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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 24 March 2026 has been entered.
Application Status
This action is written in response to applicant’s correspondence received 24 March 2026. Claims 1, 3-6, 10-30, and 33-41 are currently pending. Claims 16-17, 21-23, and 34-38 are withdrawn from prosecution as being drawn to non-elected subject matter. Accordingly, claims 1, 3-6, 10-15, 18-20, 24-30, 33, and 39-41 are examined herein. The restriction requirement mailed 11 February 2025 is still deemed proper. Applicant's elected Group I, clams 1-33, alongside the species of split proteins present in claims 1 and 18 without traverse in the reply filed 11 April 2025.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant' s amendments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Claim Objections
Claim 1 is objected to because of the following informalities: the claim recites the typos “a double-stranded DNA targer” in line 8 of the claim and “engineeded” in line 9 of the claim. Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 3-6, 10-15, 18-20, 24-30, 33, and 39-41 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claim 1, the scope of the claim is unclear. The claim recites “A non-Class I engineered CRISPR-Cas polynucleotide targeting system” (see lines 1-2 of Claim 1). However, the claim later recites a genus of “two or more Cas proteins or one Cas protein…” (see line 2 of the claim). Because the genus of “Cas proteins” encompasses any type of Cas protein, it is unclear if the Cas proteins are limited to non-Class I Cas proteins or if the Cas proteins themselves may be Class I Cas proteins, wherein the resulting targeting system is defined as a “Non-Class I targeting system”.
Claim 39 recites the limitation "the first nuclease domain" and “the second nuclease domain” in lines 1-2 of the claim. There is insufficient antecedent basis for these limitations in the claim. It is unclear which Cas protein the claimed first and second nuclease domains must be present within, if it is intended that both Cas proteins comprise the claimed nuclease domains, or if only one of the at least two Cas proteins needs to comprise the claimed nuclease domains.
Regarding claim 40, the claim recites the limitation "the first Cas protein" in line 1 of the claim. There is insufficient antecedent basis for this limitation in the claim. It is unclear which Cas protein the claim is referring two because claim 1 recites that there are two or more Cas proteins in the claimed system without reference to a “first Cas protein”.
Regarding claims 3-6, 10-15, 18-20, 24-30, 33, and 39-41, as the claims are dependent on claim 1 and do not rectify the 35 USC 112(b) rejection above, the claims are also rejected under 35 USC 112(b).
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1, 3-6, 10-13, and 39-41 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Adli (Nature communications 9.1 (2018): 1911).
Regarding claim 1, Adli is drawn to a study concerned with CRISPR Cas9 toolkits for genome editing (Abstract). Adli teaches the use of a CRISPR-Cas targeting system that comprises two tandem dCas9 proteins and unique sgRNAs capable of binding to each dCas9 protein (i.e., two non-Class I engineered CRSIPR proteins that are both engineered to be catalytically inactive, wherein the guide molecules are capable of forming a complex with the Cas proteins) wherein the two dCas9 proteins complex with one another, via an allosteric interaction between a protein dimer, in order to effect change in a target nucleic acid of interest (i.e., a change in gene expression within a target nucleic acid via the alteration of chromatin topology) through its guidable DNA targeting activity (i.e., the sgRNA may be designed in order to comprise an engineered spacer sequence that replaces a naturally occurring spacer sequence that redirects site-specific binding of the proteins to the target nucleic acid) (pg. 5; see Fig. 3).
Regarding claims 3-6 and 39-40, for the purposes of examination the claims are interpreted as requiring that at least one of the Cas proteins comprise the claimed nuclease domains. Further, the claims are interpreted as claiming that at least one of the two Cas proteins comprise an HNH and a RuvC domain. Adli teaches that CRISPR Cas9 proteins comprise two catalytic domains, an HNH and RuvC domain, that act together to mediate DNA double-strand breaks (pg. 6). Adli teaches that dCas9s are generated by mutating both domains wherein cleavage activity is lost (pg. 6).
Regarding claims 10-13, Adli teaches that two tandem dCas9 proteins can complex with one another, via an allosteric interaction between a protein dimer (i.e., a first and second functional domain that is activated upon allosteric interaction between the dCas9 proteins), in order to effect a change in gene expression within a target nucleic acid via the alteration of chromatin topology (pg. 5; see Fig. 3).
Regarding claim 41, Adli teaches that the two tandem dCas9 proteins can be fused to a protein dimer (i.e., a functional domain) in order to coordinate their activity in order to alter chromatin topology (pg. 5; see Fig. 3).
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.
The factual inquiries 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.
Claim(s) 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Adli (Nature communications 9.1 (2018): 1911) as applied to claims 1, 3-6, 10-13, and 39-41 above, and further in view of Konermann (PG Pub No. WO 2015/089486 A2, cited in the IDS filed 12 December 2022).
Regarding claim 19, Adli anticipates claims 1, 3-6, 10-13, and 39-41 as described above. Aldi further teaches that two nickase Cas9 proteins may be utilized in tandem to improve targeting specificity of the proteins (pg. 6). Aldi teaches that double stranded breaks induced by Cas9 proteins can be repaired by NHEJ (pg. 3; see Fig. 1).
Adli does not teach or suggest that the first and second Cas proteins allosterically interact upon target recognition (Claim 19).
Konermann is drawn towards an invention concerned with CRISPR-Cas systems and methods of using the systems (Abstract). Konermann teaches the use of two guide nucleic acids that can be utilized to direct two Cas9 nickases to sense and antisense strands of a target nucleic acid of interest such that the target nucleic acid is nicked and NHEJ is induced (i.e., the two Cas nickases allosterically interact to coordinate the nicking of a first and second strand of the same dsDNA molecule upon target recognition) ([00336]).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the tandem nickases and guide RNAs of Aldi for the nickases and guide RNAs of Konermann because it would have merely amounted to a simple substitution of one known Cas9 protein and guide RNA for another to obtain predictable results. Because both Adli and Konermann teach the coordination of two nickase Cas9 molecules for the targeting and editing of a nucleic acid of interest via the use of guide RNA molecules, one of ordinary skill in the art would have expected the nickases of Konermann to have functioned identically to the tandem nickases of Adli when present in a tandem construct in order to effect a DSB (i.e., a double-stranded break) in a target nucleic acid. Further, because Adli provides evidence that DSBs mediated by Cas9 proteins can be repaired by NHEJ, and Konermann teaches that the break induced by the nickases can be repaired by NHEJ (i.e., the break induced by the nickases of Konermann result in a DSB), one of ordinary skill in the art would have expected that the substitution would have predictably resulted in the generation of a DSB at the target nucleic acid.
Claim(s) 14-15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Adli (Nature communications 9.1 (2018): 1911) as applied to claims 1, 3-6, 10-13, and 39-41 above, and further in view of Stynen (Microbiology and molecular biology reviews 76.2 (2012): 331-382).
Regarding claims 14-15, Adli anticipates claims 1, 3-6, 10-13, and 39-41 as described above.
Adli does not teach or suggest that the functional domain is a nucleotide deaminase (Claims 14-15).
Stynen is drawn towards a study concerned with protein-protein interactions utilizing a yeast two-hybrid system (Abstract). Stynen teaches the use of a split yeast cytosine deaminase that comprises two monomers that can each be fused to different proteins such that the monomers can form a dimer (i.e., allosterically interact) and form a functional deaminase complex between the two different proteins (i.e., form a functional domain comprising a nucleotide deaminase) (pg. 352).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the protein dimer of Aldi for the split cytosine deaminase of Stynen because it would have merely amounted to a simple substitution of one known protein dimer for another to obtain predictable results. Because both Aldi and Stynen teach the use of split protein dimers that can be fused to heterologous nucleic acids and still maintain the ability to allosterically interact with one another, one of ordinary skill in the art would have expected utilizing the split deaminase of Stynen to similarly allow for the coordination of the two dCas9 molecules of Aldi.
Claim(s) 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Adli (Nature communications 9.1 (2018): 1911) as applied to claims 1, 3-6, 10-13, and 39-41 above, and further in view of Amoutzias (Trends in biochemical sciences 33.5 (2008): 220-229).
Regarding claim 18, Adli anticipates claims 1, 3-6, 10-13, and 39-41 as described above.
Adli does not teach or suggest that the first portion and the second portion comprise a split transcription protein (Claim 18).
Amoutzias is drawn towards a review study concerned with dimerization of eukaryotic transcription factors (Abstract). Amoutzias teaches the use of multiple different homotypic transcription factors (i.e., TFs), including bHLH, bZIP, NR, MADS-box, HD-ZIP NF-κB, and STATs, that can form dimers (pg. 221). Amoutzias teaches that TF families that can combine in homotypic and dimeric protein complexes create a large number of TF dimers with distinct properties, equaling or even exceeding the actual number of sequence-specific TF genes in a genome (pg. 227-228).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the protein dimer of Aldi for the split transcription factor of Amoutzias because it would have merely amounted to a simple substitution of one known protein dimer for another to obtain predictable results. Because both Aldi and Amoutzias teach the use of split protein dimers that can allosterically interact with one another, one of ordinary skill in the art would have expected utilizing the split deaminase of Amoutzias to similarly allow for the coordination of the two dCas9 molecules of Aldi.
Claim(s) 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Adli (Nature communications 9.1 (2018): 1911) as applied to claims 1, 3-6, 10-13, and 39-41 above, and further in view of Tóth (Biology direct 11 (2016): 1-14).
Regarding claim 20, Adli anticipates claims 1, 3-6, 10-13, and 39-41 as described above.
Adli does not teach or suggest the use of a Cas protein that has at least 10-35% identity to a Cas12a protein (Claim 20).
Tóth is drawn to a study concerned with Cpf1 nucleases (i.e., Cas12a nucleases) (Abstract). Tóth teaches that Cpf1 is a known CRISPR nuclease that is an equally or more effective tool than the most frequently used orthogonal Cas9 counterparts of SpCas9 (pg. 1). Tóth teaches that AsCpf1 proteins can be mutated such that the protein becomes a nickase (pg. 2). Tóth also teaches that cleavage-dead Cpf1 proteins were, and could be, generated, albeit no experiments were carried out with the dCpf1 molecules (pg. 11).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the Cas9 proteins of Aldi for the Cpf1 proteins of Tóth because it would have merely amounted to a simple substitution of one known CRISPR protein for another to obtain predictable results. Because both Adli and Tóth teach the use of CRISPR proteins that could target nucleic acids of interest and be mutated such that their cleavage activity is reduced or fully eliminated, one of ordinary skill in the art would have expected the dCpf1 proteins of Tóth to have functioned similarly to the dCas9 proteins of Adli when present in a tandem construct. Additionally, because Tóth teaches that Cpf1 proteins are equally as effective at mediating targeted nucleic acid modifications as Cas9 proteins, one of ordinary skill in the art would have expected the tandem dCpf1 construct to have successfully performed the same function of the tandem dCas9 construct of Aldi.
Claim(s) 24-30 is/are rejected under 35 U.S.C. 103 as being unpatentable over Adli (Nature communications 9.1 (2018): 1911) as applied to claims 1, 3-6, 10-13, and 39-41 above, and further in view of Lone (Genetics research international 2018.1 (2018): 3797214).
Regarding claims 24-32, Adli anticipates claims 1, 3-6, 10-13, and 39-41 as described above. Adli further teaches that AAV vectors are attractive therapeutic delivery vehicles for Cas9 (pg. 9).
Adli does not teach or suggest the use of a polynucleotide that encodes one or more components of the system of claim 1 (Claim 24). Adli does not teach or suggest that one or more regions of the polynucleotide is codon optimized for expression in a eukaryotic cell (Claim 25). Adli does not teach or suggest the use of a vector comprising the polynucleotide encoding one or more components of the system (Claim 26). Adli does not teach or suggest the use of a vector system comprising two or more vectors (Claim 27). Adli does not teach or suggest the use of a modified isolated cell comprising the polynucleotide of claim 24 (Claim 28) or a eukaryotic cell comprising the polynucleotide (Claim 29). Adli does not teach or suggest the use of a non-human organism comprising one or more cells of claim 28 (Claim 30).
Lone is drawn to a study concerned with CRISPR Cas9 systems (Abstract). Lone teaches the use of a polynucleotide that encodes Cas9 and is codon-optimized for expression in mammalian cells (pg. 3). Lone teaches that AAVs can be utilized to encode Cas9 and successfully deliver the Cas9 protein to target cells (pg. 9). Lone teaches that multiple AAVs can be utilized to deliver two different Cas9 proteins (pg. 9). Lone teaches that CRISPR/Cas9 systems can be delivered to cultured cells (i.e., a modified isolated cell) (pg. 10; see Figure 7). Lone teaches that utilizing AAVs to deliver Cas9 to target living cells is favored for gene delivery in vivo because the AAV is associated with minor immune responses and little pathogenesis (pg. 9).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the system of Adli such that a vector system comprising codon optimized polynucleotides that encode one or more components of the system and can be delivered to isolated or living non-human organisms is utilized because it would have merely amounted to a combination of prior art elements according to known methods to yield predictable results. Because Lone teaches that the disclosed AAV vector did not produce an immune response, one would have been motivated to have modified the system of Aldi in order to achieve a similar cellular phenotype when it is delivered to the cell. Additionally, because both Lone and Aldi teach the successful delivery of Cas9 proteins to cells of interest via the use of vectors, one of ordinary skill in the art would have expected codon optimizing the vector encoding the tandem dCas9 system and delivering it to different cell types to have predictably allowed for the successful expression of the system.
Claim(s) 33 is/are rejected under 35 U.S.C. 103 as being unpatentable over Adli (Nature communications 9.1 (2018): 1911) in view of Lone (Genetics research international 2018.1 (2018): 3797214) as applied to claims 24-30 above, and further in view of Liu (Acta pharmaceutica sinica B 7.3 (2017): 292-302).
Regarding claim 33, Adli in view of Lone renders obvious claims 24-30 as described above.
Adli in view of Lone does not teach or suggest the use of a plant cell (Claim 33).
Liu is drawn to a study concerned with the utilization of CRISPR/Cas9 proteins in plant cells (Abstract). Liu teaches the use of a plant codon-optimized Cas9 (pg. 294). Liu teaches that Cas9 was known to be able to be utilized in plant cells in order to edit target nucleic acids in the plant cells (pg. 297). Liu teaches that utilizing Cas9 editing in plant cells can be advantageous in developing plants that have increased yield and desirable traits (pg. 299).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the eukaryotic cells of Aldi and Lone for the plant cell of Liu because it would have merely amounted to a simple substitution of one known eukaryotic cell for another to obtain predictable results. Because both Adli and Liu teach the use of CRISPR proteins that could target nucleic acids of interest and be expressed within eukaryotic cells, one of ordinary skill in the art would have expected expressing the system of Aldi and Lone within a plant cell to have predictably resulted in the alteration of gene expression in plant cells. Further, because Liu teaches that Cas9 systems can be used to produce desirable traits in plants, one would have been motivated to have done so.
Response to Arguments
Applicant's arguments filed 24 March 2026 have been fully considered but they are not persuasive.
Applicant alleges that claim 1 requires a "non-Class I engineered CRISPR-Cas polynucleotide targeting system" and that the Examiner appears to treat this as synonymous with the Class 2 systems Adli reviews (Remarks; pg. 8). Applicant alleges that this conflates taxonomic classification with system architecture (Remarks; pg. 8).
This is not found persuasive because, as conceded by Applicant in the following sentence, “’non-Class I’ excludes natural Class 1 multi-protein systems (types I and III) and encompasses Class 2 systems (single effector proteins like Cas9)” (Remarks; pg. 8). Accordingly, the Cas9 proteins of Adli are drawn towards non-Class I Cas proteins as claimed.
Applicant alleges while Adli may review Class 2 systems extensively, Applicant's claim describes something fundamentally different: an engineered multi-protein targeting complex that uses Class 2-derived components but assembles them into a novel architecture with split functionality across multiple proteins (Remarks; pg. 8). Applicant alleges that Adli reviews conventional Class 2 systems where each Cas9 is a complete, independent single-protein effector while the instant disclosure takes Class 2 protein components and engineers them into an integrated multi-protein system with split nuclease domains, coordinated activity, and engineered structural features (Remarks; pg. 8). Applicant alleges that the claimed "non-Class I engineered" system is neither a natural Class 1 multi-protein system nor a conventional Class 2 single-protein system; it is a novel engineered architecture that uses Class 2-derived proteins as building blocks (Remarks; pg. 8).
This argument is not found persuasive because Adli teaches the use of two dCas9 proteins (i.e., two non-Class I Cas proteins) that can be assembled into a novel architecture via the use of a protein dimer in order to alter chromatin topology (i.e., Adli teaches the use of an engineered multi-protein targeting complex that can be assembled such that the non-Class I Cas proteins can have novel functionality across multiple proteins) (pg. 5; see Fig. 3). Adli further teaches that the protein dimer allows for the two individual dCas9 proteins to be utilized as building blocks order to effect change in a target nucleic acid of interest (i.e., a change in gene expression within a target nucleic acid via the alteration of chromatin topology) (pg. 5; see Fig. 3).
It is noted that the structural components of claim 1 are limited to a system comprising the following motifs: (1) two or more non-Class I Cas proteins; (2) a guide molecule capable of forming a complex with at least one Cas protein; and (3) a requirement wherein both Cas proteins are engineered to be catalytically inactive (see Claim 1). It is noted that the features upon which applicant relies (i.e., “an integrated multi-protein system with split nuclease domains, coordinated activity, and engineered structural features”) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KYLE T REGA whose telephone number is (571)272-2073. The examiner can normally be reached M-R 8:30-4:30, every other F 8:30-4:30 (EDT/EST).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached at 571-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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