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 .
Applicant’s response of 03/26/2026, including replacement drawings and a substitute specification, has been received and entered into the application file.
Claims 1, 7, 8, 11, 19, 24, 25, 30, 31, 32, 42, 47, and 49 were amended in the claim set filed 03/26/2026.
Claims 20-23 and 43 were canceled in the claim set filed 03/26/2026.
Claims 1-19, 24-42, and 44-50 are pending, of which claims 33-40 were previously withdrawn.
Accordingly, claims 1-19, 24-32, 41-42, and 44-50 are pending and under consideration.
Election/Restrictions
Applicant’s previous election without traverse of claims 1-32 and 41-50 (Group I) in the reply filed on 09/22/2025 is acknowledged. Claims 20-23 and 43 were canceled in the claim set filed 03/26/2026.
In the restriction requirement dated 07/22/2025, the Examiner indicated that claims 12-32 and 41-50 were in improper multiple dependent form. The amendments to the claims have obviated the basis of multiple dependency set forth in the restriction requirement dated 07/22/2025. The amendments to the claims have further required regrouping of claims 41-50 of Group II such that claims 41-50 are grouped with Group I only.
Accordingly, claims 33-40 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 09/22/2025.
Accordingly, claims 1-19, 24-32, 41-42, and 44-50 are pending and under consideration.
Information Disclosure Statement
Receipt of an information disclosure statement on 04/22/2026 is acknowledged. The signed and initialed PTO-1449 has been mailed with this action.
Status of Prior Objections/Rejections
RE: Drawings
►The drawings were previously objected to for minor informalities.
The replacement drawings filed 03/26/2026 have obviated most, but not all, of the objections of record. Those objections not repeated below are hereby withdrawn.
The Examiner notes that Applicant has filed a petition for color drawings. Said petition was filed on 03/26/2026 and is still awaiting a decision.
RE: Nucleotide and/or Amino Acid Sequence Disclosures
The previously-filed specification did not contain the requisite incorporation by reference paragraph referring to the sequence listing. The substitute specification filed 03/26/2026 has been amended to include the requisite incorporation by reference paragraph.
RE: Specification
The disclosure was previously objected to because of various minor informalities.
The substitute specification filed 03/26/2026 has obviated the basis of the objections of record. The objections of record are hereby withdrawn.
RE: Claim Objections
►Claims 2, 7, 8, 20-25, 30, 31, 47, and 49 were previously objected to for various minor informalities.
The cancellation of claims 20-23 renders the objections thereof moot.
The amendments to the instant claim set filed on 03/26/2026 have obviated the basis of the objections of record. The objections of record are hereby withdrawn.
RE: Claim Rejections - 35 USC § 112(a)
►Claims 1, 7, 8, and 20-25 were previously rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The cancellation of claims 20-23 renders the rejection thereof moot.
The amendments to instant claims 1, 7, and 8 have obviated the basis of the rejection of record. The rejection of record is hereby withdrawn.
Regarding the rejection of claims 24 and 25, the rejection of record asserts that the claimed sequence identity of 70% is too low, as such a recitation comprises a set of amino acid sequences with a large number of variable residues, all variants of which must produce functional RecT. Applicant has not presented arguments regarding the claimed threshold of 70% sequence identity, nor have the claims been amended to raise the claimed threshold. As set forth in the rejection of record, RecT sequence homologs are known to exhibit strong conservation of certain sequence motifs, such as long helices that participate in the protein-protein and protein-DNA interactions typical of the associated superfamily (reviewed in Iyer et al., 2002; see particularly page 2, column 2, 3-page 3, column 1, paragraph 1). The instant specification is silent as to the essentiality of these highly conserved sequence motifs, and the instant claim language does not limit sequence variation to regions that do not exhibit such high conservation. Accordingly, the rejection of record is hereby maintained.
RE: Claim Rejections - 35 USC § 112(b)
►Claims 11, 21-25, 30, and 47-50 were previously 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.
The cancellation of claims 20-23 renders the rejection thereof moot.
The amendments to the instant claim set have obviated the basis of most, but not all, of the rejections of record. Those rejections not repeated below are hereby withdrawn.
RE: Claim Rejections - 35 USC § 102
►Claims 1, 19-22, 26-32, and 41-44 were previously rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by WO 2019/123014 A1 (hereinafter Yoon; as cited in the IDS filed 05/11/2023).
The cancellation of claims 20-22 renders the rejection thereof moot.
Applicant has traversed the rejection of record, asserting that Yoon does not anticipate the system of amended instant claim 1, from which all other claims directly or indirectly depend.
In response, this is found persuasive. The rejection of record is hereby withdrawn. However, new grounds of rejection necessitated by amendment are set forth below.
►Claims 1, 23, 32, and 42 were previously rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhou et al., 2019 (as cited in the IDS filed 05/11/2023), as evidenced by Jiang and Doudna, 2017.
The cancellation of claim 23 renders the rejection thereof moot.
Applicant has traversed the rejection of record, asserting that Zhou (as evidenced by Jiang and Doudna) does not anticipate the system of amended instant claim 1, from which all other claims directly or indirectly depend.
In response, this is found persuasive. The rejection of record is hereby withdrawn. However, new grounds of rejection necessitated by amendment are set forth below.
RE: Claim Rejections - 35 USC § 103
►Claims 2-7, 9-11, 13, 14, 16, 18, and 45-50 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2019/123014 A1 (hereinafter Yoon; as cited in the IDS filed 05/11/2023) and Zhou et al., 2019 (as cited in the IDS filed 05/11/2023), as applied to claims 1 and 42 above, and further in view US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023), as evidenced by Iyer et al., 2002 and Kleiner et al., 2018.
►Claim 8 was previously rejected under 35 U.S.C. 103 as being unpatentable over WO 2019/123014 A1 (hereinafter Yoon; as cited in the IDS filed 05/11/2023) and Zhou et al., 2019 (as cited in the IDS filed 05/11/2023) in view of US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023), as applied to claim 2 above, and further in view of US 2016/0319260 A1 (hereinafter Joung), as evidenced by Mascini et al., 2012.
►Claim 12 was previously rejected under 35 U.S.C. 103 as being unpatentable over WO 2019/123014 A1 (hereinafter Yoon; as cited in the IDS filed 05/11/2023) and Zhou et al., 2019 (as cited in the IDS filed 05/11/2023) in view of US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023) as applied to claim 2 above, and further in view of Morita et al., 2020.
►Claim 15 was previously rejected under 35 U.S.C. 103 as being unpatentable over WO 2019/123014 A1 (hereinafter Yoon; as cited in the IDS filed 05/11/2023) and Zhou et al., 2019 (as cited in the IDS filed 05/11/2023) in view of US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023) as applied to claim 14 above, and further in view of US 9,388,430 B2 (hereinafter Liu).
►Claim 17 was previously rejected under 35 U.S.C. 103 as being unpatentable over WO 2019/123014 A1 (hereinafter Yoon; as cited in the IDS filed 05/11/2023) and Zhou et al., 2019 (as cited in the IDS filed 05/11/2023) in view of US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023) as applied to claim 16 above, and further in view of US 2014/0377868 A1 (hereinafter General Hospital; as cited in the IDS filed 04/18/2024).
►Claims 24 and 25 were previously rejected under 35 U.S.C. 103 as being unpatentable over Zhou et al., 2019 (as cited in the IDS filed 05/11/2023), as applied to claim 1 above, and further in view of US 6,787,316 B2 (hereinafter Stewart).
Applicant has traversed the rejections of record, asserting that claims 1 and 42 are amended to recite RecT as the microbial recombination protein of the instantly claimed system, which must target a nucleic acid in a eukaryotic cell. Applicant further asserts that one of ordinary skill in the art would not have reasonably expected that an annealing protein like RecT could be used interchangeably with an exonuclease like RecE in Cas9-based gene-editing systems and methods, particularly given that their mechanisms for facilitating recombination are entirely different.
In response, this is not found persuasive. As set forth in greater detail below, it was known in the field prior to the effective filing date of the instant application that RecT functions with Cas9 to enhance knock-in. WO 2020/264016 A1 (hereinafter Čermák; effectively filed 6/25/2019) discloses eukaryotic cells and related reagents, systems, methods, and compositions for increasing the frequency of homology directed repair of target editing sites with genome editing molecules (abstract). Čermák further discloses that said systems comprise a single-stranded DNA annealing protein (such as RecT), a sequence-specific endonuclease (such as Cas9 with a guide RNA), and a donor molecule (paragraphs [0009], [0055], and [0089]). Thus, the system of Čermák reads on the instantly claimed genome editing system, as set forth in greater detail below.
While Applicant’s arguments are not found persuasive, the amended claim set has necessitated new grounds of rejection, which are set forth in detail below.
RE: Double Patenting
►Claims 1-18, 23-32, and 41-50 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 4-29, and 35-43 of copending Application No. 18/687,090 (reference application; US 2025/0034594 A1), as evidenced by Iyer et al., 2002. Although the claims at issue are not identical, they are not patentably distinct from each other.
The cancellation of claims 23 renders the rejection thereof moot.
Applicant’s response filed 03/26/2026 has been fully considered but is not persuasive, as there are no arguments presented to overcome the double patenting rejection of record. As set forth in MPEP § 804, only 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. An application must not be allowed unless the required compliant terminal disclaimer is filed and/or the withdrawal of nonstatutory double patenting rejection(s) is made of record by the examiner (see 37 CFR § 1.111(b)). Accordingly, the double patenting rejection of record is maintained, as set forth in greater detail below.
►Claims 1, 2, 20, 23, 41, 42, and 47 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 23, 25, 30, 31, and 36, of copending Application No. 18/832,052 (reference application; not yet published), as evidenced by Iyer et al., 2002. Although the claims at issue are not identical, they are not patentably distinct from each other.
The cancellation of claims 20 and 23 renders the rejection thereof moot.
Upon further review of the reference application, the rejection of record is hereby withdrawn.
New/Maintained Grounds of Objection/Rejection
Drawings
The drawings are objected to because:
The legends of Figures 12A and 12B include grayscale color bars to distinguish between depicted species. However, there is very little visible difference between the various grayscale colors in the legends and in the figures themselves. It would be remedial to ensure that there are sufficient visible differences between the colors in the legend and that these differences are also clearly visible in the figures themselves in order to facilitate interpretation of the same.
Figure 15 is of insufficient quality to be clearly legible and readily interpretable. It would be remedial to increase the image quality such that it is clearly legible and readily interpretable. Additionally, each individual image set of Figure 15 includes an unlabeled image box at the bottom left (i.e. not the image boxes labeled EGFP or Merge). The associated description in the instant specification is silent as to any identification of the unlabeled image box (paragraph [0028]). It would be remedial to clearly label each image box such that one of ordinary skill in the art may readily interpret the subject matter depicted therein.
The legends of Figures 17A-17D include grayscale color bars to distinguish between depicted species. However, there is very little visible difference between the various grayscale colors in the legends and in the figures themselves. It would be remedial to ensure that there are sufficient visible differences between the colors in the legend and that these differences are also clearly visible in the figures themselves in order to facilitate interpretation of the same.
The legend of Figure 29D includes grayscale color bars to distinguish between depicted species. However, there is very little visible difference between the various grayscale colors in the legend and in the figure itself. It would be remedial to ensure that there are sufficient visible differences between the colors in the legend and that these differences are also clearly visible in the figure itself in order to facilitate interpretation of the same.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 24 and 25 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 24 and 25 are drawn to a set of RecT recombination proteins (or derivatives or variants thereof) comprising an amino acid sequence with at least 70% similarity (i.e. identity) to amino acid sequences selected from the group consisting of SEQ ID NOs: 9-14 or 9, respectively. The rejected claims thus comprise a set of amino acid sequences with a large number of variable residues, all variations of which must produce functional RecT.
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of a complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, and any combination thereof. The specification describes SEQ ID NOs: 9-14, which correspond to RecT. While Example 1 discloses systematic searching of the NCBI database of RecE/T homologs (paragraph [00127]; depicted in Figure 2A), the Examples and the specification overall are silent as to a suite of amino acid sequences with at least 70% similarity (i.e. identity) to SEQ ID NOs: 9-14 and corresponding to RecT. As shown in Appendix I, SEQ ID NOs: 9-14 (RecT) exhibit wide sequence variability within each group. For example, SEQ ID NOs: 9 and 10 are 75.2% identical, while SEQ ID NOs: 9 and 14 are 3.7% identical. Thus, both the instant specification and the sequence listing reflect a suite of amino acid sequences corresponding to RecT, but these amino acid sequences do not necessarily themselves have at least 70% similarity (i.e. identity) to each other. Accordingly, it is not clear whether a sequence that has at least 70% similarity (i.e. identity) to any one of the recited sequences would necessarily function as RecT, as instantly claimed.
Even if one accepts that the examples described in the specification meet the claim limitations of the rejected claims with regard to structure and function, the examples are only representative of SEQ ID NOs: 9-14 (RecT). The results are not necessarily predictive of any amino acid sequence with at least 70% similarity to any one of the recited sequences corresponding to RecT. Thus, it is impossible for one to extrapolate from the few examples described herein those amino acid sequences that would necessarily meet the structural/functional characteristics of the rejected claims.
The prior art does not appear to offset the deficiencies of the instant specification in that it does not describe a set of amino acid sequences with at least 70% identity to the instantly recited sequences, all variations of which must produce functional RecT. RecT sequence homologs are known to exhibit strong conservation of certain sequence motifs, such as long helices that participate in the protein-protein and protein-DNA interactions typical of the associated superfamily (reviewed in Iyer et al., 2002 (of record); see particularly page 2, column 2, 3-page 3, column 1, paragraph 1). While the instant specification does demonstrate that the conserved central core of RecT is sufficient for function (paragraph [00141]), nothing in the instant claim language requires limiting sequence variation to regions that are not the conserved central core. The instant claim language thus encompasses a wide range of amino acid sequences and derivatives or variants thereof, all versions of which must function as RecT, as set forth in greater detail below.
As set forth above, the recitation of species with at least 70% similarity (i.e. identity) to the sequence of a given SEQ ID NO encompasses a set of amino acid sequences with a large number of variable residues, all variations of which must produce functional proteins, such as RecT. However, as set forth above, under broadest reasonable interpretation, the recitation of “a derivative or variant thereof” (recited at independent claim 1 and inherited by dependent claims 24 and 25) is considered to encompass a genus of structural and functional derivatives that includes structural derivatives that are structurally related but not necessarily functionally related, as well as functional derivatives that are functionally related by not necessarily structurally related. The breadth of interpretations encompassed by these phrases is even broader than the breadth of interpretations encompassed by the recited sequence percent identities. As set forth above regarding instant claims 24 and 25, the instant disclosure provides only a few examples from which it is impossible for one to extrapolate those amino acid sequences that would necessarily meet the structural/functional characteristics of the rejected claims, and the prior art does not appear to offset these deficiencies in that it does not describe a set of amino acid sequences that would satisfy the instantly claimed “derivative or variant thereof.”
Therefore, the skilled artisan would have reasonably concluded applicants were not in possession of the claimed invention for claims 24 and 25.
Claim Rejections - 35 USC § 112(b)
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.
Claim 50 is 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.
Additionally, with regard to claim 50, which depends from instant claim 47, recites the limitation "the system, composition, or vector" in lines 2-3. There is insufficient antecedent basis for the limitation of the composition or the vector in the claim, as neither a composition nor a vector is recited at amended instant claims 1, 42, or 47, from which instant claim 50 ultimately depend. It would be remedial to amend the instant claim set such that there is sufficient antecedent basis.
Claim Rejections - 35 USC § 102
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 27, 29, 31, 32, 41, 42, and 44-50 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by WO 2020/264016 A1 (hereinafter Čermák; effectively filed 06/25/2019), as evidenced by Mathews et al., 2003 (hereinafter Mathews).
With regard to amended instant claim 1, which recites “a system for editing a nucleic acid in a eukaryotic cell, comprising:
a Cas protein;
a nucleic acid molecule comprising a guide RNA sequence that is complementary to a target DNA sequence; and
a microbial recombination protein,
wherein the microbial recombination protein is RecT, or a derivative or variant thereof,
wherein the target DNA sequence is in a eukaryotic cell,” Čermák discloses eukaryotic cells and related reagents, systems, methods, and compositions for increasing the frequency of homology directed repair of target editing sites with genome editing molecules (abstract). Čermák further discloses that said systems comprise a single-stranded DNA annealing protein (such as RecT), a sequence-specific endonuclease (such as Cas9 or Cas12a with a guide RNA), and a donor molecule (paragraphs [0009], [0055], [0089], and [0090]). The guide RNAs of Čermák are disclosed to have exact complementarity to the target sequence (paragraph [0094]). Thus, Čermák discloses a system for editing a nucleic acid in a eukaryotic cell, said system comprising a Cas protein, a guide RNA molecule, and a RecT microbial recombination protein, as instantly claimed. Accordingly, Čermák discloses each and every limitation of amended instant claim 1.
With regard to claim 27, which recites “the Cas protein [of the system of claim 1] is Cas9 or Cas12a,” as set forth above, the sequence-specific endonuclease of Čermák may be Cas9 or Cas12a (paragraphs [0089] and [0090]). Thus, Čermák discloses each and every additional limitation of instant claim 27.
With regard to claim 29, which recites “the Cas9 protein [of the system of claim 27] is a Cas9 nickase,” as set forth above, the sequence-specific endonuclease of Čermák may be Cas9 or Cas12a (paragraphs [0089] and [0090]). Čermák further discloses that the Cas9 protein may be a Cas9 nickase (paragraph [0090]). Thus, Čermák discloses each and every additional limitation of instant claim 29.
With regard to claim 31, which recites “the system of claim 1, further comprising a donor nucleic acid,” as set forth above, the systems of Čermák comprise a single-stranded DNA annealing protein (such as RecT), a sequence-specific endonuclease (such as Cas9 or Cas12a with a guide RNA), and a donor molecule (paragraphs [0009], [0055], [0089], and [0090]). Thus, Čermák discloses each and every additional limitation of instant claim 31.
With regard to claim 32, which recites “the system of claim 1, wherein the target DNA sequence is a genomic DNA sequence in a host eukaryotic cell,” as set forth above, the systems of Čermák target the genomes of eukaryotic cells (abstract; paragraph [0008]). Thus, Čermák discloses each and every additional limitation of instant claim 32.
With regard to claim 41, which recites “a eukaryotic cell comprising the system of claim 1,” as set forth above, the systems of Čermák target eukaryotic cells (abstract). Čermák further discloses cells comprising said systems (paragraph [0015]). Thus, Čermák discloses each and every limitation of instant claim 41.
With regard to claim 42, which recites “a method of altering a target genomic DNA sequence in a eukaryotic cell, comprising introducing the system of claim 1 into a eukaryotic cell comprising a target genomic DNA sequence,” as set forth above, the systems of Čermák target eukaryotic cells (abstract). Čermák further discloses methods of using said systems to edit the genomes of eukaryotic cells (abstract; paragraphs [0006]-[0008]). Thus, Čermák discloses each and every limitation of instant claim 42.
With regard to claim 44, which recites “the cell [of the method of claim 42] is a human cell,” Čermák discloses targeting human cells with the systems taught therein (paragraph [0204]). Thus, Čermák discloses each and every additional limitation of instant claim 44.
With regard to claim 45, which recites “the cell [of the method of claim 42] is a stem cell,” Čermák discloses targeting stem cells with the systems taught therein (paragraph [0205]). Thus, Čermák discloses each and every additional limitation of instant claim 45.
With regard to claim 46, which recites “the target genomic DNA [of the method of claim 42] encodes a gene product,” as set forth above, the systems of Čermák target the genomes of eukaryotic cells (abstract; paragraph [0008]). Čermák further discloses targeting the ANT1 gene of tomato plants (paragraph [0226]). As is known to those of ordinary skill in the art, the ANT1 gene encodes a MYB-factor protein (reviewed in Mathews). Thus, Čermák discloses each and every additional limitation of instant claim 46.
With regard to claim 47, which recites “the method of claim 42, wherein the introducing into a cell comprises administering the system to a subject,” as set forth above, Čermák discloses targeting the ANT1 gene of tomato plants (paragraph [0226]). As part of this procedure, Čermák discloses administering the systems taught therein to tomato protoplasts (paragraphs [0227] and [0228]), which reads on the instantly claimed administration of the system to a subject. Čermák further discloses modifying human subjects via the methods taught therein (i.e. administration of the systems taught therein) (paragraph [0134]). Thus, Čermák discloses each and every additional limitation of instant claim 47.
With regard to claim 48, which recites “the method of claim 47, wherein the subject is a human,” as set forth above, Čermák discloses modifying human subjects via the methods taught therein (i.e. administration of the systems taught therein) (paragraph [0134]). Thus, Čermák discloses each and every additional limitation of instant claim 48.
With regard to claim 49, which recites “the method of claim 47, wherein the administering comprises in vivo administration of the system,” as set forth above, Čermák discloses modifying human subjects via the methods taught therein (i.e. administration of the systems taught therein) (paragraph [0134]). Čermák further discloses that in vivo treatments are envisaged (paragraphs [0134] and p0135]). Thus, Čermák discloses each and every additional limitation of instant claim 49.
With regard to claim 50, which recites “the method of claim 47, wherein the administering comprises transplantation of ex vivo treated cells comprising the system, composition, or vector,” as set forth above, while Čermák discloses that in vivo treatments are envisaged, ex vivo treatments are also disclosed (paragraph [0135]). Thus, Čermák discloses each and every additional limitation of instant claim 50.
Claim Rejections - 35 USC § 103
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.
Claims 2-7, 9-11, 13, 14, 16, and 18 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2020/264016 A1 (hereinafter Čermák; effectively filed 06/25/2019), as applied to claim 1 above, and further in view of US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023; of record).
The disclosure of Čermák is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the additional limitations of instant claims 2-7, 9-11, 13, 14, 16, and 18.
With regard to amended claim 2, which recites “the system of claim 1, further comprising a recruitment system comprising:
at least one aptamer sequence; and
an aptamer binding protein functionally linked to the microbial recombination protein as part of a fusion protein,” as set forth above, Čermák discloses the system of claim 1. However, Čermák does not disclose the aptamer sequence and aptamer binding protein of instant claim 2. This deficiency is cured by Rutgers. Rutgers discloses a targeted gene editing system comprising a sequence targeting protein or polynucleotide encoding the same (i.e. dCas9), an RNA scaffold or DNA polynucleotide encoding the same, a non-nuclease effector fusion protein with enzymatic activity comprising an RNA binding domain, a linker sequence, and an effector domain (paragraphs [0007]-[0009]). Rutgers further discloses that in the RNA scaffold set forth above, the recruiting RNA motif and the RNA binding domain can be a pair of a non-natural RNA aptamer and a corresponding aptamer ligand or an RNA-binding section thereof (paragraph [0010]). Per Rutgers, the utilization of aptamers in the targeted gene editing system taught therein allows artificial design to target a user-specified locus for recruitment of editing machinery (paragraphs [0049]-[0053]). While Rutgers does not disclose fusion of this aptamer binding protein to the instantly claimed microbial recombination protein (rather, they disclose fusion of the same to a Cas species), Čermák discloses that the SSAPs taught therein (i.e. RecT) may be provided as fusion proteins (paragraph [0055]). Accordingly, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to fuse the aptamer binding protein of Rutgers to RecT (as disclosed in Čermák) and thus by extension to a Cas species (as disclosed in Rutgers) to predictably facilitate targeting of a user-specified locus for recruitment of editing machinery, as disclosed in Rutgers, to effectively and efficiently modify a targeted eukaryotic genome, as disclosed in Čermák. One would have been motivated to make such a modification in order to receive the expected benefit of specifically targeting a user-specified locus for recruitment of editing machinery that effectively and efficiently modifies a targeted eukaryotic genome. Accordingly, Čermák and Rutgers are considered to disclose each and every additional limitation of instant claim 2.
With regard to claim 3, which recites “the at least one aptamer sequence [of the system of claim 2] is an RNA aptamer sequence,” as set forth above regarding instant claim 2, Rutgers discloses that in the RNA scaffold set forth above, the recruiting RNA motif and the RNA binding domain can be a pair of non-natural RNA aptamer and a corresponding aptamer ligand or an RNA-binding section thereof (paragraph [0010]). Accordingly, Rutgers discloses each and every additional limitation of instant claim 3.
With regard to claim 4, which recites "the nucleic acid molecule [of the system of claim 3] comprises the at least one RNA aptamer sequence," as set forth above regarding instant claim 2, Rutgers discloses in the RNA scaffold set forth above, the recruiting RNA motif and the RNA binding domain can be a pair of a non-natural RNA aptamer and a corresponding aptamer ligand or an RNA-binding section thereof (paragraph [0010]). Rutgers additionally discloses that the aforementioned RNA scaffold component comprising an aptamer and its corresponding binding protein ligands further comprises the gRNA motif for specific DNNRNA sequence recognition (paragraph [0053]). As recited in instant claim 1, the claimed nucleic acid molecule comprises a guide RNA sequence that is complementary to a target DNA sequence. Accordingly, it is considered that the RNA scaffold component comprising an aptamer and its corresponding binding protein ligands further comprising the gRNA motif for specific DNA/RNA sequence recognition of Rutgers (paragraph [0053]) reads on the instantly claimed nucleic acid molecule comprising a guide RNA sequence and the at least one RNA aptamer sequence. Accordingly, Rutgers discloses each and every additional limitation of instant claim 4.
With regard to claim 5, which recites "the nucleic acid molecule [of the system of claim 4] comprises two RNA aptamer sequences," Rutgers discloses that increasing the number of RNA recruitment scaffolds enhances mutation frequency of the system without altering its specificity and further that adding tandem multimeric recruiting scaffolds (such as the RNA aptamers disclosed therein) increases effector presence on the target region, thereby enhancing the system's efficacy (paragraphs [0182] and [0183]). This modular design facilitates the engineering process and opens up the possibility of further improving the system (paragraph [0184]). Accordingly, Rutgers discloses each and every additional limitation of instant claim 5.
With regard to claim 6, which recites "the two RNA aptamer sequences [of the system of claim 5] comprise the same sequence," as set forth above, Rutgers discloses that increasing the number of RNA recruitment scaffolds (that comprise the instantly claimed RNA aptamers) enhances mutation frequency of the system without altering its specificity (paragraphs [0182]-[0184]). Additionally, Rutgers discloses two RNA aptamer sequences comprising the same sequence of two MS2 loops (3xMS2), thereby enhancing mutation frequency (paragraph [0183]). Accordingly, Rutgers discloses each and every additional limitation of instant claim 6.
With regard to amended claim 7, which recites "the aptamer binding protein [of the system of claim 2] comprises an MS2 coat protein," Rutgers discloses that the recruiting RNA motif and the RNA binding domain of the RNA scaffold can be a pair of a non-natural RNA aptamer and corresponding aptamer ligand (as set forth above regarding instant claim 2; paragraph [001 0]). Rutgers also discloses that an MS2 coat protein is a suitable RNA binding domain (paragraph [001 0]). Given the disclosure that the utilization of aptamers in the targeted gene editing system taught therein allows artificial design to target a user-specified locus for recruitment of editing machinery (paragraphs [0049]-[0053]), it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the claimed invention to utilize an MS2 coat protein as an RNA binding domain while designing an artificial RNA aptamer associated with the same. One would have been motivated to make such a modification in order to receive the expected benefit of targeting a user-specified genomic locus with gene editing machinery, thereby editing the targeted locus. Accordingly, Rutgers discloses each and every additional limitation of instant claim 7.
With regard to claim 9, which recites "the at least one peptide aptamer sequence [of the system of claim 3] is conjugated to the Cas protein," as set forth above regarding instant claim 2, Rutgers discloses a targeted gene editing system comprising a sequence targeting protein or polynucleotide encoding the same (i.e. dCas9), an RNA scaffold or DNA polynucleotide encoding the same, a non-nuclease effector fusion protein with enzymatic activity comprising an RNA binding domain, a linker sequence, and an effector domain (paragraphs [0007]-[0009]). Rutgers further discloses obtaining the Cas proteins utilized therein as a recombinant polypeptide by linking the nucleic acid encoding the same to another nucleic acid encoding a fusion partner such as a 6x-His epitope tag (paragraph [0036]). Per paragraph [0078] of the instant specification, His tags are considered to be peptide aptamers. Accordingly, Rutgers discloses each and every additional limitation of instant claim 9.
With regard to claim 10, which recites "the at least one peptide aptamer sequence [of the system of claim 9] comprises between 1 and 24 peptide aptamer sequences," as set forth above regarding instant claim 9, Rutgers discloses obtaining the Cas proteins utilized therein as a recombinant polypeptide by linking the nucleic acid encoding the same to another nucleic acid encoding a fusion partner such as a 6x-His epitope tag (paragraph [0036]). Per paragraph [0078] of the instant specification, His tags are considered to be peptide aptamers. Thus, the recombinant polypeptide produced by linking the nucleic acid encoding the Cas protein to another nucleic acid encoding a fusion partner such as a 6x-His epitope tag reads on the instantly claimed 1 peptide aptamer sequence. Accordingly, Rutgers discloses each and every additional limitation of instant claim 10.
With regard to amended claim 11, which recites “the at least one peptide aptamer sequence [of the system of claim 9] comprises at least 2 peptide aptamer sequences and each of the at least 2 peptide aptamer sequences comprise the same sequence,” as set forth above regarding instant claims 9 and 10, Rutgers discloses obtaining the Cas proteins utilized therein as a recombinant polypeptide by linking the nucleic acid encoding the same to another nucleic acid encoding a fusion partner such as a 6xHis epitope tag (paragraph [0036]), which is considered to be a peptide aptamer per paragraph [0078] of the instant specification. While Rutgers discloses use of the 6x-His epitope tag, one of ordinary skill in the art would have been aware, prior to the effective filing date of the claimed invention, that there are multiple available His epitope tags, including the 12x-His epitope tag disclosed in Kleiner et al., 2018 (page e2, paragraph 2) that is considered to effectively comprise two 6x-His epitope tags. Per the disclosure of Kleiner et al., 2018, the 12x-His epitope tag taught therein effectively functions for protein pulldown and purification (Figure 2; page 2, paragraph 2). As disclosed in Rutgers, the fusion proteins taught therein may comprise at least one purification tag and/or epitope tag (paragraph [0087]). Therefore, as part of normal experimental optimization regarding the development of gene editing systems, one of ordinary skill in the art would have been motivated by the disclosure of Rutgers to fuse at least one purification tag and/or epitope tag, such as the 6x-His tag taught therein, or the 12x-His tag taught in Klein et al., 2018, which is considered to effectively comprise two identical 6x-His epitope tags. Accordingly, Rutgers, as evidenced by Klein et al., 2018, discloses each and every additional limitation of instant claim 11.
With regard to claim 13, which recites “the microbial recombination protein N-terminus [of the system of claim 2] is linked to the aptamer binding protein C-terminus,” as set forth above regarding instant claim 2, Rutgers discloses a targeted gene editing system comprising a sequence targeting protein or polynucleotide encoding the same (i.e. dCas9), an RNA scaffold or DNA polynucleotide encoding the same, a non-nuclease effector fusion protein with enzymatic activity comprising an RNA binding domain (i.e. an aptamer ligand or an RNA-binding section thereof), a linker sequence, and an effector domain (paragraphs [0007]-[0010]). Rutgers further discloses that the fusion protein set above comprises two or more domains (i.e. the non-nuclease effector protein and the aptamer ligand or an RNA-binding section thereof) joined by linkers, either at the N or the C terminus (paragraphs [0081]-[0083]). Accordingly, Rutgers discloses each and every additional limitation of instant claim 13.
With regard to claim 14, which recites "the fusion protein [of the system of claim 2] further comprises a linker between the microbial recombination protein and the aptamer binding protein," as set forth above regarding instant claim 13, Rutgers discloses that the fusion protein set above comprises two or more domains (i.e. the non-nuclease effector protein and the aptamer ligand or an RNA-binding section thereof) joined by linkers, either at the N or the C terminus (paragraphs [0081 ]-[0083]). Accordingly, Rutgers discloses each and every additional limitation of instant claim 14.
With regard to claims 16 and 18, which respectively recite "the fusion protein [of the system of claim 2] further comprises a nuclear localization sequence," "on the microbial recombination protein C terminus," as set forth above regarding instant claim 2, Rutgers discloses a targeted gene editing system comprising a sequence targeting protein or polynucleotide encoding the same (i.e. dCas9), an RNA scaffold or DNA polynucleotide encoding the same, a non-nuclease effector fusion protein with enzymatic activity comprising an RNA binding domain (i.e. an aptamer ligand or an RNA-binding section thereof), a linker sequence, and an effector domain (paragraphs [0007]-[0010]). Rutgers further discloses that the fusion protein set above may comprise at least one nuclear localization sequence at either the N or the C terminus of the non-nuclease effector protein, which reads on the instantly claimed microbial recombination protein (paragraphs [0084] and [0085]).
Given that Čermák discloses the system of instant claim 1, as set forth above, and that Rutgers discloses a targeted gene editing system comprising a sequence targeting protein or polynucleotide encoding the same (i.e. dCas9), an RNA scaffold or DNA polynucleotide encoding the same, a non-nuclease effector fusion protein with enzymatic activity comprising an RNA binding domain, a linker sequence, and an effector domain in which the recruiting RNA motif and the RNA binding domain can be a pair of a non-natural RNA aptamer and a corresponding aptamer ligand or an RNA-binding section thereof, as well as obtaining the Cas proteins utilized therein as a recombinant polypeptide by linking the nucleic acid encoding the same to another nucleic acid encoding a fusion partner such as a 6x-His epitope tag (i.e. a peptide aptamer), it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to fuse the aptamer and aptamer binding protein of Rutgers to the fusion RecT of Čermák to predictably facilitate targeting of a user-specified locus for recruitment of editing machinery, as disclosed in Rutgers. One would have been motivated to make such a modification in order to receive the expected benefit of specifically targeting of a user-specified locus for recruitment of editing machinery.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over WO 2020/264016 A1 (hereinafter Čermák; effectively filed 06/25/2019) in view of US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023; of record), as applied to claim 2 above, and further in view of US 2016/0319260 A1 (hereinafter Joung; of record), as evidenced by Mascini et al., 2012 (hereinafter Mascini; of record).
The combined disclosures of Čermák and Rutgers are described above and applied as before. However, these disclosures do not teach the phage N peptide aptamer binding protein of instant claim 8.
With regard to amended claim 8, which recites "the aptamer binding protein [of the system of claim 2] comprises a phage N peptide, or a functional derivative or variant thereof," as set forth above, Čermák and Rutgers collectively disclose the system of claim 2. However, neither Čermák nor Rutgers disclose a phage N peptide aptamer binding protein. This deficiency is cured by Joung, which discloses engineered CRISPR-Cas9 nucleases with altered and improved specificities, including fusion proteins comprising said engineered CRISPR-Cas9 nucleases and biological tethers including lambda N protein, which reads on the instantly claimed phage N peptide (abstract; paragraph [0012]). Joung discloses that the lambda N protein taught therein is a fixed RNA binding sequence that functions as a biological tether to recruit RNA molecules containing a specific stem-loop structure to a locale specified by the gRNA targeting sequences (paragraphs [0083] and [0087]). As reviewed in Mascini, nucleic acids and peptides have inherent stable three-dimensional structures dependent on their sequences that make them efficient binding molecules (see section 2.1). Accordingly, the biological tethers taught in Joung (such as lambda N protein) are considered to be capable of recruiting the instantly claimed RNA aptamers, which have an inherent stable three-dimensional structure (i.e. stem-loop structure) as per Mascini. Accordingly, Joung discloses each and every additional limitation of instant claim 8.
Given that Čermák and Rutgers collectively disclose the system of claim 2, as set forth above, and that Joung discloses that lambda N protein (i.e. a phage N peptide) is a fixed RNA binding sequence that functions as a biological tether to recruit RNA molecules containing a specific stem-loop structure (i.e. an RNA aptamer as per Mascini) to a locale specified by the gRNA targeting sequences of the gene editing system taught therein, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize a lambda N protein as an RNA binding domain (as disclosed in Joung) while designing an artificial RNA aptamer associated with the same (as disclosed in Rutgers). One would have been motivated to make such a modification in order to receive the expected benefit of producing a system capable of targeting a user-specified genomic locus with gene editing machinery, thereby editing the targeted locus.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over WO 2020/264016 A1 (hereinafter Čermák; effectively filed 06/25/2019) in view of US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023; of record) as applied to claim 2 above, and further in view of Morita et al., 2020 (hereinafter Morita; of record).
The combined disclosures of Čermák and Rutgers are described above and applied as before. However, these disclosures do not teach the aptamer sequence comprising a GCN4 peptide sequence of instant claim 12.
With regard to claim 12, which recites “the aptamer sequence [of the system of claim 2] comprises a GCN4 peptide sequence,” as set forth above, Čermák and Rutgers collectively disclose the system of claim 2. However, neither Čermák nor Rutgers disclose an aptamer sequence comprising a GCN4 peptide sequence. This deficiency is cured by Morita, which discloses synergistic upregulation of target genes using dCas9 attached to a SunTag, which comprises multiple copies of a GCN4 peptide tag and is capable of recruiting multiple copies of fusion proteins of anti-GCN4 peptide antibody (with TET1 and Factor X), which synergistically activate the target gene (abstract; Figures 1 and 2). Accordingly, Morita discloses the utility of a GCN4 peptide sequence fusion in recruiting components to synergistically activate a target gene, as in instant claim 12.
Given that Čermák and Rutgers collectively disclose the system of claim 2, as set forth above, and that Morita discloses the utility of a GCN4 peptide sequence fusion in recruiting components to target and synergistically activate a target gene, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to fuse the GCN4 peptide sequence of Morita to the RecT fusion protein of Čermák and Rutgers to predictably facilitate targeting of a user specified locus for recruitment of Cas9 machinery. One would have been motivated to make such a modification in order to receive the expected benefit of specifically targeting of a user specified locus for recruitment of Cas9 machinery.
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over WO 2020/264016 A1 (hereinafter Čermák; effectively filed 06/25/2019) in view of US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023; of record) as applied to claims 2 and 14 above, and further in view of US 9,388,430 82 (hereinafter Liu; of record).
The combined disclosures of Čermák and Rutgers are described above and applied as before. However, these disclosures do not teach the specific linker sequence of instant claim 15.
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With regard to claim 15, which recites "the linker [of the system of claim 14] comprises the amino acid sequence of SEQ ID NO: 15," as set forth above, Čermák and Rutgers collectively disclose the system of instant claim 14. Furthermore, Liu discloses that the XTEN linker of SEQ ID NO: 16 taught therein is a linker suitable for use with gene editing machinery (column 20, lines 57-59). As shown in the alignment below, SEQ ID NO: 16 of Liu is 100% identical to instant SEQ ID NO: 15. Accordingly, Liu discloses each and every additional limitation of instant claim 15.
Given that Čermák and Rutgers collectively disclose the system of claim 14, as set forth above, and that Liu discloses that the XTEN linker of SEQ ID NO: 16 (which is 100% identical to instant SEQ ID NO: 15) taught therein is a linker suitable for use with gene editing machinery, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the XTEN linker of SEQ ID NO: 16 taught in Liu as the linker in the system of claim 14 ( collectively disclosed by Čermák and Rutgers, as set forth above) to predictably link the microbial recombination protein (i.e. RecE) and the aptamer binding protein (as disclosed in Rutgers). One would have been motivated to make such a modification in order to receive the expected benefit of linking the microbial recombination protein and the aptamer binding protein (as disclosed in Čermák and Rutgers), thereby forming a functional gene editing complex that performs recombineering.
Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over WO 2020/264016 A1 (hereinafter Čermák; effectively filed 06/25/2019) in view of US 2018/0327784 A1 (hereinafter Rutgers; as cited in the IDS filed 05/11/2023; of record) as applied to claims 2 and 16 above, and further in view of US 2014/0377868 A1 (hereinafter General Hospital; as cited in the IDS filed 04/18/2024; of record).
The combined disclosures of Čermák and Rutgers are described above and applied as before. However, these disclosures do not teach the specific nuclear localization sequence of instant claim 17.
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With regard to claim 17, which recites "the nuclear localization sequence [of the system of claim 16] comprises the amino acid sequence of SEQ ID NO: 16," as set forth above, Čermák and Rutgers collectively disclose the system of instant claim 16. Furthermore, General Hospital discloses that SEQ ID NO: 1 taught therein is a nuclear localization sequence that is compatible with gene editing machinery (paragraph [0027]). This is consistent with the disclosure of Čermák, which discloses that the SSAP (i.e. RecT) taught therein further comprises an operably linked nuclear localization signal (paragraph [0164]). As shown in the alignment below, SEQ ID NO: 1 of General Hospital is 100% identical to instant SEQ ID NO: 16. Accordingly, General Hospital discloses each and every additional limitation of instant claim 17.
Given that Čermák and Rutgers collectively disclose the system of claim 16, as set forth above, and that General Hospital discloses that the nuclear localization sequence of SEQ ID NO: 1 (which is 100% identical to instant SEQ ID NO: 16) taught therein is a linker suitable for use with gene editing machinery, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the nuclear localization sequence of SEQ ID NO: 11 taught in General Hospital as the nuclear localization sequence in the fusion protein of the system of claim 16 (collectively disclosed by Čermák and Rutgers, as set forth above) to predictably recruit the labeled fusion protein to the nucleus, which houses the cell's genetic material. One would have been motivated to make such a modification in order to receive the expected benefit of recruiting the labeled fusion protein to the nucleus, which houses the cell's genetic material.
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over WO 2020/264016 A1 (hereinafter Čermák; effectively filed 06/25/2019) as applied to claim 1 above, and further in view of US 2004/0014220 A1 (hereinafter Siebenkotten).
The disclosure of Čermák is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the RecT origin of instant claim 19.
With regard to claim 19, which recites “the RecT recombination protein [of the system of claim 1] is derived from E. coli, a homolog thereof or a truncation variant thereof,” as set forth above, Čermák discloses the system of claim 1. However, Čermák does not disclose that the RecT taught therein is derived from E. coli, as instantly claimed. This deficiency is cured by Siebenkotten, which discloses a novel method allowing the transport of DNA into the nucleus of eukaryotic cells, said method comprising complexing the nucleic acid for insertion with a RecT derived from E. coli (abstract; paragraph [0039]). Thus, Siebenkotten discloses each and every additional limitation of instant claim 19.
Given that Čermák discloses the system of claim 1 comprising RecT, as set forth above, and that Siebenkotten discloses a method of editing eukaryotic genomes comprising complexing the nucleic acid for insertion with a RecT derived from E. coli, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to derive the RecT of Čermák from E. coli (as disclosed in Siebenkotten) to predictably produce a functional RecT for use in the editing systems disclosed in Čermák. One would have been motivated to make such a modification in order to receive the expected benefit of producing a functional RecT for use in the editing systems disclosed in Čermák.
Claims 24 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2020/264016 A1 (hereinafter Čermák; effectively filed 06/25/2019), as applied to claim 1 above, and further in view of US 6,787,316 82 (hereinafter Stewart; of record).
The disclosure of Čermák is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the RecT sequences thereof of instant claims 24 and 25.
With regard to claims 24 and 25, which recite "the system of claim 23, wherein the RecT, or derivative or variant thereof, comprises an amino acid sequence with at least 70% [identity] to [the] amino acid sequence ... of SEQ ID NO: 9," as set forth above, Čermák discloses the system of claim 1. However, while Čermák discloses the utility of RecT in the gene editing system taught therein, they are silent as to the sequence of the same. This deficiency is cured by Stewart, which discloses that SEQ ID NO: 5 taught therein is RecT, which is suitable for use in DNA cloning and manipulation (column 10, lines 31-63).
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As shown in the alignment below, SEQ ID NO: 5 of Stewart comprises 100% identity to instant SEQ ID NO: 9. Accordingly, Steward discloses each and every additional limitation of instant claims 24 and 25.
Given that Čermák discloses the system of instant claim 1, said system comprising the microbial recombination protein RecT, as set forth above, and that Stewart discloses that SEQ ID NO: 5 taught therein (which comprises 100% identity to instant SEQ ID NO: 9) is RecT and is suitable for use in DNA cloning and manipulation, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the RecT sequence taught in Stewart (SEQ ID NO: 5) in the system of Čermák to predictably target a specified locus for gene editing with said system. One would have been motivated to make such a modification in order to receive the expected benefit of targeting a specified locus for gene editing with said system.
Claim 26, 28, and 30 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2020/264016 A1 (hereinafter Čermák; effectively filed 06/25/2019), as applied to claims 1, 27, and 29 above, and further in view of WO 2019/123014 A1 (hereinafter Yoon; as cited in the IDS filed 05/11/2023; of record).
The disclosure of Čermák is described above and applied as before (see section Claim Rejections - 35 USC § 102). However, this disclosure does not teach the catalytically dead Cas protein of instant claim 26, the Cas9 derivation of instant claim 28, or the D10A mutation of instant claim 30.
With regard to claim 26, which recites “the Cas protein [of the system of claim 1] is catalytically dead,” as set forth above, while Čermák discloses that the Cas proteins taught therein may be nickase Cas proteins (paragraphs [0089] and [0090]), they do not disclose that the Cas proteins taught therein may be catalytically dead. This deficiency is cured by Yoon. As previously set forth, Yoon discloses compositions and methods involving chimeric genome engineering molecules for increasing mutation efficiency and homologous recombination rates of site-specific endonucleases such as Cas9 (abstract). While the compositions of Yoon are drawn to RecE rather than RecT, Čermák discloses that RecT is capable of facilitating targeted genome modification in eukaryotic cells in addition to the RecE of Yoon. Yoon further discloses that the chimeric polypeptides taught therein may comprise one or more domains of Cas proteins, such as a nuclease domain that may be mutated to eliminate or reduce catalytic activity thereof (paragraph [00194]). Yoon specifically discloses that the chimeric polypeptides taught therein may comprise a deactivated Cas9 lacking all nuclease activity (paragraph [00200]). Accordingly, Yoon discloses each and every limitation of instant claim 26.
With regard to claim 28, which recites "the Cas9 protein [of the system of claim 27] is wild-type Streptococcus pyogenes Cas9...," as set forth above, Čermák discloses the system of instant claims 1 and 27 (comprising a wild-type or nickase Cas9 per paragraphs [0089] and [0090]), while Yoon discloses compositions and methods involving chimeric genome engineering molecules for increasing mutation efficiency and homologous recombination rates of site-specific endonucleases such as Cas9 (abstract). Yoon specifically discloses that the chimeric polypeptides taught therein may comprise a Cas9 polypeptide derived from Streptococcus pyogenes (paragraphs [00200] and [00201]). Yoon further discloses that this Cas9 may be in wild-type form (paragraph [00195]). Accordingly, Yoon discloses each and every limitation of instant claim 28.
With regard to claim 30, which recites "the Cas9 nickase [of the system of claim 29] comprises an amino acid substitution of D10A as compared to wild-type Streptococcus pyogenes," as set forth above, Čermák discloses the system of instant claims 1 and 27 (comprising a wild-type or nickase Cas9 per paragraphs [0089] and [0090]), while Yoon discloses compositions and methods involving chimeric genome engineering molecules for increasing mutation efficiency and homologous recombination rates of site-specific endonucleases such as Cas9 (abstract). Yoon discloses that the chimeric polypeptides taught therein may comprise a Cas9 polypeptide (wild-type or a variant thereof) derived from Streptococcus pyogenes (paragraphs [00194], [00195], [00200] and [00201]). Furthermore, Yoon specifically discloses that the chimeric polypeptides taught therein may comprise a D10A variant Cas9 with nickase activity (paragraph [00200]). Accordingly, Yoon discloses each and every limitation of instant claim 30.
Given that Čermák discloses the system of claim 1 (further comprising Cas species such as a nickase Cas9), and that Yoon discloses compositions and methods involving chimeric genome engineering molecules for increasing mutation efficiency and homologous recombination rates of site-specific endonucleases such as wild-type, nickase, or catalytically dead Cas9 derived from Streptococcus pyogenes, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to substitute the catalytically dead Cas9 of Yoon for the nickase Cas9 of Čermák (and the D10A Cas9 of Yoon for the nickase Cas9 of Čermák) to predictably generate a system capable of targeting eukaryotic genomes for highly efficient mutations and homologous recombination. One would have been motivated to make such a modification in order to receive the expected benefit of generating a system capable of targeting eukaryotic genomes for highly efficient mutations and homologous recombination.
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 1-18, 24-32, and 41-50 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 4-29, and 35-43 of copending Application No. 18/687,090 (reference application; corresponds to US 2025/0034594 A1; of record; claims amended 10/01/2024), as evidenced by Iyer et al., 2002 (hereinafter Iyer; of record). Although the claims at issue are not identical, they are not patentably distinct from each other.
Copending application '090 recites a system comprising a Cas protein, a nucleic acid molecule comprising a guide RNA sequence that is complementary to a target DNA sequence, and a recombination protein, wherein the recombination protein comprises a single stranded DNA annealing protein at claim 1. Given that microbial recombination protein RecT of instant claim 1 is known to be a single stranded DNA annealing protein (Iyer: abstract), copending claim 1 discloses each and every limitation of instant claim 1.
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Copending claims 2 and 5 recite that the recombination protein comprises an amino acid sequence with at least 95% identity to a number of SEQ ID NOs, which include amino acid sequences corresponding to RecT such as copending SEQ ID NO: 171, which is 99% identical to instant SEQ ID NO: 9, as shown in the alignment below and recited at instant claims 24 and 25.
Copending claim 4 also recites that the recombination protein comprises an amino acid sequence with at least 95% identity to a number of SEQ ID NOs and/or species. SEQ ID NO: 179 of the copending application is disclosed to correspond to a Bet protein, which is recited at claim 1 of the instant application. Accordingly, copending claim 4 anticipates instant claim 1, as both recite the inclusion of Bet proteins in the editing systems taught therein.
Copending claims 6-18 recite that the system taught therein further comprises a recruitment system comprising at least one aptamer sequence and an aptamer binding protein functionally linked to the microbial recombination protein as part of a fusion protein, said aptamer(s) being RNA aptamer sequences or peptide aptamer sequences (copending claims 6-9 and 14-15) that may comprise the same sequence (claims 10 and 15). The aptamer binding protein is recited to comprise an MS2 coat protein, a phage N peptide, or a GCN4 peptide sequence (copending claims 11, 12, and 16) and is recited to be conjugated to the Cas protein (claim 13). The linkage of the recombination protein and the aptamer binding protein is addressed at copending claims 17 and 18. These same limitations are recited at instant claims 2-14.
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Copending claim 19 recites that the linker comprises the amino acid sequence of SEQ ID NO: 15, which is identical to the linker comprising the amino acid sequence of SEQ ID NO: 15 of instant claim 15 (see alignment below).
Copending claims 23-29 recite limitations regarding the Cas protein utilized in the claimed invention, as well as that the system taught therein further comprises a donor nucleic acid. These limitations are identical to those recited at instant claims 26-32.
Copending claim 34 recites a eukaryotic cell comprising the system of copending claim 1, which is patentably indistinct from the eukaryotic cell comprising the system of instant claim 1 recited at instant claim 41.
Copending claims 35-43 recite a method of altering a target genomic DNA sequence in a cell comprising introducing the system of copending claim 1 into said cell, which may be a mammalian cell, a human cell, or a stem cell. This method may target a genomic DNA sequence encoding a gene product, and the cells produced therein may be utilized in human subjects (either in vivo or ex vivo). These limitations are patentably indistinct from the methods recited at instant claims 42-50, which recite identical limitations.
Thus, copending claims 1, 2, 4-29, and 35-43 are not patentably distinct from instant claims 1-18, 24-32, and 41-50.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
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 Sarah E Allen whose telephone number is (571)272-0408. The examiner can normally be reached M-F 8-5.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Jennifer Dunston can be reached at 571-272-2916. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SARAH E ALLEN/Examiner, Art Unit 1637
/J. E. ANGELL/Primary Examiner, Art Unit 1637
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Appendix I: Multiple Sequence Alignment of Instant SEQ ID NOs: 9-14
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