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
1. Claims 1-18 are pending and are examined on merits in the present Office action.
Drawings
2. No drawings have been submitted in the instant application.
Specification
3. The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code. See MPEP § 608.01. In the instant case, see for example, line 29 at page 11; line 16at page 17.
Information Disclosure Statement
4. Initialed and dated copy of Applicant’s IDS form 1449 filed in the papers of 06/21/2024 is attached to the instant Office action. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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.
5. Claims 1–18 are rejected under 35 U.S.C. §103(a) as being unpatentable over Begemann et al. (U.S. Patent No. 10,113,179 B2, Issued October 30, 2018) in view of Yamano et al. (Cell, 67(4):633–645, 2017; doi:10.1016/j.molcel.2017.06.035 (pages1-24 and supplementary data included)) and further in view of Kleinstiver et al. (Nature Biotechnology, 37:276–282, 2019).
Begemann et al. teach methods of modifying a nucleotide sequence at a target site in a eukaryotic or prokaryotic cell using a CRISPR-Cpf1 system comprising introduction of a Cpf1 nuclease and a DNA-targeting RNA into a cell. Begemann et al. further teach Cpf1 polypeptides comprising an RNA-binding portion and an enzymatic activity portion that exhibits site-directed DNA cleavage. Begemann et al. also teach SEQ ID NO:133, which shares 99.7% sequence identity with instant SEQ ID NO:2, thereby teaching a Cpf1 polypeptide having well above 95% identity to the claimed sequence Begemann et al. also teach introduction of a DNA-targeting RNA (crRNA) comprising a segment complementary to a target genomic sequence. Begemann et al. further teach that the genomic target may be located in chromosomal, plasmid, mitochondrial, plastid, or other intracellular DNA. Begemann et al. also teach that Cpf1 recognizes a PAM sequence adjacent to the target site and cleaves DNA in a site-specific manner. Begemann et al. also teach that Cpf1-mediated cleavage results in insertions, deletions, or mutations via endogenous DNA repair mechanisms. Begemann et al also teach insertion of heterologous DNA, including sequences encoding proteins conferring antibiotic or herbicide tolerance, particularly in plant cells. Furthermore, Begemann et al. teach expression of Cpf1 from polynucleotides operably linked to heterologous promoters, including codon-optimized constructs for plant expression Additionally, Begemann et al. also teach regeneration of plants and production of seeds comprising Cpf1 constructs. See examples 1-14, Tables I-II, claims 1-25; See in particular, col. 5, lines 10–40; col. 7, lines 10–40; col. 4, lines 20–55; col. 6, lines 5–25; Sequence Listing; col. 7, lines 10–25; col. 5, lines 20–45; col. 3, lines 15–45; col. 6, lines 45–65; Fig. 2; col. 8, lines 25–55; Examples 3–5; col. 12, lines 20–45; col. 13, lines 5–35; col. 14, lines 10–30; cols 18-22, part IV; Example 7.
The sequence homology between instant SEQ ID NO: 2 and Begemann et al. SEQ ID NO: 133 is shown as below:
Qy: SEQ ID NO: 2 (instant); Db: SEQ ID NO: 133 (US PATENT 10,113,179 B2) Query Match 99.7%; Score 6635; DB 1; Length 1264;
Best Local Similarity 99.6%;
Matches 1259; Conservative 2; Mismatches 3; Indels 0; Gaps 0;
Qy 1 MLFQDFTHLYPLSKTMRFELKPIGKTLEHIHAKNFLSQDETMADMYQKVKAILDDYHRDF 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MLFQDFTHLYPLSKTMRFELKPIGKTLEHIHAKNFLSQDETMADMYQKVKAILDDYHRDF 60
Qy 61 IADMMGEVKLTKLAEFYDVYLKFRKNPKDDGLQKQLKDLQAVLRKEIVKPIGNGGKYKAG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 IADMMGEVKLTKLAEFYDVYLKFRKNPKDDGLQKQLKDLQAVLRKEIVKPIGNGGKYKAG 120
Qy 121 YDRLFGAKLFKDGKELGDLAKFVIAQEGESSPKLAHLAHFEKFSTYFTGFHRNRKNMYSD 180
||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Db 121 YDRLFGAKLFKDGKELGDLAKFVIAQEGESSPKLAHLAHFEKFSTYFTGFHDNRKNMYSD 180
Qy 181 EDKHTAITYRLIHENLPRFIDNLQILATIKQKHSALYDQIINELTASGLDVSLASHLDGY 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 EDKHTAITYRLIHENLPRFIDNLQILATIKQKHSALYDQIINELTASGLDVSLASHLDGY 240
Qy 241 HKLLTQEGITAYNTLLGGISGEAGSRKIQGINELINSHHNQHCHKSERIAKLRPLHKQIL 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 HKLLTQEGITAYNTLLGGISGEAGSRKIQGINELINSHHNQHCHKSERIAKLRPLHKQIL 300
Qy 301 SDGMGVSFLPSKFADDSEMCQAVNEFYRHYADVFAKVQSLFDGFDDHQKDGIYVEHKNLN 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 SDGMGVSFLPSKFADDSEMCQAVNEFYRHYADVFAKVQSLFDGFDDHQKDGIYVEHKNLN 360
Qy 361 ELSKQAFGDFALLGRVLDGYYVDVVNPEFNERFAKAKTDNAKAKLTKEKDKFIKGVHSLA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 ELSKQAFGDFALLGRVLDGYYVDVVNPEFNERFAKAKTDNAKAKLTKEKDKFIKGVHSLA 420
Qy 421 SLEQAIEHYTARHDDESVQAGKLGQYFKHGLAGVDNPIQKIHNNHSTIKGFLERERPAGE 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 SLEQAIEHYTARHDDESVQAGKLGQYFKHGLAGVDNPIQKIHNNHSTIKGFLERERPAGE 480
Qy 481 RALPKIKSGKNPEMTQLRQLKELLDNALNVAHFAKLLTTKTTLDNQDGNFYGEFGALYDE 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 RALPKIKSGKNPEMTQLRQLKELLDNALNVAHFAKLLTTKTTLDNQDGNFYGEFGALYDE 540
Qy 541 LAKIPTLYNKVRDYLSQKPFSTEKYKLNFGRPTLLRGWDLNKEKDNFGIILQKDGCYYLA 600
|||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||
Db 541 LAKIPTLYNKVRDYLSQKPFSTEKYKLNFGNPTLLNGWDLNKEKDNFGIILQKDGCYYLA 600
Qy 601 LLDKAHKKVFDNAPNTGKNVYQKMIYKLLPGPNKMLPRVFFAKSNLDYYNPSAELLDKYA 660
|||||||||||||||||||||||||||||||||||||:||||||||||||||||||||||
Db 601 LLDKAHKKVFDNAPNTGKNVYQKMIYKLLPGPNKMLPKVFFAKSNLDYYNPSAELLDKYA 660
Qy 661 QGTHKKGNNFNLKDCHALIDFFKAGINKHPEWQHFGFKFSPTSSYQDLSDFYREVEPQGY 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 QGTHKKGNNFNLKDCHALIDFFKAGINKHPEWQHFGFKFSPTSSYQDLSDFYREVEPQGY 720
Qy 721 QVKFVDINADYINELVEQGQLYLFQIYNKDFSPKAHGKPNLHTLYFKALFSKDNLANPIY 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 QVKFVDINADYINELVEQGQLYLFQIYNKDFSPKAHGKPNLHTLYFKALFSKDNLANPIY 780
Qy 781 KLNGEAQIFYRKASLDMNETTIHRAGEVLENKNPDNPKKRQFVYDIIKDKRYTQDKFLLH 840
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||:||
Db 781 KLNGEAQIFYRKASLDMNETTIHRAGEVLENKNPDNPKKRQFVYDIIKDKRYTQDKFMLH 840
Qy 841 VPITMNFGVQGMTIKEFNKKVNQSIQQYDEVNVIGIDRGERHLLYLTVINSKGEILEQRS 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 VPITMNFGVQGMTIKEFNKKVNQSIQQYDEVNVIGIDRGERHLLYLTVINSKGEILEQRS 900
Qy 901 LNDITTASANGTQMTTPYHKILDKREIERLNARVGWGEIETIKELKSGYLSHVVHQISQL 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 LNDITTASANGTQMTTPYHKILDKREIERLNARVGWGEIETIKELKSGYLSHVVHQISQL 960
Qy 961 MLKYNAIVVLEDLNFGFKRGRFKVEKQIYQNFENALIKKLNHLVLKDEADDEIGSYKNAL 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 MLKYNAIVVLEDLNFGFKRGRFKVEKQIYQNFENALIKKLNHLVLKDEADDEIGSYKNAL 1020
Qy 1021 QLTNNFTDLKSIGKQTGFLFYVPAWNTSKIDPETGFVDLLKPRYENIAQSQAFFGKFDKI 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1021 QLTNNFTDLKSIGKQTGFLFYVPAWNTSKIDPETGFVDLLKPRYENIAQSQAFFGKFDKI 1080
Qy 1081 CYNADKDYFEFHIDYAKFTDKAKNSRQIWKICSHGDKRYVYDKTANQNKGATKGINVNDE 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1081 CYNADKDYFEFHIDYAKFTDKAKNSRQIWKICSHGDKRYVYDKTANQNKGATKGINVNDE 1140
Qy 1141 LKSLFARHHINDKQPNLVMDICQNNDKEFHKSLIYLLKTLLALRYSNASSDEDFILSPVA 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1141 LKSLFARHHINDKQPNLVMDICQNNDKEFHKSLIYLLKTLLALRYSNASSDEDFILSPVA 1200
Qy 1201 NDEGMFFNSALADDTQPQNADANGAYHIALKGLWVLEQIKNSDDLNKVKLAIDNQTWLNF 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1201 NDEGMFFNSALADDTQPQNADANGAYHIALKGLWVLEQIKNSDDLNKVKLAIDNQTWLNF 1260
Qy 1261 AQNR 1264
||||
Db 1261 AQNR 1264
Begemann et al. do no expressly teach (i) specific crRNA second-segment sequences recited as SEQ ID NOs:3-8; (ii) recognition of a YCCV PAM; (iii) the specific combination of arginine substitutions corresponding to D172, N571, N576, and K638 and leucine at M838 of SEQ ID NO:2; and (iv) performance of the method at temperatures below 32°C.
Yamano et al teach the structure and function of Cpf1-crRNA complexes, including the use of a single crRNA having a guide segment complementary to a target DNA. Yamano et al. further teach that crRNA sequence and length variations are tolerated while maintaining Cpf1 activity, indicating flexibility in crRNA second-segment design. Yamano et al. also teach that Cpf1 cleavage produces staggered double-strand breaks suitable for genome modification. See in particular, summary at page 1; results & discussion at pages 3-8; Figures 1-7; Table 1 at page 24; Supplementary Fig. S3 and rest of supplementary data after page 24.
Kleinstiver et al. teach that Cpf1 PAM recognition is flexible and engineerable, including functional PAMs containing Y and CC motifs. Kleinstiver et al. further teach that amino acid substitutions in Cpf1 alter PAM specificity and nuclease activity. Kleinstiver et al. also teach that Cpf1 exhibits robust nuclease activity over a range of temperatures, including temperatures compatible with plant and microbial systems. See in particular, pp. 278–279; Fig. 2; pp. 279–281; Supplementary Fig. 5.
Given (i) Begemann et al. teach a complete Cpf1-based genome-editing system, including a Cpf1 polypeptide having 99.7% identity to SEQ ID NO:2, crRNA-guided DNA cleavage, and genome modification outcomes; (ii) Yamano et al. provides established guidance on crRNA architecture and sequence flexibility, rendering selection of specific crRNA sequences such as SEQ ID NOs:3-8 a matter of routine optimization; and (iii) Kleinstiver et al. teach that PAM diversification and amino acid substitutions enabling recognition of non-canonical PAMs such as YCCV, as well as functional activity across a range of temperatures, it would have been obvious for one of ordinary skill in the art prior to earliest filing date of the instantly claimed invention to have been motivated to combine these teachings to expand PAM compatibility, optimize RNA-guided targeting, and achieve predictable genome-editing results, which are expressly recognized goals in the art. The combination involves the use of known elements according to their established functions to yield predictable results, and therefore constitutes obviousness under KSR Int’l Co. v. Teleflex Inc.
It would have been also prima facie obvious, and within the scope of an ordinary skill in the art prior to instantly claimed invention to have chosen from a finite number of predictable variants of Begemann et al. Cpf1 polypeptide (SEQ ID NO: 133, 99.7% identity to instant SEQ ID NO: 2), including the one having 100% identity to instant SEQ ID NO: 2, and thus arrive at the instantly claimed method comprising Cpf1 polypeptide of SEQ ID NO: 2 with a reasonable expectation of success without any unexpected or surprising results. See the recent Board decision Ex parte Smith, -- USPQ2d --, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR, 82 USPQ2d at 1396). KSR forecloses the argument that a specific teaching, suggestion or motivation is required to support a finding of obviousness.
Therefore, the claimed invention as a whole is prima facie obvious over the combined teachings of the prior art.
6. Claims 1–18 are therefore rejected under 35 U.S.C. §103(a) as being obvious Begemann et al. (U.S. Patent No. 10,113,179 B2, Issued October 30, 2018) in view of Gao et al. (Nature Biotechnology, 35(8): 789-792, 2017; XP055396069, New York ISSN: 1087-0156, DOI: 10.1038/nbt.38900) and Toth et al. (Nucleic Acids Research, 46(19)10272-10285, 2018, 37:276-282,2019 with supplemental data).
Begemann et al. teach methods of modifying a nucleotide sequence at a target site in a eukaryotic or prokaryotic cell using a CRISPR-Cpf1 system comprising introduction of a Cpf1 nuclease and a DNA-targeting RNA into a cell. Begemann et al. further teach Cpf1 polypeptides comprising an RNA-binding portion and an enzymatic activity portion that exhibits site-directed DNA cleavage. Begemann et al. also teach SEQ ID NO:133, which shares 99.7% sequence identity with instant SEQ ID NO:2, thereby teaching a Cpf1 polypeptide having well above 95% identity to the claimed sequence Begemann et al. also teach introduction of a DNA-targeting RNA (crRNA) comprising a segment complementary to a target genomic sequence. Begemann et al. further teach that the genomic target may be located in chromosomal, plasmid, mitochondrial, plastid, or other intracellular DNA. Begemann et al. also teach that Cpf1 recognizes a PAM sequence adjacent to the target site and cleaves DNA in a site-specific manner. Begemann et al. also teach that Cpf1-mediated cleavage results in insertions, deletions, or mutations via endogenous DNA repair mechanisms. Begemann et al also teach insertion of heterologous DNA, including sequences encoding proteins conferring antibiotic or herbicide tolerance, particularly in plant cells. Furthermore, Begemann et al. teach expression of Cpf1 from polynucleotides operably linked to heterologous promoters, including codon-optimized constructs for plant expression Additionally, Begemann et al. also teach regeneration of plants and production of seeds comprising Cpf1 constructs. See examples 1-14, Tables I-II, claims 1-25; See in particular, col. 5, lines 10–40; col. 7, lines 10–40; col. 4, lines 20–55; col. 6, lines 5–25; Sequence Listing; col. 7, lines 10–25; col. 5, lines 20–45; col. 3, lines 15–45; col. 6, lines 45–65; Fig. 2; col. 8, lines 25–55; Examples 3–5; col. 12, lines 20–45; col. 13, lines 5–35; col. 14, lines 10–30; cols 18-22, part IV; Example 7.
The sequence homology between instant SEQ ID NO: 2 and Begemann et al. SEQ ID NO: 133 is shown as below:
Qy: SEQ ID NO: 2 (instant); Db: SEQ ID NO: 133 (US PATENT 10,113,179 B2) Query Match 99.7%; Score 6635; DB 1; Length 1264;
Best Local Similarity 99.6%;
Matches 1259; Conservative 2; Mismatches 3; Indels 0; Gaps 0;
Qy 1 MLFQDFTHLYPLSKTMRFELKPIGKTLEHIHAKNFLSQDETMADMYQKVKAILDDYHRDF 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MLFQDFTHLYPLSKTMRFELKPIGKTLEHIHAKNFLSQDETMADMYQKVKAILDDYHRDF 60
Qy 61 IADMMGEVKLTKLAEFYDVYLKFRKNPKDDGLQKQLKDLQAVLRKEIVKPIGNGGKYKAG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 IADMMGEVKLTKLAEFYDVYLKFRKNPKDDGLQKQLKDLQAVLRKEIVKPIGNGGKYKAG 120
Qy 121 YDRLFGAKLFKDGKELGDLAKFVIAQEGESSPKLAHLAHFEKFSTYFTGFHRNRKNMYSD 180
||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Db 121 YDRLFGAKLFKDGKELGDLAKFVIAQEGESSPKLAHLAHFEKFSTYFTGFHDNRKNMYSD 180
Qy 181 EDKHTAITYRLIHENLPRFIDNLQILATIKQKHSALYDQIINELTASGLDVSLASHLDGY 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 EDKHTAITYRLIHENLPRFIDNLQILATIKQKHSALYDQIINELTASGLDVSLASHLDGY 240
Qy 241 HKLLTQEGITAYNTLLGGISGEAGSRKIQGINELINSHHNQHCHKSERIAKLRPLHKQIL 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 HKLLTQEGITAYNTLLGGISGEAGSRKIQGINELINSHHNQHCHKSERIAKLRPLHKQIL 300
Qy 301 SDGMGVSFLPSKFADDSEMCQAVNEFYRHYADVFAKVQSLFDGFDDHQKDGIYVEHKNLN 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 SDGMGVSFLPSKFADDSEMCQAVNEFYRHYADVFAKVQSLFDGFDDHQKDGIYVEHKNLN 360
Qy 361 ELSKQAFGDFALLGRVLDGYYVDVVNPEFNERFAKAKTDNAKAKLTKEKDKFIKGVHSLA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 ELSKQAFGDFALLGRVLDGYYVDVVNPEFNERFAKAKTDNAKAKLTKEKDKFIKGVHSLA 420
Qy 421 SLEQAIEHYTARHDDESVQAGKLGQYFKHGLAGVDNPIQKIHNNHSTIKGFLERERPAGE 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 SLEQAIEHYTARHDDESVQAGKLGQYFKHGLAGVDNPIQKIHNNHSTIKGFLERERPAGE 480
Qy 481 RALPKIKSGKNPEMTQLRQLKELLDNALNVAHFAKLLTTKTTLDNQDGNFYGEFGALYDE 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 RALPKIKSGKNPEMTQLRQLKELLDNALNVAHFAKLLTTKTTLDNQDGNFYGEFGALYDE 540
Qy 541 LAKIPTLYNKVRDYLSQKPFSTEKYKLNFGRPTLLRGWDLNKEKDNFGIILQKDGCYYLA 600
|||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||
Db 541 LAKIPTLYNKVRDYLSQKPFSTEKYKLNFGNPTLLNGWDLNKEKDNFGIILQKDGCYYLA 600
Qy 601 LLDKAHKKVFDNAPNTGKNVYQKMIYKLLPGPNKMLPRVFFAKSNLDYYNPSAELLDKYA 660
|||||||||||||||||||||||||||||||||||||:||||||||||||||||||||||
Db 601 LLDKAHKKVFDNAPNTGKNVYQKMIYKLLPGPNKMLPKVFFAKSNLDYYNPSAELLDKYA 660
Qy 661 QGTHKKGNNFNLKDCHALIDFFKAGINKHPEWQHFGFKFSPTSSYQDLSDFYREVEPQGY 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 QGTHKKGNNFNLKDCHALIDFFKAGINKHPEWQHFGFKFSPTSSYQDLSDFYREVEPQGY 720
Qy 721 QVKFVDINADYINELVEQGQLYLFQIYNKDFSPKAHGKPNLHTLYFKALFSKDNLANPIY 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 QVKFVDINADYINELVEQGQLYLFQIYNKDFSPKAHGKPNLHTLYFKALFSKDNLANPIY 780
Qy 781 KLNGEAQIFYRKASLDMNETTIHRAGEVLENKNPDNPKKRQFVYDIIKDKRYTQDKFLLH 840
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||:||
Db 781 KLNGEAQIFYRKASLDMNETTIHRAGEVLENKNPDNPKKRQFVYDIIKDKRYTQDKFMLH 840
Qy 841 VPITMNFGVQGMTIKEFNKKVNQSIQQYDEVNVIGIDRGERHLLYLTVINSKGEILEQRS 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 VPITMNFGVQGMTIKEFNKKVNQSIQQYDEVNVIGIDRGERHLLYLTVINSKGEILEQRS 900
Qy 901 LNDITTASANGTQMTTPYHKILDKREIERLNARVGWGEIETIKELKSGYLSHVVHQISQL 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 LNDITTASANGTQMTTPYHKILDKREIERLNARVGWGEIETIKELKSGYLSHVVHQISQL 960
Qy 961 MLKYNAIVVLEDLNFGFKRGRFKVEKQIYQNFENALIKKLNHLVLKDEADDEIGSYKNAL 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 MLKYNAIVVLEDLNFGFKRGRFKVEKQIYQNFENALIKKLNHLVLKDEADDEIGSYKNAL 1020
Qy 1021 QLTNNFTDLKSIGKQTGFLFYVPAWNTSKIDPETGFVDLLKPRYENIAQSQAFFGKFDKI 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1021 QLTNNFTDLKSIGKQTGFLFYVPAWNTSKIDPETGFVDLLKPRYENIAQSQAFFGKFDKI 1080
Qy 1081 CYNADKDYFEFHIDYAKFTDKAKNSRQIWKICSHGDKRYVYDKTANQNKGATKGINVNDE 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1081 CYNADKDYFEFHIDYAKFTDKAKNSRQIWKICSHGDKRYVYDKTANQNKGATKGINVNDE 1140
Qy 1141 LKSLFARHHINDKQPNLVMDICQNNDKEFHKSLIYLLKTLLALRYSNASSDEDFILSPVA 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1141 LKSLFARHHINDKQPNLVMDICQNNDKEFHKSLIYLLKTLLALRYSNASSDEDFILSPVA 1200
Qy 1201 NDEGMFFNSALADDTQPQNADANGAYHIALKGLWVLEQIKNSDDLNKVKLAIDNQTWLNF 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1201 NDEGMFFNSALADDTQPQNADANGAYHIALKGLWVLEQIKNSDDLNKVKLAIDNQTWLNF 1260
Qy 1261 AQNR 1264
||||
Db 1261 AQNR 1264
Begemann et al. do no expressly teach (i) specific crRNA second-segment sequences recited as SEQ ID NOs:3-8; (ii) recognition of a YCCV PAM; (iii) the specific combination of arginine substitutions corresponding to D172, N571, N576, and K638 and leucine at M838 of SEQ ID NO:2; and (iv) performance of the method at temperatures below 32°C.
Gao et al. teach engineered Cpf1 variants with altered PAM specificities generated by introducing positively charged amino acid substitutions into PAM-interacting residues. Gao et al. specifically teach a Cpf1 variant from Acidaminococcus sp. comprising mutations S542R and K607R, which, when aligned to SEQ ID NO: 2 of the instant claims, correspond to positions N576 and K638, respectively. Gao et al. further teach that these arginine substitutions significantly enhance cleavage activity at TCCC PAM sites, as demonstrated by comparative activity assays. Gao et al. further teach that the engineered Cpf1 variants also cleave targets adjacent to ACCC and CCCC PAM sequences, demonstrating expanded PAM recognition consistent with a YCCV motif. See in particular, abstract; 790, right column, paragraph 1; page 790, right column, paragraphs 1–2; Fig. 1 and Fig. 2; page 790, right column, paragraph 3; pages 791-792; Figs. 1, 3.
Toth et al. teach engineered Cpf1 nucleases from Moraxella bovoculi with altered PAM specificity achieved by introducing arginine substitutions at residues involved in PAM interaction. Toth et al. specifically teach a double-arginine mutant comprising substitutions N576R and K637R, which correspond to N576 and K638 when aligned to SEQ ID NO: 2 of the instant claims. Toth et al. further teach that the resulting “RR MbCpf1” variant recognizes and cleaves DNA adjacent to a TCCC PAM with high efficiency, thereby confirming that such arginine substitutions confer expanded PAM recognition and are transferable across Cpf1 orthologs. See in particular, abstract; page 10280, left column, paragraph 2; Supplementary Fig. S13; Fig.11; pages 10273-10279, pages 10281-10283 through first paragraph of left column at page 10284; Figs. 1-12.
Given (i) Begemann et al. teach a complete Cpf1-based genome-editing system, including a Cpf1 polypeptide having 99.7% identity to SEQ ID NO:2, crRNA-guided DNA cleavage, and genome modification outcomes; and (ii) Gao et al. and Toth et al. teach that introducing arginine substitutions at positions corresponding to N576 and K638 predictably alters PAM specificity to include TCCC-type PAMs, which fall within the claimed YCCV PAM sequence. The combination therefore teaches a Cpf1 polypeptide sharing high sequence identity with a reference sequence such as SEQ ID NO: 2 and comprising the claimed arginine substitutions, as well as the associated methods, nucleic acids, cells, plants, and progeny.
One of ordinary skill in the art would have been motivated to combine the teachings of Begemann et al. with those of Gao et al. and Toth et al. because all three references address improving Cpf1-based genome editing by optimizing PAM recognition, which Begemann et al. teach is a critical determinant of target site selection. Gao et al. teach that specific arginine substitutions at PAM-interacting residues expand PAM compatibility while maintaining nuclease activity (Gao et al., page 790), and Toth et al. teach that analogous substitutions function across different Cpf1 orthologs (Toth et al., Fig. 11). Applying the PAM-altering substitutions taught by Gao et al. and Toth et al. to the Cpf1 system of Begemann et al. would have been a predictable modification yielding a Cpf1 nuclease capable of recognizing YCCV PAM sequences with a reasonable expectation of success. It would have been obvious and within the scope of an ordinary skill in the art to have performed instantly claimed method at an optimum temperature, such as less than 32oC, which is compatible for growth of living cells (e.g. plant cells of economically important plant species), and enzymes therein, including recombinant Cas9 nucleases, and thus arrive at the Applicant’s invention with a reasonable expectation of success and without any surprising results. Such a combination represents the routine optimization of a known genome editing system using known techniques to achieve a predictable result, consistent with KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398 (2007).
It would have been also prima facie obvious, and within the scope of an ordinary skill in the art prior to instantly claimed invention to have chosen from a finite number of predictable variants of Begemann et al. Cpf1 polypeptide (SEQ ID NO: 133, 99.7% identity to instant SEQ ID NO: 2), including the one having 100% identity to instant SEQ ID NO: 2, and thus arrive at the instantly claimed method comprising Cpf1 polypeptide of SEQ ID NO: 2 with a reasonable expectation of success without any unexpected or surprising results. See the recent Board decision Ex parte Smith, -- USPQ2d --, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR, 82 USPQ2d at 1396). KSR forecloses the argument that a specific teaching, suggestion or motivation is required to support a finding of obviousness.
Therefore, the claimed invention as a whole is prima facie obvious over the combined teachings of the prior art.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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7. Claims 1-18 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6 and 8-19 of copending Application No.17/638,605 (‘605 thereafter) in view of Toth et al. (Nucleic Acids Research, 46(19)10272-10285, 2018, 37:276-282,2019 with supplemental data).
Although the conflicting claims are not identical, they are not patentably distinct from each other because the copending application ’605 claims subject matter directed to: a CRISPR-Cpf1 (Cas12a) genome editing method in eukaryotic and prokaryotic cells (Claims 1–5), and nucleic acid compositions (claims 6, 13, 15, 18, 19)encoding engineered, non-naturally occurring Cpf1 variants sharing ≥95% identity to selected ortholog sequences including SEQ ID NO:52, wherein the nuclease comprises arginine at residue corresponding to the position 172 and leucine at residue corresponding to the position 838. However, SEQ ID NO: 52 comprises asparagine at residues corresponding to positions 571 and 576, respectively, and lysine at residue corresponding to position 638 of SEQ ID NO: 52 (Claims 1-6, 8–19), and transformed cells, regenerated plants, seeds, and compositions using such variants (Claims 8–12, 13–19). The instant application likewise claims: the same genome editing method steps (Claims 1–5, 18), the same Cpf1 nuclease genus defined by ≥95% identity to SEQ ID NO:2, with arginine residues at positions corresponding to D172, N576, N576, and K638, and leucine at M838 (Claim 1-18), and cells, plants, seeds, and polypeptide products comprising the identical engineered nuclease construct (Claims 10–14), and express recitation of SEQ ID NO:2 and SEQ ID NO:8, which are 99.7% identical to SEQ ID NO: 52 and 100% identical to SEQ ID NO:17, respectively, of the copending ‘605 case or differ only by predictable, routine PAM-engineering substitutions at 571, 576 and 638.
Toth et al. confirm that: double arginine substitutions at residues N576R/K637R (aligned to instant N576/K638) confer high-efficiency cleavage at TCCC PAMs, and arginine substitutions at residue 571 enhance editing efficiency, and such substitutions are transferable across orthologs and represent predictable design choices. See in particular, abstract; page 10280, left column, paragraph 2; Supplementary Fig. S13; Fig.11; pages 10273-10279, pages 10281-10283 through first paragraph of left column at page 10284; Figs. 1-12.
Thus, the only sequence differences between instant SEQ ID NO:2 (571R, 576R, 638R) and copending ‘605 SEQ ID NO:52 (571N, 576N, 638L positions) fall within a class of routine and predictable PAM-interacting residue substitutions previously validated to expand YCCV/TCCC recognition. These substitutions would have been obvious variant selections from the copending ‘605 genus, and therefore do not render the claims patentably distinct.
This is a provisional nonstatutory double patenting rejection.
Conclusion
8. Claims 1-18 are rejected.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Vinod Kumar whose telephone number is (571) 272-4445. The examiner can normally be reached on 8.30 a.m. to 5.00 p.m.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad A. Abraham can be reached on (571) 270-7058 The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/VINOD KUMAR/Primary Examiner, Art Unit 1663