
Regarding claim 5, Persikov discloses the above method, wherein a series of at least four assays is performed (e.g., “After subsequent sequencing and filtering of recovered C2H2-ZF domains, the resulting data consist of a vast collection of DNA-binding interfaces that arise from four primary data sets (i.e. corresponding to protein selections in either F2 or F3 and at either low or high stringency)” as per p. 1971, left column).
Regarding claim 6, Persikov discloses the above method, wherein the segment of the DNA substrate configured to detect the binding in each assay in the series comprises at least one variable segment, wherein the variable segment comprises three base pairs (bp) targets for use in determining the binding.
Regarding claim 7, Persikov discloses the above method, wherein 64 distinct 3bp segments are included in each assay in the series (e.g., “screening all 64 possible 3bp targets for interactions with C2H2-ZF domains” as per p. 1967, left column).
Regarding claims 8-9, Persikov discloses the above method, wherein the series of assays is such that 64 independent selections can identify zinc fingers comprising helices that may be able to interact with each of the 64 distinct 3bp targets, and wherein sufficient selections are performed such that at least 16 billion unique zinc finger-DNA substrate interactions may be present and can be analyzed for expression of the selectable marker or the detectable marker or a combination thereof (e.g., seven positions randomized with 20 amino acids and 64 nucleotide combinations = 64 x 207 > 80 billion possible interactions), and wherein the sufficient selections comprise 384 selections (e.g., as per the MATERIALS AND METHODS section).
Regarding claim 10, Persikov discloses the above method, wherein the selectable marker is present and comprises HIS3 (e.g., “when these cells are grown on minimal media that requires the activation of HIS3 transcription, only a functional protein–DNA interaction will lead to survival of the bacteria” as per p. 1967, right column and as depicted in Fig. 1B).
Regarding claim 11, Persikov discloses the above method, wherein the detectable marker is present and comprises a fluorescent protein (e.g., GFP as per p. 1968, right column).
Regarding claims 12-14, Persikov discloses a contiguous polypeptide of claim 1, comprising a set of zinc fingers, one of which comprises an amino acid sequence of an F3 identified by the method of claim1, and a second of which comprises an F2 that was present in an assay of the method of claim 1, and wherein said contiguous polypeptide can bind with specificity to a 3bp segment of a DNA substrate that was also present in said assay, and further comprising an F1 that was present in an assay of the method of claim 1, wherein said contiguous polypeptide can bind with specificity to the 3bp segment of the DNA substrate (e.g., as per the RESULTS section).
However, it is noted that Persikov is silent as to the limitation of in each assay the F2 comprises at least one amino acid difference relative to domain 1 of other zinc fingers in other assays in the series, as set forth in claim 1, and wherein said amino acid difference is at position 6 of the F2, as set forth in claim 3.
Choo discloses randomizing position 6 in F2 in addition to several positions in F3 (e.g., as per Examples 1 and 3).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to screen the library of Persikov and including randomizing position 6 of F2. One of ordinary skill in the art would have been motivated to do so since Choo teaches that “[t]he resultant synergy between zinc fingers is overlooked in classical zinc finger library design, in which only a single zinc finger is randomised [sic] in each library” as per [0010]).
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since doing so would merely require the inclusion of randomizing an additional position in the construct with methods well known in the art (e.g., using commercially available kits and primers) and would readily be within reach for the skilled artisan.
Conclusion
No claims are allowed.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684