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 .
DETAILED ACTION
RESPONSE TO AMENDMENT
Status of Application/Amendments/claims
2. Applicant’s amendment filed November 13, 2025 is acknowledged. Claims 1-3 are canceled. Claims 4-5 are amended. Claims 4-5 are pending in this application Election was treated as without traverse in the reply filed on July 25, 2025.
3. Claims 4-5 are under examination in this office action.
4. Applicant’s arguments filed on November 13, 2025 have been fully considered but they are not deemed to be persuasive for the reasons set forth below.
Claim Rejections/Objections Withdrawn
5. The rejection of claims 4-5 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite is withdrawn in response to Applicant’s amendment to the claims.
Claim Rejections/Objections Maintained
In view of the amendment filed on November 13, 2025, the following rejections are maintained.
Claim Objections
6. Claim 1 is objected to because of the following informalities: The recitation “introducing into….of an effective amount of….” is objected to because the recitation should be “introducing into….an effective amount….”. Appropriate correction is required.
Claim Rejections - 35 USC § 103
7. 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 of this title, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 4-5 stand rejected under 35 U.S.C. 103 as being unpatentable over Charpentier et al. (WO2013176772; issued as US10266850; the citations are based on WO2013176772) in view of Chylinski et al. (Nucleic Acids Res. 2014; 42:6091-6105), Karvelis et al. (Methods, 2017; 121-122; 3-8) and Chen et al. (Nat. Comm 2017; 8:14958). The rejection is maintained for the reasons of record and the reasons set forth below.
Claims 4-5 as amended are drawn to a method for generating a double-strand break in a genomic DNA sequence of a unicellular or multicellular organism directly adjacent to the sequence 5'- NNNNGNA-3', the method comprising introducing into a of the unicellular or multicellular organism an effective amount of: a) a protein comprising the amino acid sequence of SEQ ID NO: 1, or a nucleic acid encoding the protein thereof, and b) a guide RNA comprising a sequence that forms a duplex with the nucleotide sequence of the genomic DNA region sequence of the unicellular or multicellular organism directly adjacent to the sequence 5'-NNNNGNA-3' and interacts with the protein comprising the amino acid sequence of SEQ ID NO:1 following the formation of the duplex, or a DNA sequence encoding the guide RNA, wherein the interaction of the protein comprising the amino acid sequence of SEQ ID NO:1 with the guide RNA and the nucleotide sequence 5'-NNNNGNA-3' results in the formation of a double-strand break in the genomic DNA sequence immediately adjacent to the sequence 5'-NNNNGNA-3'.
Response to Arguments
On p. 3-7 of the response, Applicant argues that i) Karvelis teaches NNNGTA Pam sequences. ii) There is no association between CRISPR-Cas Type II-C and NNNGTA PAM sequence; iii) A skilled artisan would not appreciate the relationship between a specific PAM sequence and its related Cas9 sequence; iv) identification and determining possible PAM sequences and how Type II-C CRISPR-Cas systems operate is not trivial.
Applicant's arguments have been fully considered but they are not found persuasive. Contrary to Applicant's arguments, the examiner asserts that based on MPEP §2141, MPEP2141-I, rationales identified by the Court in KSR (KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 398, 82 USPQ2d 1385 (2007)), MPEP2141-II, the basic factual inquires of Graham v. John Deere Co.(Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966)),and MPEP §2141.01-2147.03, the cited references do render the claimed invention obvious because:
i. Applicant cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
ii. In response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007).
In this case, Charpentier (WO2013176772) teaches a method of generating a double strand break in a DNA molecule immediately before a PAM sequence, comprising introducing into target cells including eukaryotic cells (i) a Cas9 protein; and (ii) a guide RNA comprising: a targeting sequence that hybridizes to a target sequence of the target DNA, and a protein-binding segment that interacts with the Cas9 protein (see abstract; paragraphs [0022]-[0026]; [00126]-[0149]; [0163]-[0193]), wherein the Cas9 protein includes Cas9 of Clostridium Cellulolytium having the amino acid sequence of SEQ ID NO:80, which is 100% identical to instant SEQ ID NO:1 (see the sequence alignment below; paragraphs [0013]-[0014]).
While Charpentier does not explicitly teach that the PAM sequence of the cas9 of Clostridium Cellulolytium having the amino acid sequence of instant SEQ ID NO:1 is the sequence 5’-NNNNGNA-3’, Chylinksi, Karvelis and Chen teach these limitations and provide motivation and an expectation of success because Chylinksi teaches that the Cas9 of Clostridium Cellulolytium used in the method of Charpentier is categorized as CRISPR-Cas type II-C Cas9, and Karvelis and Chen teach that the pam sequence for the CRISPR-Cas type II-C Cas9 system includes 5’-NNNNGTA-3’.
Chylinski et al. teach that type II CRISPR-Cas systems in bacteria include Cas9 isolated from Clostridium Cellulolytium and is categorized as CRISPR-Cas type II-C Cas9 (p. 6098, 2nd col, 2nd paragraph, Figures 4-5). Karvelis and Chen teach that a method of determining the PAM sequence for CRISPR-Cas type II-C and the PAM sequence for CRISPR-Cas type II-C includes 5’-NNNNGTA-3’ (see p. 4-5, table 1; Figure 2 in Karvelis and see abstract; p. 6, 2nd col., 2nd paragraph in Chen).
A person of ordinary skill in the art would have recognized that selecting and applying the known PAM sequence for CRISPR-Cas type II-C Cas9 derived from Clostridium Cellulolytium including 5’-NNNNGTA-3 disclosed by Chylinski, Karvelis, and Chen to the method of Charpentier would have yielded the predictable result of generating a double strand break in a DNA molecule directly adjacent to the PAM sequence: 5’-NNNNGNA-3’ or 5’-NNNNGTA-3, and resulted in an improved method because the Cas9 derived from Clostridium Cellulolytium used in the Charpentier’s method is a CRISPR-Cas type II-C Cas9 and the pam sequence for the CRISPR-Cas type II-C Cas9 includes 5’-NNNNGNA-3’ or 5’-NNNNGTA-3.
Using the CRISPR-Cas type II-C Cas9 derived from Clostridium Cellulolytium including 5’-NNNNGTA-3 in the Charpentier’s method would result in generating a double strand break in a DNA molecule directly adjacent to the PAM sequence: 5’-NNNNGNA-3’ or 5’-NNNNGTA-3, and expand application of the method of Charpentier in using CRISPR-Cas type II-C Cas9 in therapeutic purposes, and would increase the use of CRISPR-Cas type II-C Cas9 for pharmaceutical application and research because the Cas9 used in the Charpentier’s method is from Clostridium Cellulolytium, which is a CRISPR-Cas type II-C Cas9 and the pam sequence for the CRISPR-Cas type II-C Cas9 includes 5’-NNNNGNA-3’ or 5’-NNNNGTA-3.
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to select and apply the known PAM sequence for CRISPR-Cas type II-C Cas9 derived from Clostridium Cellulolytium including 5’-NNNNGTA-3 disclosed by Chylinski, Karvelis, and Chen to the method of Charpentier, and yield the predictable result of generating a double strand break in a DNA molecule directly adjacent to the PAM sequence: 5’-NNNNGNA-3’ or 5’-NNNNGTA-3.
Accordingly, the rejection of claims 4-5 under 35 U.S.C. 103 as being unpatentable over Charpentier in view of Chylinski, Karvelis and Chen is maintained.
Conclusion
8. NO CLAIM IS ALLOWED.
9. THIS ACTION IS MADE FINAL. 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.
10. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Chang-Yu Wang whose telephone number is (571)272-4521. The examiner can normally be reached on Monday-Thursday, 7:00am-5:30pm EST.
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Chang-Yu Wang
January 7, 2026
/CHANG-YU WANG/Primary Examiner, Art Unit 1675
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