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 16 October 2025. Claims 1-5, 16-19, and 32-39 are currently pending. Claims 2-3 are withdrawn from prosecution as being drawn to non-elected subject matter. Accordingly, claims 1, 4-5, 16-19, and 32-39 are examined herein. The restriction requirement mailed 29 December 2022 is still deemed proper. Applicant's elected Group I without traverse in the reply filed 24 February 2023.
Applicant’s arguments have been thoroughly reviewed and are deemed persuasive. Applicant alleges that Zhang’s SEQ ID NO: 109 is missing an additional alanine residue when compared to the instantly claimed SEQ ID NO: 12 (Remarks; pg. 3-5). Accordingly, the previously pending 35 USC 102 rejections of record, filed 16 July 2025, have been withdrawn. Because the newly pending rejections of record were not necessitated by amendment, this action is NON-FINAL.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1, 4-5, 16-19, and 32-39 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zhang (PG Pub No. US 2016/0208243 A1) in view of Tanaka (FEBS letters 271.1-2 (1990): 41-46).
Regarding claims 1, 16-17, and 33, for the purposes of examination, the functional limitations of “wherein the engineered Cas12a nucleases exhibits a reduced rate of non-specific cleavage of single-stranded DNA (ssDNA) as compared to a reference wildtype Cas12a nuclease comprising the amino acid sequence of SEQ ID NO: 2” (see Claim 1), “wherein the engineered Cas12a nuclease exhibits a ssDNA cleavage rate that is less than 50% of the ssDNA cleavage rate of a reference wildtype Cas12a nuclease comprising the amino acid sequence of SEQ ID NO: 2” (see Claim 16), “wherein the reduced rate of non-specific cleavage of ssDNA is measured within 180 minutes of introducing the engineered Cas12a nuclease to ssDNA” (see Claim 17), and “wherein the engineered Cas12a nuclease cleaves dsDNA at a rate that is at least 50% of the cleavage rate of the cleavage rate of a reference wildtype Cas12a nuclease comprising the amino acid sequence of SEQ ID NO: 2” (see Claim 33) are interpreted as not structurally altering the claimed engineered Cas12a nuclease comprising the amino acid sequence of SEQ ID NO: 12. Accordingly, the claimed limitations are not given patentable weight.
Regarding claim 1, Zhang is drawn to an invention concerned with systems, methods, and compositions for targeting nucleic acids via Cpf1 enzymes (Abstract). Zhang teaches the use of a wild-type LbCpf1 enzyme having 100% sequence identity to the claimed SEQ ID NO: 12 except for a single amino acid mismatch at position R1138 of the sequence and a missing alanine at the C-terminus of the LbCpf1 enzyme (pg. 217; see SEQ ID NO: 109 in previously attached sequence alignment). Zhang teaches that an NLS may be attached to the C-terminal of the Cpf1 protein so that the protein may be optimally expressed and targeted to the nucleus of eukaryotic cells ([0049]). Zhang teaches that a reaction comprising the engineered Cpf1 may be incubated at 37 C for 30 minutes followed by a determination of successful cleavage of a PCR amplicon of a human Emx1 locus ([1647]-[1648]).
Zhang does not explicitly teach the use of an engineered Cas12a protein comprising the amino acid sequence of SEQ ID NO: 12 (Claim 1).
However, one of ordinary skill in the art would have further considered the teachings of Zhang and Tanaka as both references are common fields of endeavor pertaining to the use of Cpf1 proteins and NLS sequences.
Zhang further teaches that the LbCpf1 enzyme may be modified by a mutation at R1138 ([0238], [1716]). Zhang teaches that R1138 is a good target for mutagenesis as it is one of the positive charge residues of interest within a RuvC domain of the LbCpf1 enzyme and can enhance Cpf1 specificity when mutated ([1714]-[1715]). Zhang teaches that the disclosed wild-type CRISPR proteins may be modified via the substitution of an unmodified residue with a glutamic acid ([0280]).
Tanaka is drawn towards a study concerned with mechanisms of nuclear translocation (Abstract). Tanaka teaches that NLS sequences comprise a consensus sequence XXKK(R)XK(R) that is sufficient for nuclear translocation of proteins that are imported into the nucleus of a cell (pg. 42). Tanaka teaches the use of a human c-myc NLS sequence comprising the sequence AAKRVK (pg. 43; see Table II).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to try to modify the LbCpf1 sequence of Zhang such that it comprised an R1138E mutation and the C-terminal NLS sequence was substituted with a human c-myc NLS sequence, such that the resulting LbCpf1 sequence comprised the claimed SEQ ID NO: 12, as described by Tanaka. A person of ordinary skill in the art would have recognized that Zhang identified a need in the art to mutate the LbCpf1 protein at position R1138 in order to increase the specificity of the LbCpf1 protein. A person of ordinary skill in the art would have recognized that there are a finite number of amino acids that could be substituted at position R1138 and Zhang further teaches that utilizing a glutamic acid as a substitution in the wild type Cpf1 proteins was a preferred amino acid substitution. A person of ordinary skill in the art would have recognized that the known potential solutions could have been pursued because Zhang teaches that the Cpf1 proteins of the disclosure could be mutated and their editing efficiencies measured via cleavage assays. Further, a person of ordinary skill in the art would have had a reasonable expectation of success in substituting the C-terminal NLS sequence of Zhang for the NLS sequence of Tanaka because both references teach the use of NLS sequences that can localize a protein to the nucleus of a eukaryotic cell.
Regarding claims 4-5 and 34, Zhang teaches that the Cpf1 enzyme may be used in conjunction with a guide RNA (i.e., the engineered Cas12a nuclease is part of a ribonucleoprotein) ([0012]).
Regarding claim 17, Zhang teaches that a reaction comprising the engineered Cpf1 may be incubated at 37 C for 30 minutes followed by a determination of successful cleavage of a PCR amplicon of a human Emx1 locus (i.e., a cleavage assay may be performed within 180 minutes of introducing the engineered Cas12a) ([1647]-[1648]).
Regarding claims 18-19 and 32, Zhang teaches that the target nucleic acid may be double stranded DNA ([0221]). Zhang teaches that the Cpf1 may be expressed in a eukaryotic cell ([0212]). Zhang teaches that the eukaryotic cell may be a plant cell ([0218]).
Regarding claim 35, Zhang teaches that the guide RNA may be 15 to 35 nucleotides in length ([0049]).
Regarding claim 36, Zhang teaches that the Cpf1 ribonucleoprotein does not require a tracrRNA ([0186]).
Regarding claim 37, Zhang teaches that the Cpf1 enzyme may be provided via a polynucleotide encoding the enzyme ([0024]).
Regarding claims 38-39, Zhang teaches the use of a delivery system that can comprise the nucleic acid molecule encoding the Cpf1 enzyme and a nucleic acid molecule encoding at least one guide nucleic acid ([0350]-[0358]).
Response to Arguments
Insofar as Applicant’s arguments are applicable to the currently utilized Zhang reference, Applicant’s arguments have been fully considered but are not found persuasive.
Applicant alleges that Zhang teaches that any residue in any Cpf1 protein can be substituted with any amino acid; therefore, Zhang teaches an infinite number of possible sequences (Remarks; pg. 5).
This argument is not found persuasive because MPEP 2143(I)(E) teaches that utilizing the “obvious to try” rationale requires the following:
“(1) a finding that at the relevant time, there had been a recognized problem or need in the art, which may include a design need or market pressure to solve a problem;
(2) a finding that there had been a finite number of identified, predictable potential solutions to the recognized need or problem;
(3) a finding that one of ordinary skill in the art could have pursued the known potential solutions with a reasonable expectation of success; and
(4) whatever additional findings based on the Graham factual inquiries may be necessary, in view of the facts of the case under consideration, to explain a conclusion of obviousness.”
In the instant case, Zhang teaches that (1) there was a need in the art to mutate LbCpf1 proteins at position R1138 with an amino acid other than the wild type amino acid, (2) that the possible amino acid substitutions at position R1138 were finite and that a preferred substitution was a glutamic acid substitution, and (3) the known potential solutions could have been pursued with a reasonable expectation of success because Zhang teaches that cleavage assays could be performed with mutated Cpf1 proteins and their cleavage activities measured. Thus, as required by MPEP 2143(I)(E), Zhang in view of Tanaka renders obvious the claimed engineered nuclease.
Applicant alleges that Zhang does not provide any teaching that specifically suggests changing position 1138 from a positively charged arginine an oppositely charged glutamic acid because Zhang teaches that conservative amino acid substitutions are preferred (Remarks; pg. 6).
This argument is not found persuasive because Zhang teaches that conservative amino acid substitutions may be made according to the table present in paragraph [0921] ([0920]-[0921]). Zhang teaches that arginine and glutamic acid are both polar amino acids that are grouped together in a known set of polar amino acids ([0920]-[0921]). Thus, Zhang teaches that arginine can be substituted with a glutamic acid.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KYLE T REGA whose telephone number is (571)272-2073. The examiner can normally be reached M-R 8:30-4:30, every other F 8:30-4:30 (EDT/EST).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached at 571-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636