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 .
Priority
This application is a CIP of PCT CN2024/119862 filed 09/19/2024. Acknowledgment is made of applicant's claim for foreign priority based on applications CN202410388592.2 and CN202311214330.6 filed in China on 04/01/2024 and 09/19/2023. It is noted, however, that applicant has not filed a certified copy of the either application as required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement filed 10/27/2025 has been considered.
Application Status
The Amendments and Remarks filed 05 January 2026 in response to the Office Action 31 October 2025 are acknowledged and have been entered. Claims 1, 4-6, 8, 11, 13-16, and 20 are amended. Claim 3 has been cancelled. Claims 1-2 and 4-20 are pending and being examined on the merits.
Any objection or rejection not reiterated herein has been overcome by applicant’s claim amendments.
Specification
The use of the term Cytiva, NEB, Ni Sepharose 6 Fast Flow, Thermo Scientific, Beckman COULTER, SPRISelect, Illumina, Invitrogen, Q5 Hot-Start 2x Master Mix, Qubit, Vidyabiotech, Viagen, Yeasen Biotechnology, Opti-MEM, GeneBank, Thermofisher, DirectPCR Lysis Reagent, to name a few, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term. A cursory review of the specification has revealed these trade names or marks. It would be remedial to check the specification for additional trademarks or names and amend all upon amendment.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 12-14 and 18-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a system or method that comprises a fusion protein comprising a Cas12 protein as listed in Tables 20 and 21 with editing efficiency, does not reasonably provide enablement for any Cas12 protein having at least 70% sequence identity to an amino acid sequence shown in SEQ ID NO: 696. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Nature of the Invention
The claims are directed to a method or a system that comprises a Cas12 protein having at least 70% sequence identity to an amino acid sequence shown in SEQ ID NO: 696. Enablement of the claims turns on whether one of ordinary skill in the art use any Cas12 protein having at least 70% sequence identity to an amino acid sequence shown in SEQ ID NO: 696 as in a CRISPR system which produces a function or in a method for detecting, binding, or cleaving a target nucleic acid.
State of the Art
Zhang (Zhang et al. Genome Biology (2023) 24:102) sought to conduct a de novo screen to identify mutations in LbCas12a that improve intrinsic enzymatic activity [pg. 3, last sentence]. Zhang teaches measuring cleavage activity of over 9000 point mutations with high reproducibility [pg. 4, first paragraph; Fig. 1C]. Zhang teaches that nearly all synonymous mutations (847) displayed no significant enrichment, as their scores tightly clustered around 0; and that there were 1977 point mutants with phenotype scores (i.e., natural logarithm of relative enrichment) greater than zero over three biological replicates [pg. 4, first paragraph; Table S1]. Therefore Zhang teaches that not all point mutation in LbCas12a has cleavage activity. Zhang also teaches that certain mutation at N527, G532 and K538 are detrimental to DNA cleavage in E. coli [pg. 4, paragraph 2-3; Fig. 1D].
Swarts (Swarts et al., 2017, Molecular Cell 66, 221–233) attempts to elucidate the molecular basis of both nuclease activities for Cas12a [abstract]. Swarts teaches that in the FnCas12a protein, the RuvC (E1006Q) and Nuc (R1218A0 domains impair DNA cleavage [pg. 222, col. 2, para 2]. Swarts teach that alanine substitution of Q704 or replacement of residues Thr698–Ser702 in FnCas12a with the sequence Ala-Gly3 substantially reduced DNA cleavage activity, suggesting that these residues contribute to R-loop formation by stabilizing the displaced conformation of the nontarget DNA strand [pg. 227, col. 1. Para 1; Fig. 3E].
Thereby the prior teaches that not only will certain mutation in Cas12a affect activity, some till affect conformational formation and stability, which in turns affect cleavage activity.
Breadth of the claims
The claims of the instant specification recite “the Cas12 protein comprises an amino acid sequence having at least 70% sequence identity to an amino acid sequence shown in SEQ ID NO: 696”. This recitation broadly encompass any single amino acid mutated SEQ ID NO: 696 Cas12 protein or multiple amino acid mutated SEQ ID NO: 696 Cas12 protein, as long at the mutated protein retains Cas12 protein.
Guidance of the Specification
The specification discloses some mutated C12-279 Cas12 proteins in Tables 20 and 21 and their editing efficiency. The specification do not teach all the possible mutated C12-279 Cas12 proteins that retain 70% sequence identity to an amino acid sequence shown in SEQ ID NO: 696.
Experimentation Required
In order to practice the claimed invention, an immense amount of experimentation would be required. To practice the invention as broadly claimed, it would be necessary for one of ordinary skill in the art to systematically test all possible mutation combinations for all species of Cas12 while retaining 70% sequence identity to an amino acid sequence shown in SEQ ID NO: 696. However, such experimentation would be highly unpredictable in view of the prior art. Accordingly, practicing the invention as broadly claimed would require a massive amount of highly unpredictable experimentation.
Taking into consideration the factors outlined above, including the nature of the invention, the breadth of the claims, the state of the art, the guidance provided by the applicant and the specific examples, it is the conclusion that an undue experimentation would be required to make and use the invention as claimed.
Allowable Subject Matter
The following is a statement of reasons for the indication of allowable subject matter: The closest art is Chong (US10808245 B2, published 10/20/20). Chong teaches an engineered, non-naturally occurring Cluster Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated (Cas) system comprising: (a) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence; and
(b) a CRISPR-Cas effector protein, Cas12i2, or a nucleic acid encoding Cas12i2, wherein the CRISPR-Cas effector protein comprises the amino acid sequence set forth in SEQ ID NO: 5, wherein the CRISPR-Cas effector protein binds to the RNA guide, and wherein the spacer sequence binds to a target nucleic acid [claim 1]. SEQ ID NO: 5 is 48% identical to SEQ ID NO: 696. Chong nor the prior art teaches a Cas12 protein that is at least 70% identical to SEQ ID NO: 696. Therefore, a sequence that is 70% identical to SEQ ID NO: 696 is free of the art.
Claims 2, 4-11, and 17 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
No claims allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TIFFANY N GROOMS whose telephone number is (571)272-3771. The examiner can normally be reached M-F 830-530.
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/TIFFANY NICOLE GROOMS/Examiner, Art Unit 1637