DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Application Status
This action is written in response to applicant’s correspondence received 04/16/2026. Claims 1 and 3-9 are currently pending and are examined herein. Claim 2 has been cancelled. Claims 1 and 3-6 have been amended.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Applicant’s submission of a translation of the foreign priority document and statement that the translation is accurate is acknowledged. The translation of said application has been made of record in accordance with 37 CFR 1.55. Accordingly, the foreign priority claim has been perfected, and the claims benefit from the 12/23/2020 filing date of the foreign priority document. U.S. PGPUB 2020/0399659 to Onishi, which shares a common inventor with the instant application, is excepted as prior art under 102(b)(1)(A) because it was published after the foreign priority application, on 12/24/2020.
Additionally, Applicant’s clear statement in the remarks of 04/16/2026 (pp. 6-7) that the claimed invention and the subject matter disclosed in Onishi were owned by, or subject to an obligation of assignment to, the same person no later than the effective filing date of the claimed invention, is acknowledged. Accordingly, U.S. PGPUB 2020/0399659 to Onishi is excepted as prior under 102(b)(2)(C).
As Onishi does not qualify as prior art under 102(a)(1) or 102(a)(2), the rejections of claims 1-9 over Onishi in view of Wacker, as set forth on pages 7-10 of the office action of 01/16/2026, are hereby withdrawn.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
Determining the scope and contents of the prior art.
Ascertaining the differences between the prior art and the claims at issue.
Resolving the level of ordinary skill in the pertinent art.
Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1 and 3-9 are rejected under 35 U.S.C. 103 as being unpatentable over U.S. PGPUB 2017/0121691 A1 to Wacker (of record, cited in a previous office action) in view of David (Florian David et al. Advances in yeast genome engineering. FEMS Yeast Research, Volume 15, Issue 1, February 2015, Pages 1-14.; of record, applicant’s submission), as evidenced by Moure (Moure et al. Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway. Nucleic Acids Res. 2008 Apr 19;36(10):3287–3296.).
Regarding claim 1, Wacker teaches a plasmid for recombination, the plasmid comprising a pair of homologous recombination sequences sandwiching a gene insertion site, a pair of endonuclease target sequences sandwiching the homologous recombination sequences, and a counter selection marker:
[0006] In one aspect, provided herein are methods for inserting contiguous sequences of DNA, including large, contiguous sequences of DNA, into host cell genomes.
[0015] …wherein the donor plasmid comprises: (i) from 5′ to 3′: (1) the recognition sequence of the restriction endonuclease; (2) a first homology region of at least 0.5 kilobases (kb), (3) a heterologous insert DNA of at least 8 kb; and (4) a second homology region of at least 0.5 kb; and (ii) a counterselection marker.
Please see also FIG. 1, which is a “schematic map of the donor plasmid pDOC-C and relevant elements” (para [0037]) and clearly shows two SceI recognition sites flanking, or sandwiching, the homology regions. In this context, the two SceI recognition sites are interpreted as equivalent to a first and second endonuclease target sequence. Moure evidences that SceI specifically cleaves double-stranded DNA at its cognate target sequences (Abstract).
Wacker does not teach that the plasmid further comprises a target-specific endonuclease gene (capable of) specifically cleaving double strands of the endonuclease target sequences in an expressible manner (i.e., operably linked to a promoter). Instead, Wacker teaches that the gene is present on a helper plasmid, under the control of an inducible promoter (see above).
David teaches a variety of plasmid configurations for recombination which all comprise some combination of homologous recombination sequences, endonuclease recognition sites, selection markers, and, in multiple cases, an expression cassette for a SceI endonuclease (see Figure 1, especially (b) and (d). These include systems such as the TREC system (Figure 1(b)), which places the SceI coding sequence on the same plasmid as the other elements. David also states that methods that “require as few transformation steps as possible” are preferred (p. 2 1st para). Therefore, David provides a teaching, suggestion or motivation to limit the number of plasmids which must be constructed and introduced to the host cell, because this would have reduced the number of transformation steps.
It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have combined the donor and helper plasmids for recombination, collectively comprising all of the recited elements, as taught by Walker, with the single plasmid approach as taught by David. One having ordinary skill would have been motivated to do so based on David’s teachings that these elements could be successfully combined on a single plasmid, as shown for the TREC system, and on David’s teachings that methods of recombination preferably should require as few transformation steps as possible.
Regarding claims 3-5, Wacker further teaches that the endonuclease recognition sites are specifically recognized by a SceI homing endonuclease and that the SceI gene is under the control of an inducible promoter:
[0037] …SceI: homing endonuclease restriction site for mobilizing the DNA from the donor plasmid
[0118] In a specific embodiment, the endonuclease encoded by the helper plasmids described herein is SceI. SceI is a member of the LAGLIDADG (SEQ ID NO: 1) DNA endonuclease family. This is a family of site-specific DNA endonucleases encoded by DNA mobile elements. Functionally, SceI is a homing restriction endonuclease that cuts an 18-base pair recognition sequence TAGGGATAACAGGGTAAT (SEQ ID NO: 3), that never occurs in the E. coli genome. The specific, rare and long recognition sequence is crucial for its application in for the invention. In certain embodiments, the SceI is under the control of an inducible promoter, e.g., the arabinose promoter.
Regarding claim 6, Wacker teaches that the plasmid comprises the gene of interest (see above).
Regarding claims 7-9, Wacker teaches the method for introducing a gene of interest into a host cell (i.e., producing a transformant per Applicant’s definition in para [0002] of the instant specification), as described above, comprising introducing the plasmid of claim 1into a host cell, where the gene of interest is incorporated into the host genome via homologous recombination, the gene of interest is expressed, and the counter selection market functions to induce the death of a host comprising the plasmid (i.e., the unintegrated plasmid):
[0091] In an exemplary embodiment, a method of inserting a large sequence of DNA (i.e., heterologous insert DNA) into the genome of a host cell comprises the use of (i) a donor plasmid comprising (a) heterologous insert DNA flanked by homology regions (HR), e.g., long homology regions (e.g., HR of any appropriate size, e.g., from 0.4-2.0 kb), which direct the site of recombination in the host cell genome (use of such HR increases efficiency of insertion), and (b) a counter selection marker that represses growth of host cells that comprise the donor plasmid, i.e., the non-integrated donor plasmid following introduction of the donor plasmid into the host cell (use of the counter selection marker eliminates false positive clones)
Response to Arguments
Applicant's arguments filed 04/16/2026 have been fully considered but they are not persuasive for the reasons that follow.
On page 8 of the remarks of 04/16/2026, Applicant notes that, “Wacker’s disclosure relates to a plasmid for recombination comprising a helper plasmid and a donor plasmid”, where, “the helper plasmid and the donor plasmid are separated, and [the] endonuclease gene exists on the helper plasmid.”. Applicant further argues that, “the function of the donor plasmid and the helper plasmid are different. In Wacker’s separate plasmid, endonuclease is expressed on the helper plasmid and [a] counter selection marker is expressed on the donor plasmid. Such design concept of Wacker’s plasmid cannot be recognized merely as a convenient arrangement but as a structure that supports operability.”. Applicant cites paragraphs [0010], [0016] and [0128] of Wacker in support of this argument. Applicant finally states that, “Wacker does not provide motivation to modify” the plasmid, “into a single transformation plasmid”, and “one of ordinary skill in the part would not have a reasonable expectation of success that equivalent operability and efficiency would be obtained” (p. 9).
Respectfully, this argument is not persuasive in part because it relies solely on the disclosures of Wacker, whereas it is the combination of Wacker and David which renders obvious the instant invention. In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Additionally, in response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, the motivation need not be found in Wacker, and in fact is found in David, which suggests combining the elements of the constructs into as few plasmids as possible to reduce transformation steps. While Applicant states that the general description of requiring as few transformation steps as possible is not sufficient, respectfully, this statement is conclusory and does not provide evidentiary support for why the motivation is not sufficient.
Applicant further argues that, “nor would a person skilled in the art be able to predict that the high transformation efficiency disclosed in the examples of the present specification could be achieved”. Respectfully, this is not persuasive at least because David provides a reasonable expectation of success by disclosing a functional single plasmid system comprising the integration cassette and the endonuclease on one plasmid (i.e., the TREC system, as discussed in the rejection above and in the previous office action). This would have led the ordinary artisan to expect that combining the endonuclease gene with the other components of the system would have led to a functional transformation plasmid.
It is noted that Applicant argues that the high transformation efficiency disclosed in the examples in the specification could not have been predicted based on the prior art. This appears to be an argument for an indication of objective evidence of nonobviousness in the form of unexpectedly improved results not taught by the prior art (MPEP 716.02(d)). However, Applicant has not supported the argument with any citations to, evidence from, or explanations of the specification or prior art, and has not shown that said evidence is commensurate in scope with the claimed plasmid.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1 and 3-9 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3 and 5-7 of U.S. Patent No. 12,338,454 B2 in view of Wacker (cited above).
Regarding claims 1 and 6, patented claims 1 and 5 recite a methods of producing a transformed yeast host comprising a plasmid which comprises the gene of interest, a pair of homologous recombination sequences, and a pair of endonuclease target sequences, wherein the circular plasmid is cleaved at the target sites to produce a fragment comprising the gene and the recombination sequences. This indicates that the structure of the plasmid has the endonuclease target sequences sandwiching the homologous sequences and gene of interest, because otherwise the fragment would not include those elements.
Patented claims 1 and 5 do not recite that the plasmid has a counter selection marker. However, Wacker teaches plasmids for transformation which comprise counter selection markers to induce the death of host cells which have the unintegrated plasmid, as already described above. It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have modified the construct used in the method of patented claim 1 by adding a counter select marker to eliminate non-transformed cells, as taught by Wacker. The ordinary artisan would have been motivated to do so and would have a reasonable expectation that such an element could be successfully included based on Wacker’s teachings that the inclusion of such a marker yields a functional plasmid able to eliminate un-transformed cells.
Regarding claim 4, patented claims 1 and 5 recites that the plasmid comprises a gene encoding the endonuclease that specifically cleaves double strands of the endonuclease target sequences.
Regarding claim 3, patented claims 2 and 6 recite that the endonuclease gene is a homing endonuclease.
Regarding claim 5, patented claims 3 and 7 recite that the plasmid comprises an inducible promoter that regulates expression of the endonuclease gene.
Regarding claims 6-9, these merely recite methods using the plasmid and describe outcomes in which the gene of interest undergoes homologous recombination and is incorporated into the host genome, as recited in patented claims 1 and 5, and further recite that a counter selection marker is used to eliminate non-transformed hosts, which is rendered obvious by Wacker.
Response to Arguments
Applicant requests that the rejection be held in abeyance pending an indication of allowable subject matter. Per MPEP 804(I)(B)(1), a complete response to a nonstatutory double patenting (NSDP) rejection is either a reply by applicant showing that the claims subject to the rejection are patentably distinct from the reference claims, or the filing of a terminal disclaimer in accordance with 37 CFR 1.321 in the pending application(s) with a reply to the Office action (see MPEP § 1490 for a discussion of terminal disclaimers). Such a response is required even when the nonstatutory double patenting rejection is provisional. As filing a terminal disclaimer, or filing a showing that the claims subject to the rejection are patentably distinct from the reference application’s claims, is necessary for further consideration of the rejection of the claims, such a filing should not be held in abeyance. Only compliance with objections or requirements as to form not necessary for further consideration of the claims may be held in abeyance until allowable subject matter is indicated. In this case, the remarks in response to the rejection do not comply with 37 CFR 1.111(b) and MPEP 714.02; see also 707.07(a). However, the response is still considered a bona fide attempt and is accepted as a complete response in the interest of compact prosecution.
Conclusion
No claim is allowed at this time.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMANDA M ZAHORIK whose telephone number is (703)756-1433. The examiner can normally be reached M-F 8:00-16:00 EST.
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/AMANDA M ZAHORIK/Examiner, Art Unit 1636
/BRIAN WHITEMAN/Primary Examiner, Art Unit 1636
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