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
Status of the Claims
Claims 77, 79 and 81-95 are pending.
Claims 79, 90-91 and 93-95 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected group or species, there being no allowable generic or linking claim.
Claims 78 and 80 are newly cancelled.
Election was made without traverse in the reply filed on 06/05/2025.
Claims 77, 81-89 and 92 have been examined on the merits.
Withdrawn Objections & Rejections
Applicant's response filed 11/06/2025 has been considered. Rejections and/or objections not reiterated from the previous Office action mailed 08/07/2025 are hereby withdrawn.
Rejections in the previous action (mailed 08/07/2025) over 35 USC § 112(a), 101, 102 and 103 are withdrawn. New rejections under 35 USC § 103 are entered.
The objections and rejections presented herein represent the full set of objections and rejections currently pending in the application.
Drawings
New corrected drawings in compliance with 37 CFR 1.121(d) are required in this application because the sequences listed in the figures do not correspond to the Seq ID NOs as listed in the Sequence Listing File.
Regarding Figure 1: Seq ID NOs: 342 and 299 in Figure 1c are not the same as the sequence in the Sequence Listing file.
Regarding Figure 7: Seq ID NO: 300 in the figure is not the same as the sequence in the Sequence Listing file.
Regarding Figure 8: Seq ID NO: 298 is not the same as the sequence in the Sequence Listing file.
Regarding Figures 15-16: Seq ID NOs: 301-308 are not the same as the sequence in the Sequence Listing file.
Regarding Figure 17: Seq ID NOs: 301 and 344-350 are not the same as the sequence in the Sequence Listing file.
Regarding Figure 18: Seq ID NO: 351-356 are not the same as the sequence in the Sequence Listing file.
Regarding Figure 19: Seq ID NO: 287 are not the same as the sequence in the Sequence Listing file.
Regarding Figure 20: Seq ID NO: 287-293 are not the same as the sequence in the Sequence Listing file.
Applicant is advised to employ the services of a competent patent draftsperson outside the Office, as the U.S. Patent and Trademark Office no longer prepares new drawings. The corrected drawings are required in reply to the Office action to avoid abandonment of the application. The requirement for corrected drawings will not be held in abeyance.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
Claims 83 and 92 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
This is a new rejection due to the Amendments filed 11/06/2025.
Regarding claims 81-83: The claims are indefinite because they require a single direct repeat (DR) and depend from claim 77 which comprises a direct repeat sequence (discussed below).
Claim 81 recites “the crRNA further comprises a direct repeat (DR) sequence”.
Claim 82 recites “the DR sequence is 3’ from the guide sequence” and depends from claim 81.
Claim 83 recites “the DR sequence comprises the sequence selected from”. The claim language “the DR sequence” suggests a single DR sequence in the claimed crRNA.
However the claims depend from claim 77 which already comprises a DR sequence because claim 77 requires Seq ID No: 348. Seq Id NO: 348 comprises a direct repeat sequence as shown below: nucleotides 31-65 of Seq ID NO 348 (Query) align with the direct repeat sequence shown in Figure 19 of the instant invention (sbjct) as shown below.
Query 31 TTGTGGAAGGTCCAGTTTTGAGGGGCTATTACAAC 65
|||||||||||||||||||||||||||||||||||
Sbjct 2 TTGTGGAAGGTCCAGTTTTGAGGGGCTATTACAAC 36
Thus the structural requirement of the claimed nucleotide sequence is unclear.
If multiple DR are required, the claims could be amended to recite “a first DR sequence comprising…” “a second DR sequence comprising” etc.
Regarding claim 92: The claim is dependent on withdrawn claim 90. A claim dependent on a withdrawn claim is indefinite.
For purposes of compact prosecution the claim is interpreted as dependent on claim 87.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 81-83 rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
As discussed above, the claims are indefinite because they require a single direct repeat (DR) and depend from claim 77 which comprises a direct repeat sequence. Thus the requirement for a single DR sequence is met by claim 77 and the dependent claims do not further limit the claims. Furthermore, claim 82 requires “the DR is 3’ from the guide sequence” which is inherent to the structure of Seq ID NO: 348, and thus does not further limit the claim.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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.
Claims 77, 81-82 and 86-88 are rejected under 35 U.S.C. 103 as being unpatentable over Nelles et al (WO 2019/236982 A1; previously cited) in view of Froelich (WO 2017/053753), as evidenced by Shariat et al (AEM(2014)80:2;1010; previously cited) and in further view of Cox et al (Science (2017) 24:358;1-23).
This is a new rejection due to the Amendments filed 11/06/2025, however relies on the references of record from the action filed 08/07/2025.
Regarding claim 77: Nelles teach a CRISPR/CAS system comprising a CRISPR/Cas protein guided by a gRNA sequence that specifically binds an RNA target sequence wherein the targeting sequence comprises sequences complementary to expanded RNA repeats including CUG (claims 1, 2, 8, and 9).
Nelles further teach the RNA-targeting Cas system fused to an endonuclease targets and cleaves disease causing RNA, and in the context of mytonic dystrophy type 1, an RNA-targeting Cas9 system cleaves a repetitive RNA composed of repeating CUG units (p14 063, Fig 1A-B).
Nelles further teach the spacer sequence of Seq ID NO:9, which comprises a sequence (CAG)6 which would target a nucleotide comprising 6 CUG repeats (p 109 embodiment 18).
The alignment of sequence 9 taught by Nelles (Sbject) and the spacer sequence of the instant Seq Id NO: 348 (1-30; Query) is shown below.
Query 1 GCAGCAGCAGCAGCAGCAGCAGCAGCAGCA 30
|||||||||||||||||||
Sbjct 3 GCAGCAGCAGCAGCAGCAG 21
Nelles teach a spacer sequence which comprises 6 “CUG” repeats while the instant disclosure teaches a spacer sequence comprising 9.6 “CUG” repeats (the “CA” at the 3’ terminus of the spacer sequence is considered the first two nucleotide in an additional “CUG” triplet, and thus 2/3 of a CUG repeat).
Nelles also teach the Cas system can comprise a Cas13 protein (p39 [00132]) and teach exemplary direct repeat sequences that can be used with Cas13 (p40 [0133]). Nelles do not teach the direct repeat that corresponds to the DR sequence of Seq ID NO: 348, which also corresponds to the DR sequence for PspCas13b sp 5-25 (as discussed below).
While Nelles teach the guide sequence directed to a (CAG)6 target, Nelles do not teach a guide sequence directed to (CAG)9, as taught by the instant Seq ID NO: 348.
Seq ID NO: 348 is a nucleic acid sequence which comprises 65 base pairs and encodes a crRNA with a spacer sequence (1-30) and a direct repeat sequence (31-65). Figure 1c of the instant specification teaches the structure of a crRNA and shows the DR sequence forms a stem/hairpin loop.
Figure 1c of the instant specification (reproduced below) teaches the crRNA structure comprises a linear spacer sequence and the direct repeat sequence which forms a stem/loop structure, as reproduced below:
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288
842
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Cox teach a Cas13 ortholog that demonstrates RNA editing (Abstract). Cox further teach the Cas13b ortholog from Prevotella sp. P5-125 (PspCas13b) is the most efficient and specific for mammalian cell applications (p3 ¶2). Cox teach a vector comprising the direct repeat sequence for PspCas13b P1-125 (Supp Table 5 pC0043 PspCas13b crRNA backbone, labeled “PspCas13b DR” in benchling sequence file).
The DR sequence of PspCas13b as taught by Cox (Sbjct) and the DR of the instant invention (Query; 31-65 of Seq ID NO:348) share 100% sequence identity (see below):
Query 1 GTTGTGGAAGGTCCAGTTTTGAGGGGCTATTACAAC 36
||||||||||||||||||||||||||||||||||||
Sbjct 1 GTTGTGGAAGGTCCAGTTTTGAGGGGCTATTACAAC 36
It would have been obvious to one of ordinary skill in the art to adapt the invention Nelles drawn to a crRNA with a Cas13 direct repeat and spacer sequence that targets a (CUG)6 by substituting the direct repeat sequence for PspCas13b as taught by Cox, and by using a spacer sequence which targets a (CUG)9.6 repeat. Using spacer sequence targeting a longer expanded repeat in place of targeting a (CUG)6 as taught by Nelles would be a matter of routine optimization to optimize the targeting of a specific expansion length.
One would have been motivated to use the direct repeat sequence for PspCas13b as taught by Cox because Cox teach PspCas13b is the most efficient and specific Cas13 ortholog for mammalian cells.
One would have had a reasonable expectation of success because Cox teach the Cas13 ortholog system is capable of robust knockdown and RNA editing (abstract).
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention.
Regarding claim 81: The claim recites “a direct repeat sequence”. As discussed supra for claim 77, Seq ID NO: 348 comprises a direct repeat sequence and thus the claim limitation is met as discussed supra.
Seq ID NO: 348 of the instant invention is a nucleic acid sequence which comprises 65 base pairs and encodes a crRNA with a spacer sequence (1-30) and a direct repeat sequence (31-65). Figure 1c of the instant specification teaches the structure of a crRNA and shows the DR sequence forms a stem/hairpin loop.
Figure 1c of the instant specification (reproduced below) teaches the crRNA structure comprises a linear spacer sequence and the direct repeat sequence which forms a stem/loop structure, as reproduced below:
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Regarding claim 82: The teachings of Nelles are discussed supra. Nelles do not explicitly teach the direct repeat is 3’ from the guide (or spacer) sequence.
As evidenced by Shariat, the smallest spacer arrays comprise one spacer (guide) flanked by direct repeats (p1 col2 para2).
Thus a guide sequence will always have a direct repeat sequence flanking the guide sequence at both the 5’ and 3’ termini. As flanking direct repeats are required for a functional CRISPR system, the working CRISPR/Cas system, as taught by Nelles in example 2, must have direct repeat sequences 3’ of the guide sequence.
Regarding claim 86: The teachings of Nelles are discussed supra. Nelles also teach a composition comprising a crRNA (claims 1, 2, 8, and 9).
Regarding claim 87: The teachings of Nelles are discussed supra. Nells also teach the composition comprises a CRISPR/Cas polypeptide (claim 2). This reads on a Cas protein.
Regarding claim 88: The teachings of Nelles are discussed supra. Nelles also teach the Cas protein is Cas 13 (claim 3).
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention.
Claims 83 is rejected under 35 U.S.C. 103 as being unpatentable over Nelles et al (WO 2019/236982 A1) in view of Froelich (WO 2017/053753) and as evidenced by Shariat et al (AEM(2014)80:2;1010) and in further view of Cox et al (Science (2017) 24:358;1-23) as applied to claim 77, 81-82 and 86-88 above, and further in view of Zhang et al (WO 2019/051318), Smargon et al (Mol Cell (2017) 65:4;1-30, hereafter referred to as Smargon(2017)), Ali et al (Cell Press Reviews (2018) 23:5;374-378) and Lin et al (Am Soc Gene and Cell Ther (2018) 26:11;2650-2657).
This is a new rejection due to the Amendments filed 11/06/2025, however relies on the references of record from the action filed 08/07/2025.
Regarding claim 83: The teachings of Nelles are discussed supra. Nelles do not teach a DR sequence with 100% sequence identity with seq ID NO: 295 of the instant invention.
As discussed supra, Cox teach a vector comprising the direct repeat sequence for PspCas13b P1-125 (Supp Table 5 pC0043 PspCas13b crRNA backbone, labeled “PspCas13b DR” in benchling sequence file).
The PspCas13b direct repeat sequence taught by Cox shares 95.6% sequence identity to Seq ID NO: 295 of the instant invention. The alignment of the instant Seq ID NO: 295 (QY) and Sequence the DR for PspCas13 as taught by Cox (Db) is shown below.
Qy 1 GTTGTGGAAGGTCCAGATTTGAGGGGCTATTACAAC 36
|||||||||||||||| |||||||||||||||||||
Db 36 GTTGTGGAAGGTCCAGTTTTGAGGGGCTATTACAAC 1
The sequences differ at a single nucleotide (A or T) in the loop of the direct repeat.
As discussed supra, it would have been obvious for one of ordinary skill in the art at the time of the effective filing date to modify the crRNA taught by Nelles with the DR taught by Cox which comprises the “AGTTTTGA” sequence for the loop of the direct repeat.
It would also have been obvious to modify the loop structure taught by Cox “TTTT” to comprise “ATTT”.
Lin teach the direct repeat loop structure is a flexible element for engineering and modification of one of the four residues in the loop can modulate the performance of the crRNA (p2653 col2 ¶1, Fig 1a). Lin further teach changing each of the nucleotides in the DR loop resulted in similar or better activity than the wild-type loop (p2652 (col1 ¶4).
Thus modifying one of the four nucleic acids in the DR loop would be a matter of routine optimization and one of ordinary skill in the art would have a reasonable expectation of predictable results because Lin teach DR loop mutants have similar or better performance than the wild type loop (p2652 col1 ¶4).
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention.
Claim 89 is rejected under 35 U.S.C. 103 as being unpatentable over Nelles et al (WO 2019/236982 A1) in view of Froelich (WO 2017/053753) and as evidenced by Shariat et al (AEM(2014)80:2;1010) and in further view of Cox et al (Science (2017) 24:358;1-23) as applied to claim 77, 81-82 and 86-88 above, and further in view of Zhang et al (Cell Res(2018)28:12;1198-1201).
Regarding claim 89: The claim recites Seq ID NO: 1, which is an amino acid sequence of 1,089 residues.
The teachings of Nelles are discussed supra. Nelles do not teach the Cas protein sequence comprises a sequence of Seq ID No 1.
Zhang teach the Cas13b sequence of Prevotella pectinovara (Accession WP_044065294.1) which is 100% identical to Seq ID NO 1.
Below is the alignment of Seq ID NO:1 (Query) of the instant application and Cas13b (Sbjct):
Alignment statistics for match #1
Score
Expect
Method
Identities
Positives
2250 bits(5830)
0.0
Compositional matrix adjust.
1089/1089(100%)
1089/1089(100%)
089(0%)
Query 1 NIPALVENQKKYFGTYSVMAMLNAQTVLDHIQKVADIEGEQNENNENLWFHPVMSHLYNA 60
NIPALVENQKKYFGTYSVMAMLNAQTVLDHIQKVADIEGEQNENNENLWFHPVMSHLYNA
Sbjct 2 NIPALVENQKKYFGTYSVMAMLNAQTVLDHIQKVADIEGEQNENNENLWFHPVMSHLYNA 61
Query 61 KNGYDKQPEKTMFIIERLQSYFPFLKIMAENQREYSNGKYKQNRVEVNSNDIFEVLKRAF 120
KNGYDKQPEKTMFIIERLQSYFPFLKIMAENQREYSNGKYKQNRVEVNSNDIFEVLKRAF
Sbjct 62 KNGYDKQPEKTMFIIERLQSYFPFLKIMAENQREYSNGKYKQNRVEVNSNDIFEVLKRAF 121
Query 121 GVLKMYRDLTNHYKTYEEKLNDGCEFLTSTEQPLSGMINNYYTVALRNMNERYGYKTEDL 180
GVLKMYRDLTNHYKTYEEKLNDGCEFLTSTEQPLSGMINNYYTVALRNMNERYGYKTEDL
Sbjct 122 GVLKMYRDLTNHYKTYEEKLNDGCEFLTSTEQPLSGMINNYYTVALRNMNERYGYKTEDL 181
Query 181 AFIQDKRFKFVKDAYGKKKSQVNTGFFLSLQDYNGDTQKKLHLSGVGIALLICLFLDKQY 240
AFIQDKRFKFVKDAYGKKKSQVNTGFFLSLQDYNGDTQKKLHLSGVGIALLICLFLDKQY
Sbjct 182 AFIQDKRFKFVKDAYGKKKSQVNTGFFLSLQDYNGDTQKKLHLSGVGIALLICLFLDKQY 241
Query 241 INIFLSRLPIFSSYNAQSEERRIIIRSFGINSIKLPKDRIHSEKSNKSVAMDMLNEVKRC 300
INIFLSRLPIFSSYNAQSEERRIIIRSFGINSIKLPKDRIHSEKSNKSVAMDMLNEVKRC
Sbjct 242 INIFLSRLPIFSSYNAQSEERRIIIRSFGINSIKLPKDRIHSEKSNKSVAMDMLNEVKRC 301
Query 301 PDELFTTLSAEKQSRFRIISDDHNEVLMKRSSDRFVPLLLQYIDYGKLFDHIRFHVNMGK 360
PDELFTTLSAEKQSRFRIISDDHNEVLMKRSSDRFVPLLLQYIDYGKLFDHIRFHVNMGK
Sbjct 302 PDELFTTLSAEKQSRFRIISDDHNEVLMKRSSDRFVPLLLQYIDYGKLFDHIRFHVNMGK 361
Query 361 LRYLLKADKTCIDGQTRVRVIEQPLNGFGRLEEAETMRKQENGTFGNSGIRIRDFENMKR 420
LRYLLKADKTCIDGQTRVRVIEQPLNGFGRLEEAETMRKQENGTFGNSGIRIRDFENMKR
Sbjct 362 LRYLLKADKTCIDGQTRVRVIEQPLNGFGRLEEAETMRKQENGTFGNSGIRIRDFENMKR 421
Query 421 DDANPANYPYIVDTYTHYILENNKVEMFINDKEDSAPLLPVIEDDRYVVKTIPSCRMSTL 480
DDANPANYPYIVDTYTHYILENNKVEMFINDKEDSAPLLPVIEDDRYVVKTIPSCRMSTL
Sbjct 422 DDANPANYPYIVDTYTHYILENNKVEMFINDKEDSAPLLPVIEDDRYVVKTIPSCRMSTL 481
Query 481 EIPAMAFHMFLFGSKKTEKLIVDVHNRYKRLFQAMQKEEVTAENIASFGIAESDLPQKIL 540
EIPAMAFHMFLFGSKKTEKLIVDVHNRYKRLFQAMQKEEVTAENIASFGIAESDLPQKIL
Sbjct 482 EIPAMAFHMFLFGSKKTEKLIVDVHNRYKRLFQAMQKEEVTAENIASFGIAESDLPQKIL 541
Query 541 DLISGNAHGKDVDAFIRLTVDDMLTDTERRIKRFKDDRKSIRSADNKMGKRGFKQISTGK 600
DLISGNAHGKDVDAFIRLTVDDMLTDTERRIKRFKDDRKSIRSADNKMGKRGFKQISTGK
Sbjct 542 DLISGNAHGKDVDAFIRLTVDDMLTDTERRIKRFKDDRKSIRSADNKMGKRGFKQISTGK 601
Query 601 LADFLAKDIVLFQPSVNDGENKITGLNYRIMQSAIA VYDSGDDYEAKQQFKLMFEKARLI 660
LADFLAKDIVLFQPSVNDGENKITGLNYRIMQSAIA VYDSGDDYEAKQQFKLMFEKARLI
Sbjct 602 LADFLAKDIVLFQPSVNDGENKITGLNYRIMQSAIA VYDSGDDYEAKQQFKLMFEKARLI 661
Query 661 GKGTTEPHPFLYKVFARSIPANAVEFYERYLIERKFYLTGLSNEIKKGNRVDVPFIRRDQ 720
GKGTTEPHPFLYKVFARSIPANAVEFYERYLIERKFYLTGLSNEIKKGNRVDVPFIRRDQ
Sbjct 662 GKGTTEPHPFLYKVFARSIPANAVEFYERYLIERKFYLTGLSNEIKKGNRVDVPFIRRDQ 721
Query 721 NKWKTPAMKTLGRIYSEDLPVELPRQMFDNEIKSHLKSLPQMEGIDFNNANVTYLIAEYM 780
NKWKTPAMKTLGRIYSEDLPVELPRQMFDNEIKSHLKSLPQMEGIDFNNANVTYLIAEYM
Sbjct 722 NKWKTPAMKTLGRIYSEDLPVELPRQMFDNEIKSHLKSLPQMEGIDFNNANVTYLIAEYM 781
Query 781 KRVLDDDFQTFYQWNRNYRYMDMLKGEYDRKGSLQHCFTSVEEREGLWKERASRTERYRK 840
KRVLDDDFQTFYQWNRNYRYMDMLKGEYDRKGSLQHCFTSVEEREGLWKERASRTERYRK
Sbjct 782 KRVLDDDFQTFYQWNRNYRYMDMLKGEYDRKGSLQHCFTSVEEREGLWKERASRTERYRK 841
Query 841 QASNKIRSNRQMRNASSEEIETILDKRLSNSRNEYQKSEKVIRRYRVQDALLFLLAKKTL 900
QASNKIRSNRQMRNASSEEIETILDKRLSNSRNEYQKSEKVIRRYRVQDALLFLLAKKTL
Sbjct 842 QASNKIRSNRQMRNASSEEIETILDKRLSNSRNEYQKSEKVIRRYRVQDALLFLLAKKTL 901
Query 901 TELADFDGERFKLKEIMPDAEKGILSEIMPMSFTFEKGGKKYTITSEGMKLKNYGDFFVL 960
TELADFDGERFKLKEIMPDAEKGILSEIMPMSFTFEKGGKKYTITSEGMKLKNYGDFFVL
Sbjct 902 TELADFDGERFKLKEIMPDAEKGILSEIMPMSFTFEKGGKKYTITSEGMKLKNYGDFFVL 961
Query 961 ASDKRIGNLLELVGSDIVSKEDIMEEFNKYDQCRPEISSIVFNLEKWAFDTYPELSARVD 1020
ASDKRIGNLLELVGSDIVSKEDIMEEFNKYDQCRPEISSIVFNLEKWAFDTYPELSARVD
Sbjct 962 ASDKRIGNLLELVGSDIVSKEDIMEEFNKYDQCRPEISSIVFNLEKWAFDTYPELSARVD 1021
Query 1021 REEKVDFKSILKILLNNKNINKEQSDILRKIRNAFDHNNYPDKGVVEIKALPEIAMSIKK 1080
REEKVDFKSILKILLNNKNINKEQSDILRKIRNAFDHNNYPDKGVVEIKALPEIAMSIKK
Sbjct 1022 REEKVDFKSILKILLNNKNINKEQSDILRKIRNAFDHNNYPDKGVVEIKALPEIAMSIKK 1081
Query 1081 AFGEYAIMK 1089
AFGEYAIMK
Sbjct 1082 AFGEYAIMK 1090
It would have been obvious for one of ordinary skill in the art at the time of the effective filing date to combine the Cas13b sequence taught by Zhang with RNA targeted CRISPR system taught by Nelles.
One of ordinary skill in the art would have been motivated to combine the Cas system taught by Nelles with the Cas13 taught by Zhang because Zhang disclose Cas13b is a type VI system which encompasses RNA-guided RNAses which would be desirable for the CRISPR/Cas system as taught by Nelles which targets RNA (p1198 col1 ¶1).
Combining the Cas system taught by Nelles with the Cas13b sequence taught by Zhang would have led to predictable results with a reasonable expectation of success because both inventions are drawn to RNA targeted CRISPR/Cas systems.
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention.
Claim 84 is rejected under 35 U.S.C. 103 as being unpatentable over Nelles et al (WO 2019/236982 A1) in view of Froelich (WO 2017/053753) and as evidenced by Shariat et al (AEM(2014)80:2;1010) ) and in further view of Cox et al (Science (2017) 24:358;1-23) as applied to claim 77, 81-82 and 86-88 above, and further in view of Cheng et al (US 2019/0002889 A1; previously cited).
This is a new rejection due to the Amendments filed 11/06/2025, however relies on the references of record from the action filed 08/07/2025.
Regarding claim 84: The claim recites the term “tandem array”. The instant specification is silent on an explicit definition for this term.
The teachings of Nelles are discussed supra. Nelles do not teach a tandem array comprising at least two crRNA.
Cheng disclose novel systems, methods and compositions of non-naturally occurring, engineered CRISPR systems (abstract). Cheng also disclose multiplexing Cas with multiple crRNAs targeting different sequences enables the manipulation of multiple RNA species for therapeutic applications requiring manipulation of multiple transcripts simultaneously (p52 para0402).
It would have been obvious for one of ordinary skill in the art at the time of the effective filing date to combine the crRNA taught by Nelles with the tandem array strategy taught by Cheng. One of ordinary skill in the art would have been motivated to combine the tandem array taught by Cheng with the crRNA taught by Nelles because doing so would allow for targeting multiple genes, or one gene at multiple sites, thus generating a more efficient CRISPR/Cas system. Combining the crRNA taught by Nelles with the tandem array taught by Cheng would have led to predictable results with a reasonable expectation of success because both inventions are drawn to CRISPR systems.
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention.
Claim 85 is rejected under 35 U.S.C. 103 as being unpatentable over Nelles et al (WO 2019/236982 A1) in view of Froelich (WO 2017/053753) and Cheng et al (US 2019/0002889 A1), and as evidenced by Shariat et al (AEM(2014)80:2;1010) ) and in further view of Cox et al (Science (2017) 24:358;1-23) as applied to claims 77, 81-82, 84 and 86-88 above, and further in view of Cheng et al (US 2019/0002889 A1, previously cited) and Tsui et al (Annu Rev Biophys (2015) 44;1036; previously cited).
This is a new rejection due to the Amendments filed 11/06/2025, however relies on the references of record from the action filed 08/07/2025.
Regarding claim 85: The claim recites “each crRNA comprises a guide sequence and a direct repeat (DR) sequence, wherein each DR sequence is different”
The teachings of Nelles are discussed supra. Nelles do not teach each direct repeat sequence is different.
Tsui disclose CRISPR direct repeat sequences are specific to the particular CRISPR-Cas system and dictate CRISPR-specific interactions (p2 para 3). Tsui also disclose a given organism may possess one, two, or all CRISPR-Cas types (p2 para1).
It would have been obvious for one of ordinary skill in the art at the time of the invention to have modified the CRISPR-Cas system taught by Nelles to incorporate different direct repeat sequences.
Use of different direct repeats in the same array would allow for the use of multiple CRISPR systems simultaneously and therefore a single array could target a host gene via both RNA and DNA, or a single array could be used directed to multiple genes via different CRISPR-Cas systems. This would provide the advantage of a more efficient and more flexible CRISPR-Cas system that could be beneficial in a therapeutic setting.
Substituting the direct repeat sequences as taught by Nelles for direct repeats that are different, as taught by Tsui, would have led to predictable results with a reasonable expectation of success because Tsui teach the direct repeat sequences are specific to a particular CRISPR-Cas type and multiple CRISPR-Cas systems can be used in parallel (the same unicellular organism can express multiple Cas systems).
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention.
Claim 92 is rejected under 35 U.S.C. 103 as being unpatentable Nelles et al (WO 2019/236982 A1) in view of Froelich (WO 2017/053753) and as evidenced by Shariat et al (AEM(2014)80:2;1010) ) and in further view of Cox et al (Science (2017) 24:358;1-23) as applied to claim 77, 81-82 and 86-88 above, and further in view of, and further in view of Moore et al (Molecular and Cellular Biology (1998) 18:2;1-10; previously cited) and Cong et al (Science (2013) 339;1-6).
Regarding claim 92: As discussed supra the claim as written is dependent on withdrawn claim 90. For purposes of compact prosecution the claim is interpreted as dependent on claim 87.
The teachings of Nelles are discussed supra. While Nelles teach the Cas protein comprises an NLS, Nelles do not teach the NLS comprises the sequence of Seq ID NO:67.
Moore teach the nuclear localization signal for integrase is sufficient for nuclear localization of integrase (abstract). Moore further teach the sequence of the NLS comprises the amino acid sequence between 591-635: “NSKKRSLEDNETEIKVSRDTWNTKNMRSLEPPRSKKRIH”, which shares 100% identity to the amino acid sequence of the instant Seq ID NO:67 (Fig 7).
Cong teach an a CRISPR/Cas system in which results in gene editing in eukaryotic cells using a Cas protein with a nuclear localization signal (1 col2 ¶2)
It would have been obvious for one of ordinary skill in the art at the time of the effective filing date to modify the crRNA taught by Nelles with the NLS of Moore because Moore teach IN nuclear localization is mediated by the C-terminal NLS (p1 col1 ¶2) and Cong teach a CRISPR/Cas system comprising a Cas protein with an NLS.
One of ordinary skill in the art would have been motivated to modify the composition taught by Nelles with the NLS taught by Moore because Cong teach attaching a nuclear localization signal ensures nuclear compartmentalization in mammalian cells (p2 col1 ¶1).
One would have had a reasonable expectation of success modifying the Cas protein as taught by Nelles with the NLS as taught by Cong because Cong teach successful gene editing with a Cas protein.
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention.
Response to Arguments
The responses are directed to the Arguments filed 11/06/2025.
Regarding Arguments directed to 35 USC § 112(a):
Applicant's arguments filed on 11/06/2025 have been fully considered and they are persuasive.
Applicant submits claim 80 has been cancelled and claims 89 and 92 has been amended to overcome the rejection.
This is persuasive because the claims no longer recite “at least 80% identical”. The rejection over 35 USC § 112(a) are withdrawn.
Regarding Arguments directed to 35 USC § 101:
Applicant's arguments filed on 11/06/2025 have been fully considered and they are persuasive.
Applicant submits the amended claims are not directed to a product of nature without significantly more. In view of the claim amendments this is found persuasive.
The rejection over 35 USC § 101 is withdrawn.
Regarding Arguments directed to 35 USC § 102:
Applicant's arguments filed on 11/06/2025 with regard to the 102 rejection based on Nelles have been fully considered and they are persuasive. The rejection under 102 based on Nelles is withdrawn due to the instant amendment.
Note that a new rejection under 35 USC § 103 based on Nelles is entered.
The claim rejections under 35 USC § 102 based on Smargon are withdrawn due to the instant amendment.
Regarding Arguments directed to 35 USC § 103:
Applicant's arguments filed on 11/06/2025 have been fully considered and they are persuasive. The rejection over 35 USC § 103 is withdrawn due to the instant amendment.
Conclusion
No claims are allowed.
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.
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/ANDREA LYNNE MORRIS SPENCER/Examiner, Art Unit 1631
/TAEYOON KIM/Primary Examiner, Art Unit 1631