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 .
Application Status
This action is written in response to applicant’s correspondence received on 10/28/2025. Claims 21 and 24-34 are pending. Claim 21 has been amended. Claims 22-23 and 35 have been cancelled. All pending claims are currently under examination.
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. This Office Action is Final.
Claim Rejections - 35 USC § 103 – Updated in Response to Amendment
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.
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 21 and 24-34 are rejected under 35 U.S.C. 103 as being unpatentable over Kleinstiver (Kleinstiver BP et al. Nat Biotechnol. 2019 Mar;37(3):276-282, of record) and GenBank MBR6223972 (hereafter “’972,” NCBI BLAST search results, accession number GenBank MBR6223972, published 4/22/2021, of record) and Toth (Tóth E et al. Nucleic Acids Res. 2020 Apr 17;48(7):3722-3733). The rejection of claims 21 and 24-34 is further evidenced by Gao (Gao P et al. Cell Res. 2016 Aug;26(8):901-13, of record), Yamano (Yamano T et al. Mol Cell. 2017 Aug 17;67(4):633-645.e3, of record), and UniProt U2UMQ6 (hereinafter “’Q6” UniProt search results, accession number U2UMQ6, published 13/11/2019, of record).
Regarding claim 21, claim 21 recites an engineered nuclease comprising the amino acid sequence of SEQ ID NO 535. With regards to SEQ ID NO 535, SEQ ID NO 535 consists of a wildtype LbCas12a (i.e., LbCpf1) enzyme with the following two mutations: E156R and K547R (see page 1 of ‘972 for an alignment of SEQ ID NO 535 to wildtype LbCas12a). As will be shown in the following rejection, these two mutational sites were known in the art and furthermore a known motivation existed in the art before the time of filing to generate an LbCas12a mutant enzyme comprising the two mutations.
Regarding claim 21, Kleinstiver is a research article which teaches methods of improving Cas12a variants with increased activities and improved targeting ranges by expanding PAM site recognition sites (Title, Abstract, and throughout). Kleinstiver teaches that arginine (i.e., “R”) substitutions are known to alter and form novel PAM motifs (page 276, right column, second paragraph). Kleinstiver teaches that they discovered four mutations which displayed higher gene editing efficiencies and expanded PAM recognition sites in Cas12a enzymes: S170R, E174R, S542R, and K548R (page 276, right column, second paragraph). Kleinstiver therefore reduced the beneficial mutations to practice. Kleinstiver teaches that they made their mutations in AsCas12a (page 276, right column, second paragraph). Kleinstiver also teaches LbCas12a enzymes and their beneficial uses in gene targeting applications, where such LbCas12a enzymes are known to have advantageous properties such as the recognition of different PAM sites, the use of short crRNA, and advantages for multiplexing (e.g., page 276, left column, second paragraph). Kleinstiver further teaches that their optimized mutations “should enable wider application of Cas12a enzymes for gene and epigenetic editing,” and thereby teaches that their findings of improvements to AsCas12a enables wider applications to the Cas12a family of enzymes in general (Abstract, final line).
Kleinstiver, while teaching the AsCas12a mutations E174R and K548R, and furthermore teaching the LbCas12a enzyme, where LbCas12a is further taught to be a known Cas enzyme with useful properties to be used in gene editing, and teaches that the two R mutations provide useful properties because they expand gene editing efficiency and PAM recognition site repertoire which should apply to Cas12a enzymes in general, does not explicitly reduce to practice the LbCas12a enzyme comprising mutations E156R and K547R as shown in SEQ ID NO: 535.
‘972 is a sequence of a known LbCas12a enzyme (page 1 of ‘972). ‘972 shows 99% identity compared with SEQ ID NO: 535, with the exception of two mutations: E156R and K547R. Thus, SEQ ID NO: 535 can be characterized as the known wildtype LbCas12a ‘972 comprising two mutations: E156R and K547R.
With regards to ‘972 and its relationship with the four mutations that Kleinstiver teaches which enhance gene editing efficiency, two of these mutations in AsCas12a are E174R and K548R (page 276, right column, second paragraph). The sequence of wildtype LbCas12a ‘972 and wildtype AsCas12a (UniProt document Q6) are shown in alignment with one another on page 1 of Q6 (Q6, page 1). As seen in the alignment on page 1 of Q6, position E174 of AsCas12a is aligned with position E156 of LbCas12a, and position K548 is aligned with position K547 of LbCas12a (see specific amino acid residues of the alignment on page 1 of Q6). Furthermore, both the E174 residue and the K548 residue appear to fall within conserved domains between both the AsCas12a and LbCas12a enzymes (compare sequence conservation between the two proteins with reference to residues 171-181 of AsCas12a and 542-552 of AsCas12a). Thus, the E174R/K548R mutations taught by Kleinstiver correspond to the same amino acids of LbCas12a ‘972 during routine sequence alignment (page 1 of Q6). Thus, the AsCas12a mutation sites taught by Kleinstiver correspond to the exact residues and amino acids of ‘972.
Furthermore, by teaching both AsCas12a and LbCas12a, Kleinstiver also inherently teaches the structures and sequences of both proteins. As evidenced by Gao and Yamano, both AsCas12a and LbCas12a overlap in structural composition, where both proteins comprise two recognition lobes near the N-terminus followed by a linker domain (see Figure 1A of Gao and Figure 2A of Yamano). Thus, the 174/548 AsCas12a mutations recited in Kleinstiver correspond to positions 156 and 547 of the LbCas12a enzyme, per Q6, where the mutation sites are part of the same functional domains of both the AsCas12a and LbCas12a proteins (i.e., the first lobe of the recognition domain for the 156/174 residue and the linker domain for the 548/547 residue). Thus, presently recited SEQ ID NO 535 is reciting two mutations in LbCas12a which are known to be advantages mutations in the homologous protein AsCas12a, where such mutations occur at the same corresponding structural domains in both LbCas12a and AsCas12a, where the structural and functional domains of both proteins have been solved. There is therefore high predictability in applying the advantageous mutations of Kleinstiver to LbCas12, as Kleinstiver suggests to do, because both protein classes AsCas12a (reduced to practice by Kleinstiver) and LbCas12a (directly suggested and taught by Kleinstiver) share the same structural and functional domains at the known advantageous mutational sites, which are furthermore aligned during routine sequence alignment.
In addition, Toth is a research article focused on improved modifications to LbCas12a nucleases (Title, Abstract, and throughout). Toth teaches LbCas12a variants, where furthermore Toth directly references the study of Kleinstiver, where Toth teaches that they made analogous mutations to those taught by Kleinstiver (see page 3731 in its entirety, where reference “39” is Kleinstiver). Toth therefore builds off of the work of Kleinstiver, with the exception that they use LbCas12a enzymes, which were also taught and suggested by Kleinstiver. Toth teaches that the analogous mutations of those taught by Kleinstiver produced similarly beneficial effects for LbCas12a mutants. Thus, Toth has reduced to practice making the mutations taught and suggested by Kleinstiver in LbCas12a, and therefore teaches that such mutations are predictable and function in LbCas12a with the same effects as those of Kleinstiver.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the AsCas12a and the mutations E174R and K548R to be applied to LbCas12a positions E156R and K547R of ‘972 because such a combination is the simple substitution of one known prior art element for another with predictable results. In the present case, a practitioner would substitute the AsCas12a enzyme and its mutations sites for the LbCas12 enzyme with corresponding mutations after aligning the proteins. Kleinstiver has already taught a motivational teaching in the practice of mutating residues in Cas12a enzymes to arginine, where such mutations are known to have beneficial results such as improved gene editing efficiencies and expanded PAM recognition. The present sequence, SEQ ID NO 535, has made the same mutations which Kleinstiver has made in AsCas12a, except that the present mutations are in LbCas12a. However, applying the mutational strategy of Kleinstiver to LbCas12a is obvious given that Kleinstiver also teaches the known LbCas12a enzyme, and further teaches that the LbCas12a enzyme is known to be a useful enzyme for multiplexing applications (Introduction). Furthermore, the results are predictable because 1) AsCas12a and LbCas12a belong the same Cas12a protein family 2) the structures of the two proteins are already solved and defined 3) the mutations recited in SEQ ID NO 535 correspond to the same mutations taught by Kleinstiver’s E174 and K548 mutations in AsCas12a when the sequence is aligned with LbCas12a and 4) the mutations occur in the exact same known functional domains in both AsCas12a and LbCas12a and 5) Toth already teaches that the mutational strategy of Kleinstiver can be applied to LbCas12a enzymes with the same beneficial effects of expanding the PAM site recognition sequences. A practitioner would therefore not only be motivated to make analogous mutations in LbCas12a as taught by Kleinstiver, but the results are predictable owing to the knowledge in the art of both the sequence and structure of the two homologous Cas enzymes. Furthermore, Kleinstiver teaches only four mutations, two of which are the instant mutations in SEQ ID NO: 535; a practitioner is not selecting from a large number of options (four) when applying the AsCas12a teachings of Kleinstiver to the homologous protein LbCas12a.
Regarding claim 24, Kleinstiver teaches fusing engineered Cas enzymes to make fusion proteins (e.g., page 278, right column, third paragraph).
Regarding claim 25, Kleinstiver teaches that the Cas enzymes can be fused with a nuclear localization signal (e.g., page 283, right column, final paragraph).
Regarding claim 26, Kleinstiver teaches that the fusion protein can comprise a tag sequence (page 283, right column, final paragraph).
Regarding claim 27, Kleinstiver teaches that the composition comprising Cas enzymes further comprise guide RNAs (e.g., page 279, left column, second paragraph, “crRNA”).
Regarding claim 28, Kleinstiver teaches that Cas12a enzymes such as AsCas12a and LbCas12a interact with guide sequences (crRNA) which target nucleic acid targets (Introduction first paragraph, page 279, left column, second paragraph).
Regarding claim 29, Kleinstiver teaches that Cas12a enzymes in combination with crRNA/guideRNA can target and modify genes (e.g., Figure 2A).
Regarding claim 30, Kleinstiver teaches that the target can be in human cells (e.g., page 279, left column, second paragraph).
Regarding claim 31, Kleinstiver teaches that guideRNA/crRNA can be encoded on a plasmid, and therefor teaches that the guide RNA is encoded in a nucleic acid (e.g., the caption beneath Figure 3).
Regarding claims 32-34, Kleinstiver teaches Cas12a enzymes introduced into human cells (e.g., page 276, right column, second paragraph).
Response to Arguments
The Applicant’s arguments filed 10/28/2025 have been considered but are not persuasive. The Applicant argues that, while Kleinstiver teaches LbCas12a, they do not inherently teach the ’972 sequence. The Office concedes that, while Kleinstiver inherently teaches the class LbCas12a enzymes, and also specific instances of such enzymes and the structural/functional characteristics of such enzymes, does not inherently teach ‘972. In view of the rejection as a whole, the rejection is based upon the known teachings in the art, where Kleinstiver teaches a known mutational strategy to be used with both AsCas12a and LbCas12a proteins, where furthermore ‘972 is a known LbCas12a protein. The prior art elements can be combined with a reasonable prediction of success for the reasons outlined in the 103 rejection; thus, while Kleinstiver may not inherently teach the sequence ‘972, such a sequence is a known prior art LbCas12a which could be predictably combined with the teachings of Kleinstiver.
With regards to the mutational strategy to arrive at SEQ ID NO: 535, the Applicant argues that there is no guidance in Kleinstiver to arrive at SEQ ID NO: 535, where such a mutational strategy would require 700 mutations starting from the ND2006 LbCas12a. This argument is not persuasive. Kleinstiver teaches that the mutational strategy has broad applicability across Cas12a enzymes, and therefore reasonably teaches a motivation to apply the mutation strategy to additional Cas12a enzymes, and in particular to LbCas12a enzymes which they teach have specific advatages. The present invention is therefore properly characterized as a known LbCas12a enzyme (i.e., ‘972) with two mutations, where the mutation sites are furthermore known and taught with a strong motivational teaching to make such mutations in enzymes such as LbCas12a. By teaching the broad applicability of making enhanced Cas12a enzymes such as enAsCas12a as taught by Kleinstiver (Abstract) and also teaching specific species of LbCas12as, a practitioner could reasonably envision applying such a strategy to other members of the same genus (i.e., other LbCas12a enzymes). In other words, the fact that Kleinstiver teaches one specific LbCas12a does not preclude a practitioner from applying the mutational strategy to other known LbCas12as.
The Applicant argues that Kleinstiver does not teach a motivation to alter any LbCas12a because they teach that the enhanced AsCas12a produced similar cleavage activity to LbCas12a ND2006. This argument is not persuasive because it does not take into consideration what the art is teaching. The mere fact that enAsCas12a had similar cleavage activity to LbCas12a ND2006 does not mean that a practitioner would not be motivated to modify LbCas12a because Kleinstiver teaches a benefit of making such modification in that the modifications expand the PAM site recognition capacity of Cas12a proteins. Thus, a practitioner would be motivated to modify LbCas12a as well, to expand the PAM site recognition capacity of LbCas12a. Contrary to the Applicant’s assertions, the fact that modified AsCas12a retains a similar cleavage activity to LbCas12a and also has expanded PAM recognition is a strong motivation to make such changes in other homologous proteins because Kleinstiver shows that such modifications are permitted and do not negatively affect activity (i.e., there is similar cleavage activity) and also add the benefit of changing/expanding PAM site recognition. Kleinstiver therefore shows that the mutations produce functional proteins with added benefits, which would motivate a practitioner to make similar changes in homologous proteins.
The Applicant argues that there is a vast number of Cas proteins available in databases, and that nothing in ‘972 would guide a person to find it. This argument is not persuasive because 1) Kleinstiver directs a practitioner to the specific sub-class of LbCas12a proteins, which significantly limits the “Cas” family, and 2) ‘972 is identified as an LbCas12a variant. The combination of motivational teachings provided by Kleinstiver with a known embodiment of LbCas12a is obvious, as a practitioner is able to identify ‘972 as an LbCas12a by its characterization and title in protein databases.
The Applicant argues that nothing technical identifies ‘972 as an LbCas12a protein, and that it is simply a sequence. This argument is not persuasive because ‘972 is in fact identified as an LbCas12a enzyme, and therefore it is specifically and directly identified by its function as an enzyme. ‘972 is therefore not merely “a sequence.” For instance, ‘972 is not identified as a “hypothetical protein” or “putative domain” as other proteins are in GenBank. Rather, ‘972 is identified with a specific function based upon
computational analysis using gene prediction/protein homology analysis (‘972, page 3). The Applicant argues that no information is provided in ‘972 with regards to its functionality or structure. This argument is not persuasive because ‘972 is specifically identified by its title as an LbCas12a, which identifies its functionality, where furthermore the functionality is based upon structural prediction/homology prediction (see title of ‘972 and page 3). Thus, the Applicant’s assertion that “nothing can be gleaned” misconstrues what ‘972 actually teaches. The Applicant argues that a practitioner could only arrive at ‘972 by serendipity. This argument is not persuasive; given the motivational teachings of Kleinstiver, who specifically teaches LbCas12a and a beneficial mutational strategy, and the fact that ‘972 is the sequence of a known, published protein entitled “type V CRISPR-associated protein Cas12a/Cpf1 [Lachnospiraceae bacterium],” serendipity hardly seems to play a role in the combination of elements. Rather, Kleistiver teaches a direct motivation to arrive at specific modifications of LbCas12a, where ‘972 teaches one such embodiment of a known LbCas12a. The practitioner is therefore armed with both a motivational teaching that directs them to the exact two positions presently recited for mutation, the class of protein to mutate (LbCas12a), and embodiments of identified LbCas12a proteins (e.g., ‘972).
The Applicant argues that the assertions surrounding the predictability of the present invention are not supported by data. This argument is not found to be persuasive because the original argument is supported by data supplied by the art. For instance, Gao and Yamano provide structural data showing the functional/structural domains of LbCas12a and AsCas12a and their similarity, ‘972 provides functional data produced based upon structural modeling, and Q6 provides alignment data showing conserved residues and domains across AsCas12a and ‘972. Thus, the argument of predictability is largely supported by data of record which was taught in the art.
The Applicant points to Figure 7 to show variability in nuclease activity and cleavage efficiency, where discernable trends are not seen between sequence similarity to ND2006 and the claimed sequence. This data in itself is not persuasive, as the argument in the rejection is directed to the combination of known LbCas12a nucleases with the mutational approach of Kleinstiver. There is no indication in the specification or drawings that the nucleases of Figure 7 are nucleases which have been identified as LbCas12a nucleases and tested. Data which would actually support a claim of non-obvious would show enzymes which are identified by structural homology predictions to be LbCas12as which in fact do not function as LbCas12a nucleases, as this is the class of enzyme to which ‘972 belongs. Merely showing that there are nucleases and nuclease variants which are non-functional or vary in functionality is not sufficient to show unpredictability in the class of LbCas12a taught in the art. For instance, the specification does not show unpredictability specifically in previously identified LbCas12a enzymes which also comprise the mutations taught by Kleinstiver. The data of record, which relies upon sequence similarity and structural/functional overlap (Gao, Yamano, ‘972, Q6) therefore appears to teach predictability in the art, where the applicant’s data is not directed to the LbCas12a genus.
Furthermore, the Applicant has amended independent claim 21 to now be drawn specifically to SEQ ID NO: 535. Such an amendment prompted a new search and consideration, where furthermore Toth was also found to be known in the art. Toth took the teachings of Kleinstiver and applied them to LbCas12a enzymes, where the outcome was similar to that taught by Kleinstiver as the analogous mutations in LbCas12a expanded the PAM recognition of LbCas12a (see Toth page 3731 as an example, and throughout). Thus, the application of Kleinstiver’s teachings of mutations to LbCas12a enzymes have already been taught and reduced to practice by Toth, rendering the results predictable for other LbCas12as such as ‘972.
Double Patenting – Updated in Response to Amendment
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 21, 24-25, and 27-31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of copending applciation 19/261,682 (‘682, reference application). Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 21, claim 14 of ‘682 recites a composition comprising a nuclease, where the nuclease comprises a sequence with between 70-100% identity to SEQ ID NOs 1-1096. SEQ ID NOs 535 of both the instant application and ‘682 are identical. Claim 14 of ‘682 therefore recites overlapping subject matter of instant claim 21.
Regarding claim 24, claim 16 of ‘682 recites that the protein is comprised in a fusion protein.
Regarding claim 25, claim 17 of ‘682 recites that the fusion protein comprises an NLS.
Regarding claim 27, claim 18 of ‘682 recites that the composition further comprises at least on gRNA.
Regarding claim 28, claim 19 recites a system comprising a nuclease having the sequence of SEQ ID NO 535 and a gRNA, where the gRNA comprises a first region configured to interact with the nuclease and a second region configured to hybridize with a portion of the first target nucleic acid.
Regarding claim 29, claim 19 recites that the system is for modifying a first target nucleic acid.
Regarding claim 30, the limitations of claim 30 recite that the nuclease is capable of modifying a target in a human cell. Thus, the claim is drawn to an intrinsic property of the nuclease. Thus, claim 19 of ‘682 broadly encompasses the claim limitations of claim 30 because both claims recite the same nuclease (i.e., SEQ ID NO: 535).
Regarding claim 31, claim 18 of ‘682 recites a nucleic acid comprising a sequence encoding the at least one gRNA.
This is a provisional rejection.
Claims 26 and 32-34 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of copending Application No. 19/261,682 in view of Kleinstiver (Kleinstiver BP et al. Nat Biotechnol. 2019 Mar;37(3):276-282).
Regarding ‘682, a discussion of what is disclosed in ‘682 is given in the rejection above.
Claim 19 of ‘682 discloses a system for modifying a target DNA comprising a nuclease of SEQ ID NO 535 and a gRNA.
Regarding claim 26, ‘682 does not recite that the fusion protein comprises a tag sequence.
Regarding claims 32-34, ‘682 does not recite that the composition is in a cell (mammalian, human, or otherwise).
Kleinstiver is a research article which teaches engineered Cas12a nucleases, including LbCas12a, of which SEQ ID NO 535 was derived (Title, Abstract, Introduction). Kleinstiver and ‘682 therefore directly overlap in subject matter and field of endeavor because they concern the same enzymes and the same applications.
Regarding claim 26, Kleinstiver teaches that nuclear localization-tagged Cas12a enzymes can further comprise a purification tag sequence (page 283, right column, final paragraph). Thus, Kleinstiver teaches the presently recited design concept, where the inclusion of a purification tag allows for the recovery of the engineered nuclease.
Regarding claims 32-34, Kleinstiver teaches that such engineered nucleases are used practically in cells in order to carry out their designed functions, and furthermore are useful for gene editing purposes in cells including human/mammalian cells, and that such uses are widely known (Introduction, particularly the first line of the Introduction).
It would have been obvious to a person of ordinary skill in the art, before the effective filing date of the claimed invention, to combine the nucleases recited in ‘682 with the teachings of Kleinstiver to include a tag sequence and furthermore to introduce the systems of ‘682 into human cells as taught by Kleinstiver because such a combination of references is the simple combination of known prior art elements to yield predictable results. A practitioner would be motivated to include a sequence tag as taught by Kleinstiver, in order to recover the engineered nuclease. The inclusion of a purification tag is a known technique, as taught by Kleinstiver. Furthermore, Kleinstiver teaches that it is common to express Cas enzymes in cells for useful purposes such as gene editing, particularly in human cells. Thus, a practitioner would be motivated to express the nucleases and systems in human cells, simply to carry out the function of the nuclease (i.e., modifying a nucleic acid target, as recited in for instance claim 20 of ‘682). Furthermore the combination of references yields predictable results because both ‘682 and Kleinstiver teach the same class of enzyme (Cas12a) and the same subspecies of enzyme (LbCas12a, of which SEQ ID NO 535 is derived, see 103 rejection, above).
This is a provisional nonstatutory double patenting rejection.
Claims 21, 24-25, 27-34 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of copending Application No. 19/344,313 (‘313 reference application). Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding claim 21, claim 1 of ‘313 recites:
“A composition comprising a nuclease, wherein the nuclease comprises an amino acid sequence with at least 90% sequence identity to SEQ ID No. 535 and wherein the nuclease comprises an arginine at position 156 and an arginine at position 547 relative to the numbered positions of SEQ ID NO: 535.”
SEQ ID NOs 535 are identical in both the instant application and ‘313, where instant SEQ ID NO: 535 comprises an arginine at positions 156 and 547. Thus, ‘313 and instant claim 21 are not distinct from one another.
Regarding claim 24, claim 4 of ‘313 recites “further comprising a fusion protein comprising the nuclease.
Regarding claim 25, claim 5 of ‘313 recites “wherein the fusion protein comprises a nuclear localization sequence.”
Regarding claims 27 and 31, claim 6 of ‘313 recites “A kit comprising the composition of claim 1 and at least one guide ribonucleic acid (gRNA).”
Regarding claim 28, claim 7 of ‘313 recites “The kit of claim 6, wherein the at least one gRNA comprises a first region configured to interact with the nuclease and a second region configured to hybridize with a portion of a target nucleic acid.”
Regarding claim 29, claim 14 of ‘313 recites “A method of modifying a target nucleic acid, comprising contacting the target nucleic acid with the engineered nuclease of claim 11,” which reasonably a combination of a guide RNA to modify the target using a nuclease.
Regarding claims 30 and 32-34, claim 10 of ‘313 recites that a cell of the invention can be a human cell.
Claim 26 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of copending Application No. 19/344,313 (‘313 reference application), as applied to claims 21, 24-25, and 27-34 above, in view of Kleinstiver (Kleinstiver BP et al. Nat Biotechnol. 2019 Mar;37(3):276-282).
Regarding claims 21, 24-25, and 37-34, as discussion of these claims is given above.
‘313 does not teach that the nuclease fusion has a purification tag.
Kleinstiver is a research article focused on engineered Cas12a variants and therefore overlaps in subject matter with ‘313. Kleinstiver teaches that Cas nucleases can comprise His-tagged purification tags, as this is a known method to retrieve a purified protein (e.g., see “Expression and purification of Cas12a proteins” section of Methods, which details that the proteins are expressed with His tags for purification).
It would have been obvious to a person of ordinary skill in the art before the effective filing date to modify the teachings of ‘313 to include a protein purification tag as taught by Kleinstiver, as Kleinstiver teaches that such a tag is a well known addition to a protein which can be accomplished with commercially available products. Thus, the combination is the simple combination of known prior art elements to arrive at a predictable outcome, where furthermore a practitioner would be motivated to purify the Cas proteins which they have made in methods such as Kleinstiver, to retrieve the proteins which are produced using commercially available methods.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant argues that the original rejection, based upon a statutory rejection, does not apply, as the copending application is not drawn to the exact subject matter as that instantly recited. This argument is persuasive. Applicant’s amendments of the independent claim prompted further consideration. As such, the double patenting rejection is updated as detailed above.
Conclusion
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 DOUGLAS CHARLES RYAN whose telephone number is (571)272-8406. The examiner can normally be reached M-F 8AM - 5PM.
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/D.C.R./Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635