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 .
Sequence Compliance
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 through 1.825 because there are sequences in figures 4A, 5A, and 10A, for example, that do not contain a SEQ ID NO.
A complete response to this office action must correct the defects cited above regarding compliance with the sequence rules and a response to the action on the merits which follows.
The aforementioned instance of failure to comply is not intended as an exhaustive list of all such potential failures to comply in the instant application. Applicants are encouraged to thoroughly review the application to ensure that the entire application is in full compliance with all sequence rules. This requirement will not be held in abeyance.
Drawings
The drawings filed on 4/20/23 are objected to because they contain sequences that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2), but each sequence does not contain a SEQ ID NO., as explained in the “Sequence Compliance” section above. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 1 and 6 are objected to because of the following informalities: It appears that applicant inadvertently omitted “or” between parts (b) and (c) of claims 1 and 6. Appropriate correction is required.
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 1-19 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.
Claim 1 part (b) recites that one to several amino acids are deleted, inserted, substituted, or added in a portion other than amino acid positions 118, 122, 126, and 178 relative to SEQ ID NO: 1. The specification does not define what structural relationship is required to be “relative” to SEQ ID NO: 1 and therefore the claim language is indefinite. The specification does not provide a standard for what the term means.
Claim 6 recites “relative” to SEQ ID NO: 1 in part (b).
“Relative” to can be interpreted as considered in relation or in proportion to SEQ ID NO: 1. The language does not require for the deletion, insertion, or substitution to be at the exact position as located in SEQ ID NO: 1, but rather any position that is relative to it.
Amendment to claim 1 to recite “one to several amino acids are deleted, inserted, substituted, or added in a portion other than amino acid positions 118, 122, 126, and 178 of the sequence of SEQ ID NO: 1” would obviate this rejection of claim 1 and the claims depending from claim 1.
Amendment to claim 6 to recite “(b) an amino acid sequence in which one to several amino acids are deleted, inserted, substituted, or added in a portion other than amino acid positions 156 and 146 of the sequence of SEQ ID NO:1” would obviate this rejection of claim 6 and the claims depending from claim 6.
The remainder of the claims are rejected because they depend from claim 1 or 6 and do not overcome the rejection.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-19 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Instant claim 1 is directed to: A ribonucleoprotein effector complex that consists of:(i) a guide RNA and (ii) a protein comprising a sequence of any length having 80% homology to SEQ ID NO: 1 including any one amino acid sequence of the following (a) to (c):
(a) an amino acid sequence containing at least one substitution of an amino acid residue selected from the group consisting of I118, Y122, I126, and M178 in an amino acid sequence set forth in SEQ ID NO: 1,
(b) an amino acid sequence in which one to several amino acids are deleted, inserted, substituted, or added in a portion other than amino acid positions 118, 122, 126, and 178 relative to SEQ ID NO: 1, or
(c) an amino acid sequence having 95% or more identity in a portion other than the amino acid positions 118, 122, 126, and 178 of the amino acid sequence represented by (a) above,
wherein the protein forms a homodimer and forms the ribonucleoprotein effector complex with the guide RNA.
Regarding part (b), the specification does not adequately describe the structure required for the amino acid sequence in which one to several amino acids are deleted, inserted, substituted, or added in a portion other than amino acid positions 118, 122, 126, and 178 “relative” to SEQ ID NO: 1. The term “relative” does not impart a specific structural requirement. It is assumed that applicant intends for portion to be a portion other than amino acid positions 118, 122, 126, and 178 of the sequence of SEQ ID NO: 1.
Additionally, the specification does not adequately describe amino acids that have one to “several” (more than two but not many) amino acids that are deleted, inserted, substituted, or added in a portion other than amino acid positions 118, 122, 126, and 178 of the sequence of SEQ ID NO: 1 that has the required function. The specification does not disclose any additional species other than 118C, Y122C, N133R, E174R, N177R, S187R, N470R, and N483 that have the required function and therefore do not disclose species that are representative of the entire claimed genus.
Regarding part (c), the specification does not adequately describe the structure required for the amino acid sequence to be any amino acid sequence of any length that has 95% or more identity in any portion other than the amino acid positions 118, 122, 126, and 178 of the amino acid sequence represented by (a) above, and have the required function.
Instant claim 6 is directed to: A ribonucleoprotein effector complex that consists of:(i) a guide RNA and (ii) a protein comprising a sequence of any length having 80% homology to SEQ ID NO: 1 including any one amino acid sequence of (a) to (c):
(a)an amino acid sequence containing a substitution of an amino acid residue of A156 and/or Y146,
(b)an amino acid sequence in which one to several amino acids are deleted, inserted, substituted, or added in a portion other than amino acid positions 156 and 146 relative to SEQ ID NO:1, or
(c)an amino acid sequence having 95% or more identity in a portion other than the amino acid positions 156 and 146 relative to SEQ ID NO:1.
The remainder of the claims are rejected because they depend from claim 1 or 6 and do not overcome the rejection.
Regarding part (b), the specification does not adequately describe the structure required for the amino acid sequence in which one to several amino acids are deleted, inserted, substituted, or added in a portion other than amino acid positions 156 and 146 “relative” to SEQ ID NO:1. The term “relative” does not impart a specific structural requirement. It is assumed that applicant intends for portion to be a portion other than amino acid positions 156 or 146 of the sequence of SEQ ID NO: 1. Part (c) also recites “relative” to.
Additionally, the specification does not adequately describe amino acids that have one to “several” (more than two but not many) amino acids that are deleted, inserted, substituted, or added in a portion other than amino acid positions 156 and 146 of the sequence of SEQ ID NO: 1 that has the required function. The specification does not disclose any additional species other than 118C, Y122C, N133R, E174R, N177R, S187R, N470R, and N483 that have the required function and therefore do not disclose species that are representative of the entire claimed genus.
Regarding part (c), the specification does not adequately describe the structure required for the amino acid sequence to be any amino acid sequence of any length that has 95% or more identity in any portion other than other than the amino acid positions 156 and 146 of the sequence of SEQ ID NO: 1, and have the required function.
The remainder of the claims are rejected because they depend from claim 1 or 6 and do not overcome the rejection.
Additionally, claim 14 recites a “nucleic acid base converting enzyme”, although the specification only discloses cytosine deaminase, cytidine deaminase, and adenosine deaminase as species of nucleic acid converting enzymes. Without further description of the structure required for the enzyme to have the function of being nucleic acid base converting, one would not be able to readily envision which enzymes are necessarily included or excluded from the recited genus.
The MPEP states that for a generic claim, the genus can be adequately described if the disclosure presents a sufficient number of representative species that encompass the genus. See MPEP § 2163. If the genus has a substantial variance, the disclosure must describe a sufficient variety of species to reflect the variation within that genus. See MPEP § 2163. Although the MPEP does not define what constitute a sufficient number of representative species, the courts have indicated what do not constitute a representative number of species to adequately describe a broad genus. In Gostelli, the courts determined that the disclosure of two chemical compounds within a subgenus did not describe that subgenus. In re Gostelli, 872, F.2d at 1012, 10 USPQ2d at 1618. Additionally, in Carnegie Mellon University v. Hoffman-La Roche Inc., Nos. 07-1266, -1267 (Fed. Cir. Sept. 8, 2008), the Federal Circuit affirmed that a claim to a genus described in functional terms was not supported by the specification’s disclosure of species that were not representative of the entire genus. Furthermore, for a broad generic claim, the specification must provide adequate written description to identify the genus of the claim. In Regents of the University of California v. Eli Lilly & Co. the court stated:
"A written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as by structure, formula, [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." Fiers, 984 F.2d at 1171, 25 USPQ2d 1601; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284985 (CCPA 1973) ("In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus ...") Regents of the University of California v. Eli Lilly & Co., 43 USPQ2d 1398.
The Guidelines for Examination of Patent Applications under the 35 USC § 112, first paragraph, “Written Description” Requirement”, published at Federal Register, Vol. 66, No. 4, pp. 1099-1111 outline the method of analysis of claims to determine whether adequate written description is present. The first step is to determine what the claim as a whole covers, i.e., discussion of the full scope of the claim. Second, the application should be fully reviewed to understand how applicant provides support for the claimed invention including each element and/or step, i.e., compare the scope of the claim with the scope of the description. Third, determine whether the applicant was in possession of the claimed invention as a whole at the time of filing.
To achieve the desired function, it appears that the amino acid must comprise instant SEQ ID NO: 1 other than having a 118C, Y122C, N133R, E174R, N177R, S187R, N470R, or N483 mutation. The specification discloses that these variants exhibited increased enzymatic activities (example 3), whereas others were not confirmed or were degraded (examples 1 and 2).
Thus, in view of the guidelines, it is clear that the specification does not disclose a representative number of species for the instant ribonucleoprotein effector complexes within the instant enormous genus that have the structure to result in the required function. Thus, one skilled in the art would be led to conclude that Applicant was not in possession of the claimed invention at the time the application was filed.
Claims 12-15, 17, and 19 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 method of delivering a ribonucleoprotein complex that comprises instant SEQ ID NO: 1 other than having a 118C, Y122C, N133R, E174R, N177R, S187R, N470R, or N483 mutation with a resultant increase in enzymatic activity, does not reasonably provide enablement for each of the recited outcomes via delivery of any ribonucleoprotein effector complex within the instantly recited genus. 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/or use the invention commensurate in scope with these claims.
Factors to be considered in a determination of lack of enablement include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure.
In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)
The instant claims are directed to a method of editing a genome, a method for site-specific modification of a target double-stranded polynucleotide, or a method for regulating expression of a gene via delivery of any ribonucleoprotein effector complex within the instantly recited genus.
The specification discloses in vitro transfection of HEK293 cells with a plasmid containing each of the genes encoding mutant Cas12f (118C, Y122C, N133R, E174R, N177R, S187R, N470R, or N483) and a sgRNA plasmid with a resultant increase in enzymatic activity (Example 3).
Instant claims 12 and 13 encompass editing a genome or site-specific modification of a target double-stranded polynucleotide in vivo. The in vitro transfection of specific plasmids of the specification is not enabling for broad systemic delivery of any ribonucleoprotein effector complex of the genus of claim 1 or 6 with the predictable in vivo outcomes as claimed.
Cas12f, like other Cas proteins, has specific requirements for targeting, including a defined protospacer adjacent motif (PAM) sequence and complementarity between its guide RNA (gRNA) and the target DNA. However, the instant methods do not require for the target to have any of these requirements. For example, Karvelis et al. (Nucleic Acids Research, 2020, Vol. 48, No. 9, pages 5016-5023) teach that CRISPR–Cas12f nucleases recognize and cleave dsDNA in a PAM dependent manner (abstract).
Karvelis et al. teach that Cas12f proteins differ significantly in length. Due to this and their similarity to transposase associated TnpB proteins, it is hypothesized that they are remnants or intermediates of type V CRISPR–Cas system evolution and are incapable of forming the protein architecture required for dsDNA target recognition and cleavage. Karvelis et al. teach that miniature Cas12f effectors (from Cas14 and type V-U3 families), like most other Cas12 proteins, are able to cleave dsDNA targets if a 5 PAM sequence is present in the vicinity of the guide RNA target. For the Cas12f proteins from the Cas14 family, this primarily consists of 5 T-rich sequences while type V-U3 PAM recognition includes both C- and T-rich motifs (page 5017).
Additionally, in vitro transfection of specific plasmids of the specification with specific mutants is not enabling for broad delivery in vivo or to an isolated cell (in vitro) of any ribonucleoprotein effector complex of the genus of claim 1 or 6 which comprises delivery of proteins of varying lengths and having varying amounts of homology to instant SEQ ID NO: 1, as well as varying possible deletions, insertions, or substitutions.
It would involve undue experimentation to determine which proteins comprising which possible deletions, insertions, or substitutions would function as claimed.
To achieve the desired function, it appears that the amino acid must comprise instant SEQ ID NO: 1 other than having a 118C, Y122C, N133R, E174R, N177R, S187R, N470R, or N483 mutation. The specification discloses that these variants exhibited increased enzymatic activities (example 3), whereas others were not confirmed or were degraded (examples 1 and 2).
For example, Thurtle-Schmidt et al. (Biochemistry and Molecular Biology Education, 2018, vol. 46, issue 2, 195-205) teaches that there are many guidelines to consider when creating a guide RNA. Most importantly, the 20-nucleotide target region of the guide RNA must be adjacent to a PAM site, 50-NGG-30 in the case of SpCas9. Therefore, one must identify the genomic region where a desired mutation is to be generated and select a 20-nucleotide target in that region that is adjacent to a PAM site (Fig. 2A). Thurtle-Schmidt et al. teach that if target sequences are not specific enough, Cas9 can bind and cut in a different place than intended and result in background mutations that could confound experimental results. (page 199).
The instant claims are directed to a method of editing a genome, a method for site-specific modification of a target double-stranded polynucleotide, or a method for regulating expression of a gene via delivery of any ribonucleoprotein effector complex within the instantly recited genus, although the target sequence does not necessarily meet the requirements for the guide RNA or Cas protein function.
With regards to in vivo effects, Cui et al. (Adv. Sci. 2024, 11, 2308095, pages 1-10) teach that CRISPR-based gene therapies are making remarkable strides toward the clinic. But the large size of most widely used Cas endonucleases including Cas9 and Cas12a restricts their efficient delivery by the adeno-associated virus (AAV) for in vivo gene editing. Being exceptionally small, the recently engineered type V-F CRISPR-Cas12f1 systems can overcome the cargo packaging bottleneck and present as strong candidates for therapeutic applications. In this study, the pairwise editing efficiencies of different engineered Cas12f1/sgRNA scaffold combinations are systemically screened and optimized, and the CasMINI_v3.1/ge4.1 system is identified as being able to significantly boost the gene editing activity. Moreover, packaged into single AAV vectors and delivered via subretinal injection, CasMINI_v3.1/ge4.1 achieves remarkably high in vivo editing efficiencies, over 70% in transduced retinal cells (abstract). Cui et al. is evidence that packaging into AAV vectors and direct delivery to the target was needed for in vivo results. The instant claims are not directed to any specific mode of delivery or delivery complex that has been demonstrated to achieve broad systemic delivery and the recited outcomes.
As outlined above, it is well known that there is a high level of unpredictability in the CRISPR art for therapeutic in vivo applications. The scope of the claims in view of the specification as filed together do not reconcile the unpredictability in the art to enable one of skill in the art to make and/or use the claimed invention, namely a broad method of mediating the instant outcomes encompassing in vivo effects.
MPEP 2164.01
Any analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention.
Also, MPEP 2164.01(a)
A conclusion of lack of enablement means that, based on the evidence regarding each of
the above factors, the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed
invention without undue experimentation. In re Wright, 999 F.2d 1557,1562, 27
USPQ2d 1510, 1513 (Fed. Cir. 1993).
Given the teachings of the specification as discussed above, one skilled in the art could not predict a priori whether introduction of any complex of the instantly recited genus in vivo by the broadly disclosed methodologies of the instantly claimed invention, would result in successful of editing of any genome, site-specific modification of any target double-stranded polynucleotide, or regulating expression of any gene. To practice the claimed invention, one of skill in the art would have to de novo determine; the stability of the molecule in vivo, delivery of the molecule to the whole organism, specificity to the target tissue in vivo, dosage and toxicity in vivo, and entry of the molecule into the cell in vivo and the effective action therein. Without further guidance, one of skill in the art would have to practice a substantial amount of trial and error experimentation, an amount considered undue and not routine, to practice the instantly claimed invention.
A conclusion of lack of enablement means that, based on the evidence regarding each of the above factors, the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention without undue experimentation (see MPEP 2164.01(a)).
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) 1-19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Doudna et al. (WO 2019/089820 A1), in view of Eid et al. (Biochemical Journal (2018) 475 1955–1964).
Doudna et al. teach: Provided are compositions and methods that include one or more of: (1) a "CasZ" protein (also referred to as a CasZ polypeptide), a nucleic acid encoding the CasZ protein, and/or a modified host cell comprising the CasZ protein (and/or a nucleic acid encoding the same); (2) a CasZ guide RNA that binds to and provides sequence specificity to the CasZ protein, a nucleic acid encoding the CasZ guide RNA, and/or a modified host cell comprising the CasZ guide RNA (and/or a nucleic acid encoding the same); and (3) a CasZ transactivating noncoding RNA (trancRNA) (referred to herein as a "CasZ trancRNA"), a nucleic acid encoding the CasZ trancRNA, and/or a modified host cell comprising the CasZ trancRNA (and/or a nucleic acid encoding the same) (abstract).
Doudna et al. teach that the sequence of CasZ is identical to instant SEQ ID NO: 1 (see SEQ ID NO: 3, Figure 1). Doudna et al. is not required to call the sequence by the same name as instantly claimed. Doudna et al. teach that the sequence is a CasZ sequence that is combined with a gRNA to form a ribonucleoprotein complex that is targeted to a particular site in a target nucleic acid molecule. A guide RNA includes a nucleotide sequence (a guide sequence) that is complementary to a sequence (the target site) of a target nucleic acid. Thus, a CasZ protein forms a complex with a CasZ guide RNA and the guide RNA provides sequence specificity to the RNP complex via the guide sequence. The CasZ protein of the complex provides the site-specific activity [0055].
Doudna et al. teach that: [0088] A variant CasZ protein has an amino acid sequence that is different by at least one amino acid (e.g., has a deletion, insertion, substitution, fusion) when compared to the amino acid sequence of the corresponding wild type CasZ protein (instant claim 1).
Since Doudna et al. does not teach that the deletion, insertion, or substitution is specifically at amino acid positions 118, 122, 126, or 178, it would have been obvious for the deletion, insertion, or substitution to be at other sites as a matter of design choice, which renders obvious instant claim 1, part (b).
Given that there are 20 possible standard amino acid residues, selection of any one would have been a matter of design choice (instant claim 2).
The instant specification demonstrates that the amino acid must consist of instant SEQ ID NO: 1 other than having a 118C, Y122C, N133R, E174R, N177R, S187R, N470R, or N483 mutation. The specification discloses that these variants exhibited increased enzymatic activities (example 3), whereas others were not confirmed or were degraded (examples 1 and 2). However, there are not any instant claims that are closed to an amino acid consisting of instant SEQ ID NO: 1 other than having a 118C, Y122C, N133R, E174R, N177R, S187R, N470R, or N483 mutation.
The amino acid of instant claims 3 and 8 can be any length and comprise a protein sequence of any length having 80% homology to SEQ ID NO: 1.
With regards to the remainder of the recited mutations (A156, Y146, I126, and M178), applicant has not demonstrated an unexpected result in the instant claim breadth. It was known in the art to incorporate deletions, insertions, or substitutions into a Cas protein sequence that is identical to instant SEQ ID NO: 1. It is routine and well within the technical grasp of one of ordinary skill in the art to test and optimize the placement of such mutations. Doudna et al. is evidence that it was known to screen variants having desired functions and properties from variant libraries (instant claims 1 and 3-8).
Doudna et al. teach a composition comprising a guide RNA and a polynucleotide encoding the protein (abstract) (instant claims 9, 11, 16, and 18); and teach incorporation into a vector and host cell ([0043] (instant claims 10 and 12).
Doudna et al. recite a method of editing a genome (claims 1 and 6) or site specific modification (claims 1 and 2) of a target double stranded polynucleotide or a target single stranded DNA (claim 4) comprising delivery of the ribonucleoprotein complex comprising CasZ (identical to instant SEQ ID NO: 1) and a gRNA (claim 1). Doudna et al. recite additionally delivery a DNA donor template (claim 17) or a trancRNA (claim 18) (instant claims 12, 13, 15, 17, and 19).
It is noted that the method steps are obvious in view of Doudna et al. The recited outcomes are not required to be taught by the reference.
Doudna et al. does not teach incorporation of a nucleic acid base converting enzyme (disclosed in instant specification as a deaminase enzyme)
With regards to instant claim 14, it would have been obvious to incorporate a
deaminase enzyme because Eid et al. teach that the CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 adaptive immunity system has been harnessed for genome editing applications across eukaryotic species, but major drawbacks, such as the inefficiency of precise base editing and off target activities, remain. A catalytically inactive Cas9 variant (dead Cas9, dCas9) has been fused to diverse functional domains for targeting genetic and epigenetic modifications, including base editing, to specific DNA sequences. As base editing does not require the generation of double-strand breaks, dCas9 and Cas9 nickase have been used to target deaminase domains to edit specific loci. Adenine and cytidine deaminases convert their respective nucleotides into other DNA bases, thereby offering many possibilities for DNA editing. Such base-editing enzymes hold great promise for applications in basic biology, trait development in crops, and treatment of genetic diseases.
Given that Eid et al. teach base-editing enzymes hold great promise and that deaminases convert their respective nucleotides into other DNA bases, thereby offering many possibilities for DNA editing, it would have been obvious to incorporate a base converting enzyme into the complex of Doudna et al. with expectation of the benefits taught by Eid et al. given that both references address CRISPR gene editing systems.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Amy R Hudson whose telephone number is (571)272-0755. The examiner can normally be reached M-F 8:00am-6:00pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/AMY ROSE HUDSON/Primary Examiner, Art Unit 1636