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 .
Election/Restrictions
Applicant's election with traverse of Group I (claims 1-16) with a species election of Blackjack-SpCas9 (SEQ ID NO: 13) in the reply filed on 08/26/2025 is acknowledged. The traversal is on the grounds that the cited art in the restriction requirement dated 06/26/2025 (CA 3069296 A1; hereinafter Kim; previously cited) does not teach or suggest all the elements of claim 1. After searching the patent and non-patent literature for the elected invention and species, this is found persuasive. Accordingly, the restriction requirement dated 06/26/2025 is hereby withdrawn.
Accordingly, claims 1-17 are pending and under consideration.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. The earliest effective filing date to which the instant application is entitled is February 25, 2020.
Drawings
The drawings are objected to because:
The numbering of the drawings is improper (see 37 CFR 1.84). Drawings should be sequentially numbered (i.e. the instant “supplementary” drawings should be numbered sequentially rather than separated as “supplementary”). It would be remedial to update the figure numbering accordingly.
Figures 1c and 1d lack any caption or explanation in the associated brief description of the figures in the instant specification. It would be remedial to amend the instant specification to address figures 1c and 1d (see also section Specification).
The image quality of supplementary figure 1 and supplementary figures 5b and 5c is insufficient to be clearly legible and interpretable. It would be remedial to increase the image quality such that these figures are clearly legible and interpretable.
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.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
►Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
►Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. Several figures in the drawings filed 06/01/2022 include amino acid sequences with at least 4 specifically defined and enumerated residues, which must be listed with a sequence identifier (i.e. SEQ ID NO). At least figure 1b and supplementary figure 1c include such amino acid sequences.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
►Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d), at least as follows: The sequence disclosed as “Human codon optimized S. pyogenes Cas9” starting at page 59 lacks an appropriate sequence identifier. The primer sequences listed at page 62, lines 19 and 20 also lack an appropriate sequence identifier. Table 9 is disclosed to list the SEQ ID NOs associated with the sequences therein in the second column. In the interest of clarity and consistency, the Examiner notes that the second column of Table 9 is labeled “Seq#” rather than SEQ ID NO, or other such consistent nomenclature. It would be remedial to keep the labeling of sequence identifiers internally consistent, as in Tables 1 and 2 (among others).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities:
Table 4 includes identifying text boxes reading vertically to the left of the table. However, these text boxes are either not filled out or not legible at pages 47, 48, and 49 (partially). It would be remedial to correct the formatting of the vertical text boxes in Table 4.
Table 8, which begins at page 56, is formatted improperly in that it is broken at page 57 such that said break does not correspond to a page break. Furthermore, following the break in Table 8 at page 57, the structure of the table changes such that the columns from the Table 8 which begins at page 56 no longer correspond to the columns from the Table 8 which begins following the break at page 57. It would be remedial to correct the formatting of Table 8 such that it is properly broken up and the formatting is consistent.
The brief description of the drawings lacks a caption or explanation of figures 1c and 1d. It would be remedial to amend the instant specification to address figures 1c and 1d (see also section Drawings).
It appears that Applicant has incorporated superscript reference numbers at least at page 38, line 2. There is no associated numbered reference list in the instant specification. Accordingly, it is not clear what reference is being invoked. It would be remedial to remove any superscript reference numbers and replace them with a clear citation or other indication of what reference is being invoked.
Appropriate correction is required.
The disclosure is further objected to because it contains an embedded hyperlink and/or other form of browser-executable code at: page 2, lines 24 and 37; page 33, lines 18, 22, 28, and 41; page 39, line 24; and page 46, line 14. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Claim Objections
Claims 1, 2, 6-10, 12, and 15-17 are objected to because of the following informalities:
With regard to claim 1, which recites the acronyms “crRNA” and “sgRNA”, the instant claim language recites these acronyms without first defining said acronyms, which is improper. It would be remedial to amend the claim language such that it recites “CRISPR RNA (crRNA)” and “single guide RNA (sgRNA)” prior to reciting only the acronyms. Additionally, the end of line 8 into line 9 recites “an 5’ extension” (bolded emphasis added), which is grammatically improper. The article “an” is improper when preceding words articulated with an initial consonant sound. While “5” is recited as an Arabic numeral, the equivalent “five” begins with a consonant and is pronounced accordingly. It would be remedial to update the grammar of the instant claim language to be proper.
With regard to claim 2, the penultimate line of instant claim 2 recites “amino acidsand wherein” (bolded emphasis added), which is grammatically improper. It would be remedial to insert a space between “acids” and “and” for grammatical propriety and readability. Additionally, claim 2 recites the acronyms “crRNA” and “sgRNA,” which are not defined first, either in the instant claim set or in the instant claim itself. It would be remedial to amend the instant claim language to recite only the acronym(s) that are defined earlier, either in the claim set or in the claim itself.
With regard to claim 6, the Examiner notes that the grammatical structure of instant claim 6 is poorly constructed such that interpretation of claim 6 is hindered. For example, the recitation of “and the volume of insertion, and or the space filling or steric effect” (bolded emphasis added) in lines 6-7 would benefit from a slash separating “and/or” to facilitate readability and to comport with standard grammatical and/or linguistic conventions. It would be remedial to amend the language of claim 6 such that it is readily interpretable and comports with standard grammatical and/or linguistic conventions.
With regard to claim 7, the Examiner notes that the grammatical structure of instant claim 7 is poorly constructed such that interpretation of claim 7 is hindered. For example, there is no punctuation separating lines 3 and 4, 4 and 5, or 5 and 6. Additionally, the absence of any coordinating conjunction between possible species complicates the interpretation of instant claim 7 as well. It would be remedial to amend the language of claim 7 such that it is readily interpretable and comports with standard grammatical and/or linguistic conventions.
With regard to claim 8, which recites “preferably said mutation is selected from the group consisting of K848A, K1003A, R1060A” (bolded emphasis added), as set forth above regarding instant claim 7, the absence of the coordinating conjunction “or” separating the recited K1003A and R1060A substantially complicates the interpretation of instant claim 8. It would be remedial to amend the language of claim 8 such that it is readily interpretable and comports with standard grammatical and/or linguistic conventions.
With regard to claim 9, which recites “the variant Cas9 comprises a sequence selected from the group consisting of SEQ ID NOs 5 to 23, preferably SEQ ID NOs 6 to 23, more preferably SEQ ID NOs 11 to 21, highly preferably SEQ ID NO 13” (bolded emphasis added), as set forth above regarding instant claims 7 and 8, the absence of a coordinating conjunction separating the recited preferred SEQ ID NOs substantially complicates the interpretation of instant claim 9. It would be remedial to amend the language of claim 9 such that it is readily interpretable and comports with standard grammatical and/or linguistic conventions. Additionally, SEQ ID NOs 2 and 3, which are listed both in the sequence listing and in the claim itself, are also identified with their UniProt identifier. Incorporation by reference of essential material is only permitted by way of an incorporation by reference to a U.S. patent or U.S. patent application publication, which patent or patent application publication itself does not incorporate such essential material by reference. In the instant case, incorporation by reference of an electronic database which is subject to change over time (for example, UniProt entry no Q1J6W2 of SEQ ID NO 3 is no longer in the UniProt database) is improper, and the claims should only refer to the instant SEQ ID NOs. It would be remedial to remove the UniProt identifiers from the instant claim set.
With regard to claim 10, which recites “said variant Cas9 comprises a sequence selected from the following group consisting of SEQ ID NOs 6 to 23 as listed below” (bolded emphasis added), there is no such listing of SEQ ID NOs 6 to 23 below in instant claim 10. It would be remedial to amend the instant claim language to remove “as listed below” or to include the recited listing of SEQ ID NOs 6 to 23.
With regard to claim 12, which recites the acronym “crRNA,” this acronym is not defined first, either in the instant claim set or in the instant claim itself. It would be remedial to amend the instant claim language to recite only the acronym(s) that are defined earlier, either in the claim set or in the claim itself.
With regard to claim 15, which recites “a vector comprising said nucleic acid wherein preferably…” (bolded emphasis added), the grammatical structure of the instant claim language is improper, as the quoted phrase lacks a comma separating “nucleic acid” and “wherein.” It would be remedial to amend the instant claim language such that it recites “nucleic acid, wherein…” (bolded and underlined emphasis added).
With regard to claim 16, which recites “crRNA,” single guide RNA,” and “sgRNAs,” as set forth above regarding instant claim 1, it is improper to recite acronyms without first defining said acronym (i.e. at instant claim 1). Furthermore, the claim language itself should be internally consistent, meaning either the full names or the acronyms (after defining said acronym, such as at instant claim 1) of the claimed components should be recited-not a mixture thereof. It would be remedial to amend the instant claim language to be internally consistent and reflect the acronym(s) defined earlier, either in the claim set or in the claim itself.
With regard to claim 17, which recites “a method of altering the genome or epigenome of a cell, said method comprising -expressing in the cell a Cas9 protein according to claim1 or contacting the cell with said Cas9 protein, -providing a crRNA having a target specific spacer sequence, preferably a target-specific single guide RNA (sgRNA)…” (bolded emphasis added), as set forth above regarding instant claim 1, it is improper to recite acronyms such as the bolded crRNA without first defining said acronym. Furthermore, the grammatical structure of instant claim 17 is improper, as it lacks a colon or other demarcating punctuation to separate the introductory phrase regarding the claimed method and the steps of the claimed method. It would be remedial to amend the instant claim language to recite only the acronym(s) that are defined earlier, either in the claim set or in the claim itself, as well as to insert a colon or other demarcating punctuation to separate the introductory phrase and the active steps.
Appropriate correction is required.
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 1 and 11-17 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.
Claim 1 is drawn to a set of variant Cas9 proteins comprising a mutation in the surface loop proximal to the 5’ end of a target specific spacer sequence in a crRNA or sgRNA when said crRNA or sgRNA is in association with said Cas9 protein, said mutation comprising a deletion of 6 to 12 amino acids, thereby increasing both the available target space in the Cas9 protein to accommodate a 5’ extension of the spacer sequence and the fidelity of said variant Cas9 protein. Claims 11-16 are drawn to fusion proteins, ribonucleoprotein complexes, nucleic acids, vectors, cells, and kits comprising the same, while claim 17 is drawn to a method of using the same. The rejected claims thus comprise a set of variant Cas9 proteins comprising deletions of 6 to 12 amino acids in the surface loop proximal to the 5’ end of a target specific spacer sequence in a crRNA or sgRNA when said crRNA or sgRNA is in association with said Cas9 protein, all of which must retain their endogenous functions and must have increased available target space and fidelity.
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 experimentation with Streptococcus pyogenes Cas9 (SpCas9) variants. No description is provided of experimentation with any other Cas9 species, such as Cas9 from Actinomyces naeslundii (AnaCas9).
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 SpCas9 variants. The results are not necessarily predictive of variants of other Cas9 species, such as AnaCas9, as set forth below. Thus, it is impossible for one to extrapolate from the SpCas9 examples described herein those Cas9 variants 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 variant Cas9 proteins comprising a mutation in the surface loop proximal to the 5’ end of a target specific spacer sequence in a crRNA or sgRNA when said crRNA or sgRNA is in association with said Cas9 protein, said mutation comprising a deletion of 6 to 12 amino acids, thereby increasing both the available target space in the Cas9 protein to accommodate a 5’ extension of the spacer sequence and the fidelity of said variant Cas9 protein. Cas9 is a well-established and widely-known RNA-guided endonuclease that is endogenously found in many bacterial species, including (but not limited to) Streptococcus pyogenes, Staphylococcus aureus, Francisella novicida, and Actinomyces naeslundii (reviewed in Jiang and Doudna, 2017: see Figure 1b). Cas9 is a type II CRISPR endonuclease, which recognizes double stranded DNA substrates and cleaves each strand with a distinct nuclease domain (HNH or RuvC) (Jiang and Doudna, 2017: Figure 1b; page 509, paragraph 2). While Cas9 species such as SpyCas9 and AnaCas9 share a relatively conserved catalytic/functional core consisting (in part) of said RuvC and HNH domains, the orientation of these common regions relative to the nuclease lobe varies between SpyCas9 and AnaCas9 (Jiang and Doudna, 2017: page 524, paragraph 1; Jinek et al., 2014: page 1247997-5, column 1, paragraph 1-column 2, paragraph 1; Figure 3F). These differences are illustrative of the structural divergence that is thought to be responsible for the diversity of guide RNA structures and PAM specificities within the Cas9 superfamily (Jinek et al., 2014: page 1247997-5, column 2, paragraph 1). To emphasize the diversity of guide RNA structures and PAM specificities within the Cas9 superfamily and the functional implications thereof, AnaCas9 uses a distinct mechanism of PAM recognition compared to SpyCas9 (Jinek et al., 2014: page 1247997-5, column 2, paragraph 1). PAM recognition is essential for Cas9 target search and recognition (Jiang and Doudna, 2017: page 516, paragraph 2). Given that PAM recognition is essential for Cas9 function, and that PAM specificities and the structures determining these specificities are known to differ within the Cas9 superfamily, in the absence of experimental data supporting that generating the claimed mutations in non-SpyCas9 species, it is not clear to one of ordinary skill in the art whether these mutations would disrupt endogenous Cas9 function or even necessarily generate the recited functional outcomes.
Therefore, the skilled artisan would have reasonably concluded applicants were not in possession of the claimed invention for claims 1 and 11-17.
Claims 9 and 10 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 9 and 10 are drawn to variant Cas9 proteins comprising an amino acid sequence with at least 80% sequence identity to several recited SpCas9 sequences. The rejected claims thus comprise a set of amino acid sequences with a large number of variable residues, all variations of which retain their endogenous functions and must have increased available target space and fidelity.
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 variant SpCas9 proteins comprising several deletions and/or insertions, such as Blackjack-SpCas9 (Examples), as well as other defined SpCas9 variants (Table 8). However, these disclosed examples only involve the manipulation of a relatively small number of amino acid residues. These disclosed examples do not describe variant Cas9 sequences with up to approximately 273 altered amino acids, which is the threshold for sequences with at least 80% identity to the recited SpCas9 sequences.
As is known to those of skill in the art, the amino acid sequence of a protein or polypeptide determines the structure and function of said protein or polypeptide. Substitutions within said amino acid sequence that alter the sequence identity thereof may be conservative (which are more likely to preserve function and be tolerated) or nonconservative (which are less likely to preserve function and be tolerated) (reviewed in Goldstein and Pollack, 2016). Furthermore, as is known to those of skill in the art insertions or deletions of the amino acid sequence of a protein or polypeptide also necessarily have the potential to alter its structure and function. With regard to the implications of this principle for Cas9 specifically, as set forth above, the Cas9 endonuclease superfamily shares common functions of scanning and cleaving a targeted locus (reviewed in Jiang and Doudna, 2017). Furthermore, Cas9 species are known to share a relatively conserved catalytic/functional core, which may also be referred to/thought of as the active site of the Cas9 enzyme (Jiang and Doudna, 2017: page 524, paragraph 1). As is known to those of skill in the art, the active site of any enzyme is crucial to its function, as its shape and charge properties enable the enzyme to bind to a single type of substrate molecule (reviewed in Robinson, 2015; see page 4, paragraphs 2-3). Accordingly, one of ordinary skill in the art would be aware that substitutions, insertions, and/or deletions in the active site of an enzyme such as Cas9 may have profound implications for the functionality of said enzyme (such as Cas9). The instant specification is silent as to the essentiality of any particular residues or motifs that must be preserved to ensure Cas9 function, such as those that determine the Cas9 “active site” (as set forth above), which is not excluded from the “at least 80% sequence identity” recited at instant claims 9 and 10.
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 SpCas9 variant species with a relatively small number of amino acid residues being altered. The results are not necessarily predictive of any amino acid sequence with about 80% identity to the instantly recited SpCas9 sequences. 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 about 80% to the instantly recited SpCas9 species, all of which must produce a functional variant Cas9 with increased available target space and fidelity.
Therefore, the skilled artisan would have reasonably concluded applicants were not in possession of the claimed invention for claims 9 and 10.
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.
Claims 1, 2, 5, 7-9, 12, and 15-17 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 claims 1, 2, 5, 7-9, 12, and 15-17, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Allowable Subject Matter
Claims 3 and 4 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims (such that the basis of rejection set forth above is resolved following amendment). Furthermore, while claim 6 is objected to for minor informalities as set forth above (see section Claim Objections), the subject matter of claim 6 is free of the art. Therefore, upon remedying the minor informalities set forth above, claim 6 would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims (such that the basis of rejection set forth above is resolved following amendment).
The following is a statement of reasons for the indication of allowable subject matter:
While Cas9 and variants thereof (including high-fidelity variants) are well-known in the art, as set forth in the instant specification and supported by a search of both the patent and non-patent literature, the instantly-claimed Cas9 variant comprising a mutation in the surface loop as set forth at instant claim 1 does not appear to have been known in the field as of the effective filing date, nor does the state of the art as of the effective filing date provide sufficient motivation to arrive at the instant invention. While Slaymaker et al., 2016 does disclose that the RuvC domain (which comprises the region of mutated amino acid residues set forth in the instant application per UniProt entry Q99ZW2) is implicated in stabilizing the nontarget strand of the target DNA and is thus a viable target to alter in order to require more stringent Watson-Crick base pairing between the RNA guide and the target DNA strand (page 84, text column 2, paragraph 2), they do not disclose the instantly claimed mutation. Additionally, CA 3069296 A1 (hereinafter Kim; previously cited) discloses the deletion of one or more amino acids in region 2-3 of SpCas9 to improve target specificity (page 12, lines 16-19; page 94, lines 9-11), which completely encompasses the instantly claimed range of 6-12 amino acids and must necessarily produce a Cas9 with the instantly claimed structure and function (see MPEP § 2114 and § 2173.05(g)), as set forth in the restriction requirement dated 06/26/2025. However, as Applicant noted in the reply dated 08/26/2025, this disclosure constitutes “a laundry list of possible mutated amino acids”; furthermore, Kim does not motivate the deletion of 6-12 amino acids specifically, as instantly claimed.
In summary, it does not appear that a person having ordinary skill in the art would have been sufficiently motivated by what was known in the field at the time of the effective filing date of the claimed invention to alter a wild-type Cas9 to arrive at the instantly claimed variant Cas9.
Conclusion
Claims 1, 2, 5, and 7-17 are rejected.
Claims 1-4, 6-10, 12, and 15-17 are objected to.
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-Th 8-5, F 8-12.
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, Ph.D./ Primary Examiner, Art Unit 1637