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 .
Status of the Claims
This office action is in response to the communication of 2/3/2026.
Claims 1-9, and 11-12 are pending.
Applicant’s election without traverse of group I claims 1-6 in the reply filed on 2/3/2026 is acknowledged.
Claims 7, 8-9, and 11-12 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected group, there being no allowable generic or linking claim.
Claims 1, 3-4, 6-9, 11 and 12 are amended.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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.
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.
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.
Jiang
Claims 1-6 are rejected under 35 U.S.C. 103 as being unpatentable over:
Jiang (Jiang, Yu, et al. "Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system." Applied and environmental microbiology 81.7 (2015): 2506-2514.) (provided in IDS of 8/28/2023)
Regarding claim 1, Jiang teaches an efficient and traceless gene editing system that was demonstrated to function in two species of the genus Enterobacteriaceae. (Jiang, Abstract). Jiang’s system comprises a dual plasmid CRISPR/Cas9 system (Jiang, Figure 1, pg. 2508, left column).
Jiang’s system comprises two plasmids, a pCAS and a pTarget plasmid. pCas in the two-plasmid system consisted of cas9 with a native promoter, λ-Red, a temperature-sensitive replicon, and an arabinose-inducible sgRNA guiding Cas9 to the pMB1 replicon of the pTarget plasmid. The (i.e., a helper plasmid A expressing a relevant functional protein). (Jiang, 2508, left column, Figure 1).
The pTarget series had two versions, pTargetT and pTargetF, which had donor DNA for recombination supplied in the plasmid pTarget and not supplied, respectively . pTargetF consisted of the sgRNA sequence, the N20 sequence, and the multiple restriction sites, with the donor DNA supplied as fragments. The pTarget plasmid expressed a target site sgRNA with a 20-nucleotide targeting sequence complementary to the genomic locus of interest. (i.e., a targeting plasmid B). (Jiang, 2508, right column, Figure 1)
Regarding the targeting plasmid B comprising a screening marker gene, Jiang teaches that their pTarget plasmids carry a spectinomycin resistance gene aadA as a screening marker gene. (Jiang, 2508, right column, Table 1).
AmpR
Jiang does not explicitly teach that the screening marker for their targeting plasmid is for ampicillin resistance, AmpR. However, Jiang teaches that the pTarget plasmid was derived from pTrc99A, which originally carried the bla gene encoding AmpR. Jiang deliberately replaced bla for aadA for reasons not disclosed, but it appears this was for experimental design reasons.
Specifically, Jiang’s system required each plasmid to have a different antibiotic resistance markers (Jiang uses kanamycin and spectinomycin) to allow independent selection of each plasmid in a combined antibiotic selection environment (i.e., a plate with kanamycin and spectinomycin would select for cells carrying both plasmids, and not just one of them). (Jiang, Table 1: General plasmids, pTrc99A, also Figure 1 caption).
It isn’t clear why ampicillin was swapped out, but it is reasonable that a skilled artisan would likely still expect ampicillin resistance to serve as a selection antibiotic at least to some degree. A person of ordinary skill in the art would have known that ampicillin/ AmpR is a commonly and routinely used selection antibiotic/ resistance gene in plasmids, as shown by pTrc99A itself as well other “general plasmids” that even just Jiang describes.
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 use an ampicillin resistance gene (AmpR), as a selection antibiotic for the second targeting plasmid. One of ordinary skill in the art would have been motivated to do so, since this combination is a simple substitution of one known element (spectinomycin resistance) for another (ampicillin resistance) to obtain predictable results (a plasmid with a known and routinely used selection antibiotic).
One of ordinary skill in the art would have had a reasonable expectation of success, since the use of a different selection antibiotic resistance gene, including AmpR, would have the predictable result of a targeting plasmid that could be selected for with ampicillin
One-step homologus recombination
Regarding the limitation that the targeting plasmid B being constructed by one-step homologus recombination, this limitation fails to distinguish claim 1 from Jiang because claim 1 is effectively a product claim directed to a “system” consisting of these two plasmids. The limitation on the method of construction of the targeting plasmid B is a process limitation describing how the plasmid is made, and not directed to a structural feature of the resulting plasmid. Even though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process.” In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (MPEP 2113II)).
There does not appear to be any structural difference in the sequence of the plasmid itself or in how it functions between a plasmid constructed by Jiang’s overlap PCR and ligation method vs. the same plasmid constructed by a one-step homologus recombination method. Thus , this process limitation thus cannot be given patentable weight in this product claim.
Salmonella
Regarding the “system for Salmonella” limitation in the preamble, this is not limiting because the body of the claim describes a complete invention and the language recited solely in the preamble does not provide any distinct definition of any of the claimed invention' s limitations, namely the body of claim 1 only includes limitations directed to structural features for the plasmids themselves, none of which are specific to Salmonella or require the system to function in or be adapted for use in Salmonella.
Thus, the preamble of the claim as presently written is not considered a limitation and is of no significance to claim construction. See Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See MPEP § 2111.02.
However, in the interest of compact prosecution, this limitation will still be considered to be limiting as it does appear in the body of a dependent claim (claim 3).
Jiang teaches that their two-plasmid system, “without any modification”, is able to successfully modify genes with 100% efficiency in two distinct members of the Enterobacteriaceae family, E. Coli (MG 1655) and Tatumella citrea (DSM 13699). (Jiang, Abstract, Table 2, experiments 12-13, pg. 2511, right column top para). Jiang specifically suggests that the observed efficient genome editing of T.citrea without strain-specific backbone modification of the two-plasmid-based CRISPR-Cas9 system suggests a possible broader applicability of this system in various Enterobacteriaceae species. Jiang goes on to say that the successful expansion of this system without any specific modification to T. citrea indicated its wide adaptability and flexibility in other Enterobacteriaceae species. (Jiang, 2511, right column). Salmonella is a well-known member of the Enterobacteriaceae family.
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 use Jiang’s composition for Salmonella. One of ordinary skill in the art would have been motivated to do so, since Jiang provides an express suggestion that their system could be used in the entire Enterobacteriaceae family without modification. One of ordinary skill in the art would have had a reasonable expectation of success, since Jiang provides an express suggestion that their system could be used in the entire Enterobacteriaceae family without modification.
Regarding claim 2, Jiang’s helper plasmid (pCas) comprises a Cas9 with a native promoter, λ-Red recombinase, a temperature-sensitive replicon, and an arabinose-inducible sgRNA guiding Cas9 to the pMB1 replicon of the pTarget plasmid (Targeting plasmid B replicon), and a kanamycin resistance gene (a plasmid A screening marker gene). ((Jiang, 2508, left column, Figure 1).
Regarding claim 3, Jiang’s targeting plasmid B (pTarget F for instance) comprises a replicon, the sgRNA sequence for a target site, the N20 sequence, multiple restriction sites, with the donor DNA supplied as fragments. (Jiang, 2508, right column, Figure 1). Jiang expressly teaches that their plasmid B may be replicated in E. Coli, and as discussed in the rejection of claim 1, the person of ordinary skill in the art would find it obvious to use Jiang’s system in Salmonella as well. The replicons and screening marker genes of Jiang’s targeting plasmid and helper plasmid are different (repA101(Ts) in pCas and pMB1 in pTarget), and are compatible with each other. (Jiang, 2508, right column, Figure 1).
Regarding claim 4, Jiang teaches an sgRNA expression frame comprising constitutive promoter pJ23119, which is an N20 (20-nucleotide) targeting sequence, the sgRNA scaffold backbone sequence, and a terminator. (Jiang, Fig. 1 b). This reads on the claimed promoter-(N)X-sgRNA backbone-terminator structure, where X in Jiang’s case is 20. Jiang’s target site DNA has a 5’(N)X-NGG-3’ structure, where N are nucleotides and X is 20 (Jiang, 2506, right column).
Regarding claim 5, Jiang uses N20 as the X of the target site. Regarding the homologus recombinant DNA fragments, Jiang teaches that their editing templates comprise upstream and downstream homology arms flanking a deletion junction for gene knock-out (Jiang, Table 2, experiments 1-3), and knock-in ((Jiang, Table 2, experiments 4-6). Regarding the limitation that the DNA fragment is in the targeting plasmid, Jiang teaches the pTargetT comprises donor DNA (Jiang, Fig 1b, pg. 2508, right column). Jiang teaches that their system simultaneously edits multiple target sites (maeA and maeB). (Jiang, Table 2, Experiment 2, p.2510, right column)).
Regarding claim 6, Jiang teaches a pTarget plasmid that encodes three sgRNA targets (pTargetT-cadA maeA maeB) (Jiang, Table 2, experiment 2 and 3, p. 2510, right column). Thus, Jiang teaches at least 3 targets with their system, i.e., that the target sites are not greater than 3.
Conclusion
Claims 1-6 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to THOMAS RUSSE AMICK whose telephone number is (571)272-5474. The examiner can normally be reached 7:30-5 M-F.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Tracy Vivlemore can be reached at (571) 272-2914. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/THOMAS R. AMICK/ Examiner, Art Unit 1638
/Tracy Vivlemore/ Supervisory Primary Examiner, Art Unit 1638
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