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 .
Applicant’s arguments and amendments filed on 1/22/2026 have been entered.
Claim 10 has been amended and its objection has been withdrawn.
Claims 1, 5-8, 10, 11, 13, 15, 17-19 and 26-28 are examined in the instant application.
Priority
Acknowledgment is made of applicant's claim for foreign priority based on applications filed in Korea on 10/29/2019 and 10/29/2020. It is noted, however, that applicant has not filed a certified copy of the 10-2019-0135935 or the PCT/KR2020/014961 applications as required by 37 CFR 1.55.
Thus, for the reasons set forth above and for the purposes of applying prior art, Applicant’s earliest effective filing date is 3/29/2022.
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.
Claim(s) 1, 5, 8, 10, 11, 13, 15, 17, 18, 27 and 28 remain rejected under 35 U.S.C. 103 as being unpatentable over Zhu et al. (2018, National Science Rev., Vol 6, pgs. 438-451) in view of Karvelis et al. (April 2020, Nucleic Acids Res., Vol. 48(9), pgs. 5016-5023) and Moon et al. (2018, Nature Communications, Vol. 9:3651, pgs. 1-11) for reasons of record in the Non-Final Office Action mailed on 10/22/2025 (and repeated below).
Regarding claims 1, 5 and 10, Zhu et al. teach an engineered crRNA and guide RNA for a CRISPR/Cas12 system comprising a spacer sequence which is complementary to the target sequence, a tracrRNA sequence and a scaffold which interacts with a Cas12 protein (pg. 442 col. 2 parag. 2 bridge pg. 444 col. 2 parag. 1, Fig. 1 and Table 1).
Zhu teaches that the “Although CRISPR-Cas9 is the most powerful genome editing tool so far and has been successfully applied in a broad range of organisms [31,33], the high ratio of off-target effects of CRISPR-Cas9 technology cannot be ignored” (pg. 444 col. 1 parag. 2 lines 1-5) and to address this a more efficient genome editing tool using Cas12 may be an alternative to Cas9 (pg. 444 col. 1 parag. 3).
Zhu does not teach:
a vector comprising a sequence encoding Cas12f1; and
a U-rich tail sequence and multiple guide RNAs (i.e multiplexed).
Regarding Cas12f1, Karvelis et al. teach the discovery of a novel CRISPR/Cas
system comprising Cas12f1 which provides the same genome editing ability as Cas9 systems (see Abstract and Introduction).
Specifically, Karvelis teaches “Taken together, this confirms that at least some Cas12f effectors function like Cas9 and Cas12 nucleases to recognize, cleave, and protect against dsDNA invaders in a heterologous host. In all, our results significantly improve our understanding of novel CRISPR-Cas systems and pave the way for the adoption of
programmable miniature nucleases for genome editing applications.” Pg. 5023 col. 1 parag. 1).
Regarding using a U-rich tail sequence in a multiplexed vector system in claims 11 and 17, Moon et al. teach an “enhanced CRISPR/Cpf1 system, in which crRNA has a repeat sequence and a 20-nt target-complementary sequence plus a uridinylate-rich 3’-overhang. For synthetic crRNA, the addition of 8-meric uridinylates (U8) created the most efficient indel efficiency. For transcribed crRNA, T4AT6 created a maximum indel efficiency of Cpf1 when added as a 3’-overhang after a 20-base target sequence in the template DNA. The engineered U-rich crRNA enabled a highly efficient and specific genome editing by Cpf1. This engineered CRISPR-Cpf1 system will significantly contribute to enhancing the genome-editing toolbox.” (pg. 2 col. 1 parag. 3 line 13 bridge col. 2 parag. 1).
Moon continues to teach a multiplexed CRISPR/Cas12f complex comprising three guide RNAs (crRNA 1-3) with corresponding U6 promoters (pg. 3 col. 2 parag. 2 and Fig. 5A, reproduced below).
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Moon continues to teach that using a U-rich tail sequence made multiplexed genome editing easier (pg. 7 col. 1 parag. 1).
Regarding claim 8, Moon teaches that the U-rich tail can be five uridines in length (Fig. 1E).
Regarding claims 13, 15, 27 and 28, Moon teaches that the vector can be an AAV vector (pg. 9 col. 1 parag. 2).
Regarding claim 18, Moon teaches using the U6 promoter for the second and third promoter sequence (pg. 5 col. 1 parag. 1 and Fig. 5A).
Thus, at the time of filing the ordinary artisan would have found it prima facie obvious to combine the teachings of Zhu regarding a crRNA for CRISPR/Cas12 with the teachings of Karvelis regarding Cas12f1 and with the Moon regarding the benefits of using a U-rich tail in a CRISPR/Cas12 multiplex system to arrive at the claimed invention.
One of ordinary skill in the art would have been motivated to make such a combination since Karvelis teaches that Cas12f1 can be used as an alternative to Cas9 and Moon teaches that using a U-rich tail in a Cas12f system makes gene editing easier.
There would have been a reasonable expectation of success that the CRISPR/Cas system of Zhu could be modified to use a Cas12f1 since Karvelis teaches that Cas12f1 has the same ability to cut as Cas9.
Thus the cited art provides the requisite teachings and motivations to make and use the invention as claimed.
Response to Arguments
Applicant’s Arguments
Applicants argue in amendment that Karvelis primarily focuses on protein structure, PAM recognition, and cleavage activity, not guide RNA engineering. Id. at page 5017-5019. The guide RNAs employed in Karvelis are conventional and lack the claimed U-rich tail architecture. Id. at page 5017, column 2 (RNA Synthesis). Accordingly, Karvelis provides no teaching, suggestion, or motivation to modify crRNA structure in the manner claimed by Applicant.
Moon discloses a CRISPR/Cpfl (Cas12a) system in which a uridylate-rich 3' overhang is
appended to crRNA to improve genome-editing efficiency. Moon at page 2, column 2 (Results),
and pages 3-4 (crRNA with the U-tail improves Cpfl activity in vivo). While Moon teaches a U-
rich tail, it does SO exclusively in the context of Cpfl, a system that is structurally, mechanistically, and evolutionarily distinct from Cas12f1.
Critically, Moon uses different Cas proteins than Applicant's claims. The AsCpfl
disclosed in Moon consists of ~1307 amino acids and includes a Nuc domain. Moon at page 3.
In contrast, the Cas12f1 proteins recited in Applicant's claims consist of approximately 500-1050
amino acids and lack a Nuc domain. Application at paragraphs [0288]-[0304].
Moon also relies on different guide RNA requirements. Specifically, Moon's Cpfl
systems require only crRNA, while Applicant's claimed Cas12f1 systems comprise a dual-RNA
architecture, including both crRNA and tracrRNA. Moon at page 2, first column; Application at
paragraph [0421]. These differences materially affect RNA-protein interactions and system
function.
Moreover, Moon's Cpf1 system arises from different microorganisms and CRISPR
subclasses, reflecting distinct evolutionary origins and architectures.
Karvelis primarily focuses on protein structure, PAM recognition, and cleavage activity,
not guide RNA engineering. Id. at page 5017-5019. The guide RNAs employed in Karvelis are
conventional and lack the claimed U-rich tail architecture. Id. at page 5017, column 2 (RNA
Synthesis). Accordingly, Karvelis provides no teaching, suggestion, or motivation to modify
crRNA structure in the manner claimed by Applicant.
Moon discloses a CRISPR/Cpfl (Cas12a) system in which a uridylate-rich 3' overhang is
appended to crRNA to improve genome-editing efficiency. Moon at page 2, column 2 (Results),
and pages 3-4 (crRNA with the U-tail improves Cpfl activity in vivo). While Moon teaches a U-
rich tail, it does SO exclusively in the context of Cpfl, a system that is structurally,
mechanistically, and evolutionarily distinct from Cas12f1.
Critically, Moon uses different Cas proteins than Applicant's claims. The AsCpfl
disclosed in Moon consists of ~1307 amino acids and includes a Nuc domain. Moon at page 3.
In contrast, the Cas12f1 proteins recited in Applicant's claims consist of approximately 500-1050
amino acids and lack a Nuc domain. Application at paragraphs [0288]-[0304].
Moon also relies on different guide RNA requirements. Specifically, Moon's Cpfl
systems require only crRNA, while Applicant's claimed Cas12f1 systems comprise a dual-RNA
architecture, including both crRNA and tracrRNA. Moon at page 2, first column; Application at
paragraph [0421]. These differences materially affect RNA-protein interactions and system
function.
Moreover, Moon's Cpf1 system arises from different microorganisms and CRISPR
subclasses, reflecting distinct evolutionary origins and architectures.
Because of these fundamental differences, the behavior of guide RNA modifications in a
Cpfl system cannot be extrapolated to Cas12f1. Moon provides no teaching or suggestion that a
U-rich 3' tail would function - let alone enhance efficiency - in a Cas12f1 system.
Given the distinct protein architectures, guide RNA requirements, and mechanistic
differences between Cpfl and Cas12fl systems, a skilled artisan would not reasonably expect that
a crRNA modification effective in Cpfl would operate similarly in Cas12f1. At minimum, the
results would be unpredictable, and the prior art provides no guidance suggesting that the claimed configuration would improve editing efficiency in Cas12f1.
The unexpected performance improvements demonstrated in the present Application
further underscore the non-obviousness of the claimed systems and methods.
Examiner’s Response
While Applicants arguments have been fully considered they are not found persuasive. Applicant’s make the argument that there is unexpected performance improvements demonstrated in the present Application which further underscores the non-obviousness of the claimed systems and methods. However, this argument is not persuasive. There are no functional limitations recited in the claims and particularly no limitations regarding performance improvements. The claimed crRNA is only required to be capable of editing a nucleic acid. Regarding Applicants arguments with respect to Moon, they are not found persuasive. While Moon does not teaching using the claimed CRISPR/Cas12f1, Moon teaches that using a U-rich tail in a Cas system can make gene editing easier. There are no teachings in Moon that the U-rich tail would be exclusive to only the Cas of their system. While the structures of different Cas proteins may differ, they function the same, i.e. editing a nucleic acid. The ordinary artisan is provided by the teachings of Moon that a U-rich tail may be beneficial in a CRISPR/Cas system and it would be obvious to try a U-rich tail in the cRNA of Zhu and Karvelis in view of teachings in Moon.
Thus for the reasons above and of record the rejection is maintained.
Claim(s) 6 and 7 remain rejected under 35 U.S.C. 103 as being unpatentable over Zhu et al. (2018, National Science Rev., Vol 6, pgs. 438-451) in view of Karvelis et al. (April 2020, Nucleic Acids Res., Vol. 48(9), pgs. 5016-5023) and Moon et al. (2018, Nature Communications, Vol. 9:3651, pgs. 1-11) as applied to claims 1, 5, 8, 10, 11, 13, 15, 17, 18, 27 and 28 above, and further in view of Mir et al. (2018, Nature Communications, Vol. 9, pgs. 1-9) for reasons of record in the Non-Final Office Action mailed on 10/22/2025 (and repeated below).
Zhu, Karvelis and Moon are relied upon above in teaching an engineered crRNA for a CRISPR/Cas12f1 system.
Zhu, Karvelis and Moon do not teach:
Using the linker sequence 5’-gaaa-3’.
Regarding the linker sequence 5’-gaaa-3’, Mir et al. al teach that “that crRNA
and tracrRNA can be fused with a GAAA tetraloop or other linkers to yield a single guide RNA (sgRNA) with enhanced efficacy.” (pg. 6 col. 1 parag. 2 lines 1-3).
Thus at the time of filing the ordinary artisan would have found it prima facie obvious to combine the teachings of Zhu, Karvelis and Moon regarding an engineered crRNA for a CRISPR/Cas12f1 system with the teachings of Mir regarding the GAAA linker to arrive as the claimed invention.
One of ordinary skill in the art would have been motivated to make such a combination since Mir teaches that using the linker GAAA can result in enhanced efficacy fusing crRNA and tracrRNA.
There would have been a reasonable expectation of success that GAAA linker of Mir would work in the system of Zhu, Karvelis and Moon since Mir teaches that the GAAA linker is effective for increasing efficacy of the sgRNA.
Thus the cited art provides the requisite teaching and motivations to make and use the invention as claimed.
Response to Arguments
Applicants provide no specific arguments regarding this rejection, thus for the reasons of record the rejection is maintained.
Claim(s) 19 remains rejected under 35 U.S.C. 103 as being unpatentable over Zhu et al. (2018, National Science Rev., Vol 6, pgs. 438-451) in view of Karvelis et al. (April 2020, Nucleic Acids Res., Vol. 48(9), pgs. 5016-5023) and Moon et al. (2018, Nature Communications, Vol. 9:3651, pgs. 1-11) as applied to claims 1, 5, 8, 10, 11, 13, 15, 17, 18, 27 and 28 above, and further in view of Gao et al. (2019, Molecular Therapy: Nucleic Acids, Vol. 14, pgs. 32-40) for reasons of record in the Non-Final Office Action mailed on 10/22/2025 (and repeated below).
Zhu, Karvelis and Moon are relied upon above in teaching an engineered crRNA for a CRISPR/Cas12f1 system.
Zhu, Karvelis and Moon do not teach:
using a H1 promoter and a U6 promoter.
Regarding using H1 and U6 promoters, Gao et al. al teach that both the H1 and
U6 promoters can be used to drive expression in CRISPR/Cas system and that the both the H1 and U6 promoters can be used together. Specifically, Gao teaches “In vector-based
CRISPR-Cas9 systems, an RNA polymerase (Pol) III (Pol III) promoter like U6 or H1 is commonly used for gRNA production” (pg. 32 col. 1 parag. 2 lines 4-6 and Fig. 1A).
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Thus at the time of filing the ordinary artisan would have found it prima facie obvious to combine the teachings of Zhu, Karvelis and Moon regarding an engineered crRNA for a CRISPR/Cas12f1 system with the teachings of Gao regarding H1 and U6 promoters to arrive as the claimed invention.
One of ordinary skill in the art would have been motivated to make such a combination since Gao teaches that both H1 and U6 can be used in gRNA production and teaches that both the H1 and U6 can be used together as well as interchangeably. Thus as a design choice the ordinary artisan would be motivated to use the H1 and U6 promoters as claimed to drive expression in the CRISPR/Cas12f1 system of Zhu, Karvelis and Moon.
There would have been a reasonable expectation of success that the H1 and U6 promoters could function together in the CRISPR/Cas12f1 system of Zhu, Karvelis and Moon since Gao teaches successful expression of Cas9 using H1 and U6 promoters together.
Thus the cited art provides the requisite teaching and motivations to make and use the invention as claimed.
Response to Arguments
Applicants provide no specific arguments regarding this rejection, thus for the reasons of record the rejection is maintained.
Claim(s) 26 remians rejected under 35 U.S.C. 103 as being unpatentable over Zhu et al. (2018, National Science Rev., Vol 6, pgs. 438-451) in view of Karvelis et al. (April 2020, Nucleic Acids Res., Vol. 48(9), pgs. 5016-5023) and Moon et al. (2018, Nature Communications, Vol. 9:3651, pgs. 1-11) as applied to claims 1, 5, 8, 10, 11, 13, 15, 17, 18, 27 and 28 above, and further in view of Burstein et al. (2018, Nature Communications, Vol. 7:10613, pgs. 1-8) for reasons of record in the Non-Final Office Action mailed on 10/22/2025 (and repeated below).
Zhu, Karvelis and Moon are relied upon above in teaching an engineered crRNA for a CRISPR/Cas12f1 system.
Zhu, Karvelis and Moon do not teach:
a tracrRNA having a sequence of SEQ ID NO: 60 and a crRNA repeat sequence of SEQ ID NO: 58.
Regarding a tracrRNA and crRNA in SEQ ID NOs 60 and 58 respectively,
Burstein et al. al teach a tracrRNA and crRNA which are 100% identical to the sequences set forth in SEQ ID NOs 58 and 60. Specifically, Burstein teaches:
“Microorganisms play fundamental roles in the functioning of the biosphere, yet their existence depends on their ability to resist viral predation. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR associated) systems are common defence mechanisms that confer bacteria and archaea with acquired immunity to viruses. The two main parts of the system are a CRISPR array, composed of spacers matching foreign DNA flanked by repeats, and an operon of cas genes that encode for proteins that process the CRISPR array and cleave DNA targeted by the spacers1–3. Due to its high specificity and programmable nature, CRISPR-Cas has been harnessed to develop a powerful new genome editing technology4–6. Current knowledge of the frequency and distribution of CRISPR-Cas is based primarily on genomes of isolated microorganisms3,7. Here, we expand the investigation of the prevalence, variety and taxonomic distribution of these systems to include more than 40 major lineages of uncultivated bacteria and archaea.” (Abstract lines 1-18).
Burstein has identified multiple sequences in bacteria which are effective in a CRISRP/Cas system such as the nucleotide sequences set forth in SEQ ID NOs 58 and 60.
SEQ ID NO: 58
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SEQ ID NO: 60
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Thus at the time of filing the ordinary artisan would have found it prima facie obvious to combine the teachings of Zhu, Karvelis and Moon regarding an engineered crRNA for a CRISPR/Cas12f1 system with the teachings of Burstein regarding sequences effective in a CRISPR/Cas system to arrive as the claimed invention.
One of ordinary skill in the art would have been motivated to make such a combination since Burstein teaches that CRISPR/Cas sequence can be used to for editing genomic sequences.
There would have been a reasonable expectation of success that the nucleotide sequences of Burstein would work in the CRISPR/Cas12f1 system of Zhu, Karvelis and Moon since Burstein teaches specific nucleotide sequences identified for functioning in a CRISPR/Cas system.
Thus the cited art provides the requisite teaching and motivations to make and use the invention as claimed.
Response to Arguments
Applicants provide no specific arguments regarding this rejection, thus for the reasons of record the rejection is maintained.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DAVID A MONTANARI whose telephone number is (571)272-3108. The examiner can normally be reached M-Tr 8-6.
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DAVID A. MONTANARI
Examiner
Art Unit 1632
/ANOOP K SINGH/Primary Examiner, Art Unit 1632
Prosecution Insights