DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 16 October 2025 has been entered.
Application Status
This action is written in response to applicant’s correspondence received 16 October 2025. Claims 19, 23, 32-34, 36-41, and 43-46 are currently pending. Accordingly, claims 19, 23, 32-34, 36-41, and 43-46 are examined herein. The restriction requirement mailed 21 July 2022 is still deemed proper. Applicant's elected Group V and SEQ ID NOs: 27, 123, and 220 without traverse in the reply filed 30 September 2022.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 19, 32-34, 41, and 43 is/are rejected under 35 U.S.C. 103 as being unpatentable over Barrangou (PG Pub No. WO 2016/033298 A1, published 3 March 2016) in view of Briner (Molecular cell 56.2 (2014): 333-339).
Regarding claim 19, Barrangou is drawn to an invention concerned with methods and compositions comprising novel CRISPR polypeptides and polynucleotides for site-specific cleavage and nicking of nucleic acids (Abstract). Barrangou teaches a method of transcriptional control of a target DNA comprising contacting the target DNA with a chimeric sgRNA molecule and a deactivated Cas9 polypeptide (i.e., a Cas9 polypeptide that is unable to cleave target DNA but can bind to an sgRNA) that can bind to the target DNA, thereby controlling transcription of the target DNA (pg. 3, line 30 to pg. 4, line 4, pg. 9, lines 6-10; see FIG. 6C). Barrangou teaches that the chimeric sgRNA molecule comprises (a) a crRNA comprising a 3' region and a 5' region, wherein the 3' region comprises at least 10 consecutive nucleotides of a CRISPR repeat and the 5' region comprises at least 20 consecutive nucleotides of a spacer sequence located immediately upstream of the repeat (pg. 29, lines 17-27). Barrangou teaches that the chimeric sgRNA molecule comprises (b) a tracrRNA comprising a 5' and 3' region, wherein at least a portion of the 5' region of the tracrRNA is complementary to the 3' region of the crRNA and the 3' region of said tracrRNA forms secondary structures (e.g., hairpin structures) (pg. 29, lines 17-27). Barrangou teaches that the chimeric sgRNA molecule comprises, from 5’ to 3’, (i) a stem comprising a duplex between the 5’ end of the tracrRNA and the repeat of the crRNA, (ii) a nexus hairpin, and (iii) at least one terminal hairpin (pg. 8, lines 20-21; see Fig. 1). Barrangou teaches the use of a nexus hairpin having 100% identity to nucleotides 67-92 of the claimed SEQ ID NO: 428 (pg. 11, lines 9-11; see L. rhamnosus Cas9 sgRNA in Fig. 19 and in previously attached sequence alignment).
Regarding claims 41 and 43, Barrangou teaches that the sgRNA crRNA can be derived from Lactobacillus sp. (pg. 4, lines 20-26).
Barrangou does not teach or suggest that the nexus comprises at least one mutation selected from an insertion, substitution, and/or deletion of about one to five base pairs located from nucleotide 67 to nucleotide 92 of the claimed SEQ ID NO: 428 such that the GC content of the nexus hairpin is increased when compared to a construct comprising the nexus hairpin without at least one mutation (Claim 19).
However, one of ordinary skill in the art would have considered the teachings of Briner as both references are common fields of endeavor pertaining to the study of Cas9 sgRNAs.
Briner is drawn to a study concerned with identifying and modifying crRNA:tracrRNA duplexes that direct Cas9 endonuclease cleavage activity (Abstract). Briner teaches that RNA- guided Cas9 endonucleases specifically target and cleave DNA in a sequence-dependent manner and have been widely used for programmable genome editing (Abstract). Briner teaches the use of a Cas9 sgRNA that comprises secondary structures including a stem, nexus hairpin, and at least one terminal hairpin created via the hybridization of a crRNA’s 3’ CRISPR repeat and tracrRNA’s 5’ region (pg. 336; see Figure 2). Briner teaches that the Cas9’s SgRNA nexus hairpins are relatively tolerant to sequence variations, including nucleotide substitutions, insertions, and deletions (i.e., an insertion, substitution, and/or deletion of at least one nucleotide in the nexus) (pg. 334; see Table S1 and green sgRNA in Figure 2). Briner teaches that the Cas9’s nexus can have additional cytosines and guanines inserted (i.e., the GC content of the sgRNA’s nexus was increased when compared to an sgRNA’s nexus not comprising the insertions in the nexus) (Table S1, variant 17). Briner teaches that the nexus is one of the most critical features of Cas9 sgRNAs and teaches that mutating the nexus hairpins opens new avenues for the exploitation of novel Cas9 proteins, with the potential to harness the diversity of natural Cas9 orthologs, including short Cas9 variants for convenient packaging and delivery (pg. 337).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the artificial sgRNA of Barrangou via the inclusion of at least one insertion in the nexus hairpin such that its GC content increased, as described by Briner. A person of ordinary skill in the art would have been motived to do so in order to facilitate specific DNA targeting. A person of ordinary skill in the art would have had a reasonable expectation of success because both Barrangou and Briner teach the use of synthetic Cas9 sgRNAs that can bind to target DNA. Further, Briner teaches that increasing the GC content of the nexus via the insertion of one or more nucleotides did not abolish the sgRNA binding affinity for the target DNA.
Regarding claims 32-34, Barrangou does not teach or suggest that the insertion, substitution, and/or deletion in the synthetic nucleic acid construct comprises replacing a pair of complementary base pairs with a pair of non-complementary nucleotides (Claim 32), replacing a complementary base pair with a different complementary base pair (Claim 33), or replacing a pair of non-complementary nucleotides with a different pair of non-complementary nucleotides (Claim 34).
However, as discussed above and applied to claim 19, one of ordinary skill in the art would have considered the teachings of Briner as both references are analogous prior art pertaining to the use of Cas9 guide RNAs.
Briner teaches that a Cas9 sgRNA stem can be mutated such that a complementary base pair is replaced with a pair of non-complementary base pairs (Table S1, variant 3). Briner teaches that the S. pyogenes stem can be mutated such that a complementary base pair is replaced with a different complementary base pair (Table S1, variant 2). Briner teaches that the S. pyogenes stem can be mutated such that non-complementary nucleotides are replaced with different non-complementary nucleotides (Table S1, variant 7). Briner teaches that the mutations in the Cas9 sgRNA constructs can facilitate specific DNA targeting with a previously orthologous Cas9 (pg. 335). Briner teaches that Cas9 sgRNAs have stems that can comprise variable nucleotides that can be substituted for at least three different bases (pg. 336; see green sgRNA in Figure 2).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the artificial Cas9 sgRNA of Barrangou via the inclusion of at least one insertion, substitution, and/or deletion in both the stem and nexus hairpin that replaces a pair of complementary base pairs with a pair of non-complementary nucleotides, replaces a complementary base pair with a different complementary base pair, or replaces a pair of non-complementary nucleotides with a different pair of non- complementary nucleotides, as described by Briner. A person of ordinary skill in the art would have been motived to do so in order to facilitate specific DNA targeting. A person of ordinary skill in the art would have had a reasonable expectation of success because both Barrangou and Briner teach the use of synthetic Cas9 sgRNAs and Briner further teaches that the stem of the Cas9 sgRNA is tolerate to sequence variations.
Claim(s) 45 is/are rejected under 35 U.S.C. 103 as being unpatentable over Barrangou (PG Pub No. WO 2016/033298 A1, published 3 March 2016) in view of Briner (Molecular cell 56.2 (2014): 333-339) as applied to claims 19, 32-34, 41, and 43 above, and further in view of Zhang (PG Pub No. US 2014/0186919).
Regarding claim 45, Barrangou in view of Briner renders obvious claims 19, 32-34, 41, and 43 as described above.
Barrangou in view of Briner does not teach or suggest that the synthetic nucleic acid construct comprises a sequence having about 95% identity to the claimed SEQ ID NO: 404 (Claim 45).
However, one of ordinary skill in the art would have considered the teachings of Zhang as both references are common fields of endeavor pertaining to the use of synthetic guide RNAs.
Zhang is drawn to an invention concerned with compositions and methods related to components of a CRISPR complex (Abstract). Zhang teaches the use of a synthetic Cas9 guide RNA that comprises a hairpin having 94.8% sequence identity to (i.e., has about 95% identity to) the claimed SEQ ID NO: 404 ([0091]; see FIG. 8C and SEQ ID NO: 106 in previously attached sequence alignment).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute a hairpin rendered obvious by Barrangou in view of Briner for a hairpin having about 95% sequence identity to the claimed SEQ ID NO: 404, as described by Zhang. A person of ordinary skill in the art would have had a reasonable expectation of success because both Barrangou in view of Briner and Zhang are drawn towards the use of synthetic Cas9 guide RNAs comprising hairpins.
Response to Arguments
Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Applicant alleges that the repression of transcription taught in Barrangou in view of Briner is attributed to the dCas9 polypeptide and not the sgRNA. Applicant alleges that Barrangou in view of Briner does not teach an sgRNA that would necessarily result in a synthetic nucleic acid construct that prevents complete cleavage of the target DNA e.g., in the presence of a wild-type Cas9. Applicant alleges that the combination of references provides no information as to whether a mutant sgRNA would still be able to bind to a target DNA and control transcription of the same, independent of the Cas9 used.
These arguments are not found persuasive because it is noted that the claim is not limited towards a method that utilizes a specific wild-type Cas9 molecule, or any Cas9 molecule that is not deactivated, in combination with the synthetic nucleic acid construct. The functional limitations regarding the prevention of complete cleavage of target DNA is met by the combination of Barrangou and Briner because the sgRNA rendered obvious by the references can bind to the target DNA and, alongside the use of a dCas9, prevent complete cleavage of the target DNA and be utilized to control transcription of the target DNA.
Allowable Subject Matter
Regarding claims 23, 36-40, 44, and 46, the prior art does not teach the use of a synthetic nucleic acid construct comprising a stem that has at least 95% identity to the claimed SEQ ID NOs: 411-412, 414-415, 418, 420-421, 423, or 426 (see Claims 23 and 45).
The closest prior art, Barrangou (PG Pub No. US 2016/0345578 A1, published 1 December 2016) is drawn towards an invention concerned with CRISPR nucleic acids to screen for essential and non-essential genes (Abstract). Barrangou teaches the use of a synthetic Cas9 guide RNA that comprises a stem having 65.4% identity to the claimed SEQ ID NO: 414 ([0037]; see FIG. 16 and SEQ ID NO: 35 in previously attached sequence alignment).
However, Barrangou does not teach or suggest the use of a synthetic nucleic acid construct comprising a stem that has at least 95% identity to the claimed SEQ ID NOs: 411-412, 414-415, 418, 420-421, 423, or 426 (see Claims 23 and 45).
Therefore, the closest prior art does not teach or suggest the use of a synthetic nucleic acid construct comprising a stem that has at least 95% identity to the claimed SEQ ID NOs: 411-412, 414-415, 418, 420-421, 423, or 426. Accordingly, claims 23, 36-40, 44, and 46 are allowed.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KYLE T REGA whose telephone number is (571)272-2073. The examiner can normally be reached M-R 8:30-4:30, every other F 8:30-4:30 (EDT/EST).
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636