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 .
Claims Status
Claims 3-14, 17-18, 21-26, 29-34, 37-39, 41, 43-44, 48-52, 55-57, 59-78, 80-88 is/are cancelled. Claims 1-2, 15-16, 19-20, 27-28, 35-36, 40, 42, 45-47, 53-54, 58, 79 is/are currently pending. Claims 1-2, 15-16, 19-20, 27-28, 35-36, 40, 42, 45-47, 53-54, 58, 79 is/are under examination.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 112(a) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 62/865,085, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. Claim 28 of the instant application recites a method which comprises “introducing an anti-CRISPR inhibitor (aca) into [a] cell”. Provisional application ~085 does not disclose anti-CRISPR inhibitors of any kind. Provisional application 62/942,642, filed 12/02/2019, does disclose anti-CRISPR inhibitors (see ~642 specification paragraph [0013]). Accordingly, the limitations of claim 28 are considered to have an earliest priority date of 12/02/2019.
Claim Interpretation
The claims do not recite limitations regarding the structure of a “I-C CRISPR-Cas3 system”. Paragraph [0071] of the specification states that a I-C CRISPR-Cas3 system can comprise “a number of different Cas components, including Cas1, Cas2, Cas3, Cas4, Cas5, Cas7, and Cas8”. The art at the time of filing teaches that a Type I-C CRISPR-Cas3 system comprises Cas3 and a complex of Cas5, Cas7, and Cas8 (see Hochstrasser, 2016). Based on the specification and the prior art, a “I-C CRISPR-Cas3 system” is interpreted to comprise Cas3, Cas5, Cas7, and Cas8.
In claim 1, the limitation “the nucleotide sequences of the first and second repeats differ from one another at 3, 4, 5, 6, 7, 8, 9, 10, or 11 nucleotides” is interpreted to mean that the nucleotide sequences of the first and second repeats differ from one another at any 3, 4, 5, 6, 7, 8, 9, 10, or 11 nucleotides of either sequence. In order to claim that nucleotide positions 3, 4, 5, 6, 7, 8, 9, 10, or 11 are different between the two repeat sequences, the limitation would need to be amended to read “the nucleotide sequences of the first and second repeats differ from one another at nucleotides 3, 4, 5, 6, 7, 8, 9, 10, or 11” or “the nucleotide sequences of the first and second repeats differ from one another at nucleotide positions 3, 4, 5, 6, 7, 8, 9, 10, or 11”.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1, 16, 19-20, 35-36, 40, 42, 45-47, 53, 58, 79 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Gersbach (US 20180334688 A1).
Regarding claim 1, Gersbach teaches a crRNA for use with a Type I-C CRISPR-Cas3 system (claims 1-2), used for generating deletions in a cell (claim 58) or inducing HDR (claim 59). The crRNA comprises a first repeat of 20-40 nucleotides comprising a first stem and a first loop, a second repeat of 20-40 nucleotides comprising a second stem and a second loop, and a spacer of 30-40 nucleotides located between the first and second repeats and which targets a genomic locus within a cell, and wherein the first and second repeats differ in nucleotide sequences (see Fig. 11 for an example of a Type I-C crRNA, wherein the repeat sequences and spacer sequences are 30-40 nucleotides long; see paragraphs [0129] and [0232], teaching that a crRNA (also a CRISPR array) comprises at least one repeat sequence or portion thereof and a second repeat sequence or portion thereof; see paragraph [0140], a “portion” is a sequence whose length is reduced by “1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11…or more nucleotides”, thus differing by at least three nucleotides). The nucleotide sequence difference between the first and second repeats can be at either the 3’ or the 5’ end of the repeat sequence (paragraph [0234], “a spacer sequence linked at its 5’ end to the 3’ end of a portion of consecutive nucleotides of a repeat sequence”, emphasis added). A 3’ truncation of up to 11 nucleotides of the direct repeat sequence of Gersbach shown in Fig. 11 would inherently not affect the base-pairing of the stem region, as the 11 3’-terminal nucleotides are not comprised in the stem region. Gersbach also teaches that a nucleotide sequence is “almost identical (e.g., 70%...identical) to the reference nucleic acid or nucleotide sequence” (paragraph [0140]). Sequences at least 70% and less than 100% identical to a reference sequence encompass sequences that differ by substitution of nucleotides. Gersbach also teaches that a repeat sequence can be “substantially identical” to a wild-type Type I CRISPR repeat sequence, and that “substantially identical” sequences are at least 70% identical (paragraphs [0244], [0183]).
Regarding claim 16, Gersbach teaches that the crRNA (also called a CRISPR array in Gersbach, see claim 19) is under the control of a promoter (claim 20) and is comprised in an expression cassette (claim 33).
Regarding claim 19, Gersbach teaches a vector comprising the crRNA and promoter (the components of the expression vector) (claim 33).
Regarding claim 20, Gersbach teaches a method of inducing a deletion in the genome of a cell comprising a type I-C CRISPR-Cas3 system, the method comprising introducing into the cell the I-C CRISPR-Cas3 crRNA, thereby resulting in a deletion in the genome of the cell at the target genomic locus (claims 69-70 and 98).
Regarding claim 35, Gersbach teaches that the I-C CRISPR-Cas3 system is heterologous to the cell (claims 69-70 and 98; the I-C CRISPR-Cas3 system is prokaryotic, and is not endogenous in eukaryotes, see paragraph [0004]).
Regarding claim 36, Gersbach teaches introducing the I-C CRISPR-Cas3 system into the cell comprises introducing polynucleotides encoding Cas3, Cas5, Cas7, and Cas8 proteins into the cell (claims 69-70 and 98; claims 36 and 39; paragraphs [0008]; claim 1).
Regarding claim 40, Gersbach teaches that the polynucleotides encoding Cas3, Cas5, Cas7, and Cas8 are present on a single plasmid or vector (claims 69-70 call for at least one polynucleotide encoding the proteins; paragraph [0413], more than one nucleotide sequence can be assembled as part of a single nucleic acid construct).
Regarding claim 42, Gersbach teaches that the deletion is at least 5kb, 10kb, 20kb, 25kb, 50kb, 100kb, 150kb, 200kb, or 250kb in length (paragraph [0322]).
Regarding claim 45, Gersbach teaches that multiple target regions can be targeted by introduction of more than one crRNA (paragraph [0286]). Gersbach further teaches that multiple deletions can be achieved with one multiplex system (paragraph [0332]).
Regarding claim 46, Gersbach teaches that NHEJ can be used by a cell to repair the genome after a deletion event without the use of a homologous template (paragraphs [0128], [0159]), and teaches that a homologous template is merely optional for a method of introducing a deletion into the genome of a cell (claim 70).
Regarding claim 47, Gersbach teaches that for a method of introducing a deletion in a genome of a cell, a homologous repair template is introduced into the cell (claims 69-70). Gersbach teaches that this template comprises two homologous regions homologous to genomic sequences flanking the target genomic locus (paragraph [0320]; claims 75-76), wherein the genomic regions that are homologous to the homology arms of the template are separated by 1-100kb in the genome (paragraph [0322]).
Regarding claim 53, Gersbach teaches that the intervening sequence between the homology arms of the template can differ from the homologous sequence in the genome by at least one nucleotide (paragraph [0320]), and wherein HDR results in the introduction of this intervening sequence of the template into the genome, resulting in a modification of the genomic sequence (claim 77).
Regarding claim 58, Gersbach teaches a method of editing a cell’s genome by introducing a heterologous Type I-C CRISPR-Cas3 system and crRNA, which inherently produces a cell comprising the heterologous Type I-C CRISPR-Cas3 system and crRNA (claims 69-70 and 98).
Regarding claim 79, Gersbach teaches a method of modulating expression of a target gene in a cell (repressing or activating) (claims 36, 40, 53-54, 56-57), by introducing a crRNA that targets the promoter of the gene (claims 41 and 49), introducing Cas5, Cas7, and Cas8 into the cell (claims 38 and 3). Gersbach further teaches that at least one of the Cas proteins is fused to a second polypeptide domain having transcriptional activation activity (claim 55).
Response to Arguments/Amendments
Applicant argues, in arguments filed 08/08/2025, that the phrasing “the first and second repeats differ from one another at 5, 6, 7, 8, 9, 10, or 11 nucleotides” excludes truncations from the broadest reasonable interpretation. It is noted that claim 1 does not recite “at 5, 6, 7, 8, 9, 10, or 11 nucleotides”, as argued by Applicant on page 8 of the arguments, and instead recites “at 3, 4, 5, 6, 7, 8, 9, 10, or 11 nucleotides”. However, if two sequences are aligned, wherein the first sequence is truncated relative to the second sequence, the first sequence differs from the second sequence at the nucleotides that the second sequence comprises which the first sequence does not comprise. Applicant also argues that paragraph [0072] of the specification “distinguishes between differences and truncations” because repeat sequence truncations are described as additional (“can also comprise truncations”) to differences between direct repeat sequences. However, it is noted that the excerpt of paragraph [0072] provided in the arguments does not define a difference between two repeat sequences as excluding truncations. The broadest reasonable interpretation of crRNAs encompassed by the description in paragraph [0072] is that two direct repeat sequences can differ by insertions, substitutions, or deletions (including truncations), and additionally can comprise a truncation which does not necessarily create a difference between the two direct repeat sequences. As such, the rejection under 35 USC 102 is maintained.
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 and 2 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gersbach (US 20180334688 A1), in view of Cameron (CA 3163768 A1).
Regarding claim 1, Gersbach teaches a crRNA for use with a Type I-C CRISPR-Cas3 system (claims 1-2), used for generating deletions in a cell (claim 58) or inducing HDR (claim 59). The crRNA comprises a first repeat of 20-40 nucleotides comprising a first stem and a first loop, a second repeat of 20-40 nucleotides comprising a second stem and a second loop, and a spacer of 30-40 nucleotides located between the first and second repeats and which targets a genomic locus within a cell, and wherein the first and second repeats differ in nucleotide sequences (see Fig. 11 for an example of a Type I-C crRNA, wherein the repeat sequences and spacer sequences are 30-40 nucleotides long; see paragraphs [0129] and [0232], teaching that a crRNA (also a CRISPR array) comprises at least one repeat sequence or portion thereof and a second repeat sequence or portion thereof; see paragraph [0140], a “portion” is a sequence whose length is reduced by “1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11…or more nucleotides”, thus differing by at least three nucleotides). The nucleotide sequence difference between the first and second repeats can be at either the 3’ or the 5’ end of the repeat sequence (paragraph [0234], “a spacer sequence linked at its 5’ end to the 3’ end of a portion of consecutive nucleotides of a repeat sequence”, emphasis added). A 3’ truncation of up to 11 nucleotides of the direct repeat sequence of Gersbach shown in Fig. 11 would inherently not affect the base-pairing of the stem region, as the 11 3’-terminal nucleotides are not comprised in the stem region.
Regarding claim 2, Gersbach teaches that multiple different direct repeat sequences can be comprised in one crRNA (paragraph [0140]). However, Gersbach does not teach that nucleotides in the stem region of the crRNA can be substituted, as required by claim 2.
Cameron teaches that the stem region of a crRNA for use in a Type I system can be mutated.
Regarding claim 2, Cameron teaches that a crRNA for a Type I CRISPR system can be engineered to introduce one or more base changes through substitution in the repeat stem sequence (paragraph [00781]).
While Cameron does not specifically state that base pairs in the stem region can be reversed relative to their wild-type orientation, Cameron does teach that any nucleotides in the stem region can be mutated. It would be obvious to a person of ordinary skill in the art that this encompasses A[Wingdings font/0xE0]T or G[Wingdings font/0xE0]C mutations, for example. It would be further obvious to a person of ordinary skill in the art that in order to conserve base pairing (and not introduce a mismatch), the nucleotide opposite such a substitution would also need to be mutated (e.g., if one nucleotide is mutated A[Wingdings font/0xE0]T, the opposing paired nucleotide would be mutated T[Wingdings font/0xE0]A, constituting a reversal of a base pair).
Claim(s) 1 and 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gersbach (US 20180334688 A1), in view of Cameron (US 10227576 B1).
Regarding claim 1, Gersbach teaches a crRNA for use with a Type I-C CRISPR-Cas3 system (claims 1-2), used for generating deletions in a cell (claim 58) or inducing HDR (claim 59). The crRNA comprises a first repeat of 20-40 nucleotides comprising a first stem and a first loop, a second repeat of 20-40 nucleotides comprising a second stem and a second loop, and a spacer of 30-40 nucleotides located between the first and second repeats and which targets a genomic locus within a cell, and wherein the first and second repeats differ in nucleotide sequences (see Fig. 11 for an example of a Type I-C crRNA, wherein the repeat sequences and spacer sequences are 30-40 nucleotides long; see paragraphs [0129] and [0232], teaching that a crRNA (also a CRISPR array) comprises at least one repeat sequence or portion thereof and a second repeat sequence or portion thereof; see paragraph [0140], a “portion” is a sequence whose length is reduced by at least 1 nucleotide, thus differing by at least one nucleotide).
However, Gersbach does not teach that the stem and loop sequence of the crRNA comprises, SEQ ID NOs:1, 2, 7, 8, or 9, as required by claim 15.
Cameron teaches crRNA sequences which fulfill these requirements.
Regarding claim 15, Cameron teaches that for a Type I-C CRISPR-Cas3 system, a stem-loop repeat sequence of a crRNA is of SEQ ID NO:272 (SEQ ID NO:272 is 100% identical to SEQ ID NO:8 of the instant application, see alignment below).
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114
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Cameron teaches that this sequence is found in D. vulgaris (see Table 3) and can be used with Type I-C CRISPR-Cas3 gene editing systems. It would have been obvious to a person of ordinary skill in the art at the time of filing that this crRNA stem-loop repeat sequence should be used in the crRNA of Gersbach as an efficient mechanism to guide the I-C CRISPR-Cas3 system, as it was already known in the art to do so.
Claim(s) 1, 20, and 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gersbach (US 20180334688 A1), in view of Beisel (US 20170028083 A1), Hochstrasser (2016), and Chang (2016).
Regarding claim 1, Gersbach teaches a crRNA for use with a Type I-C CRISPR-Cas3 system (claims 1-2), used for generating deletions in a cell (claim 58) or inducing HDR (claim 59). The crRNA comprises a first repeat of 20-40 nucleotides comprising a first stem and a first loop, a second repeat of 20-40 nucleotides comprising a second stem and a second loop, and a spacer of 30-40 nucleotides located between the first and second repeats and which targets a genomic locus within a cell, and wherein the first and second repeats differ in nucleotide sequences (see Fig. 11 for an example of a Type I-C crRNA, wherein the repeat sequences and spacer sequences are 30-40 nucleotides long; see paragraphs [0129] and [0232], teaching that a crRNA (also a CRISPR array) comprises at least one repeat sequence or portion thereof and a second repeat sequence or portion thereof; see paragraph [0140], a “portion” is a sequence whose length is reduced by at least 1 nucleotide, thus differing by at least one nucleotide).
Regarding claim 20, Gersbach teaches a method of inducing a deletion in the genome of a cell comprising a type I-C CRISPR-Cas3 system, the method comprising introducing into the cell the I-C CRISPR-Cas3 crRNA, thereby resulting in a deletion in the genome of the cell at the target genomic locus (claims 69-70 and 98).
However, Gersbach does not teach that the method is performed in a cell which endogenously expresses a type I-C CRISPR-Cas3 system.
Regarding claim 27, Beisel teaches that such a method can be performed in E. coli (Fig. 2, paragraph [0016]).
Chang teaches a method of gene editing in E. coli with a type I-E CRISPR system, wherein the system is endogenous to the E. coli (see abstract).
Hochstrasser teaches that a type I-C CRISPR-Cas3 system is endogenously expressed in D. vulgaris (page 841).
Beisel teaches methods of gene editing utilizing multiple Type I CRISPR systems, including I-C and I-E, and teaches that the Type I-E system can be used in E. coli (paragraph [0019]), but does not specifically teach advantages to using the endogenous components of the CRISPR system. Chang teaches that by utilizing an endogenous CRISPR system (like Type I-E in E. coli), the metabolic burden is reduced, in large part because fewer exogenous nucleic acids need to be introduced to use the CRISPR system (see Chang abstract). While neither Beisel nor Chang teaches these concepts for the Type I-C CRISPR system, specifically, it would be obvious to a person of ordinary skill in the art that the benefits of using an endogenous CRISPR system, in particular the lower metabolic burden described by Chang, would not be tied to a specific CRISPR system, and instead could translate to others, like type I-C. Hochstrasser teaches that the type I-C CRISPR-Cas3 system is endogenously expressed in the bacterium D. vulgaris; given the teachings of Beisel and Chang, as discussed above, it would be obvious to a person of ordinary skill in the art that the endogenous type I-C CRISPR-Cas3 system of D. vulgaris could be used in a gene editing method as taught by Gersbach, wherein an exogenous crRNA is introduced to edit a target sequence in the D. vulgaris genome using the endogenously-expressed I-C CRISPR-Cas3 system. Such an application of the invention of Gersbach would allow for editing of the D. vulgaris genome while reducing metabolic burden through the minimization of exogenous nucleic acids introduced into the bacterium.
Claim(s) 1, 20, 28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gersbach (US 20180334688 A1), in view of Stanley (2019).
Regarding claim 1, Gersbach teaches a crRNA for use with a Type I-C CRISPR-Cas3 system (claims 1-2), used for generating deletions in a cell (claim 58) or inducing HDR (claim 59). The crRNA comprises a first repeat of 20-40 nucleotides comprising a first stem and a first loop, a second repeat of 20-40 nucleotides comprising a second stem and a second loop, and a spacer of 30-40 nucleotides located between the first and second repeats and which targets a genomic locus within a cell, and wherein the first and second repeats differ in nucleotide sequences (see Fig. 11 for an example of a Type I-C crRNA, wherein the repeat sequences and spacer sequences are 30-40 nucleotides long; see paragraphs [0129] and [0232], teaching that a crRNA (also a CRISPR array) comprises at least one repeat sequence or portion thereof and a second repeat sequence or portion thereof; see paragraph [0140], a “portion” is a sequence whose length is reduced by at least 1 nucleotide, thus differing by at least one nucleotide).
Regarding claim 20, Gersbach teaches a method of inducing a deletion in the genome of a cell comprising a type I-C CRISPR-Cas3 system, the method comprising introducing into the cell the I-C CRISPR-Cas3 crRNA, thereby resulting in a deletion in the genome of the cell at the target genomic locus (claims 69-70 and 98).
However, Gersbach does not teach that the method further comprises introducing an aca gene or encoded protein (i.e. an inhibitor of anti-CRISPRs) into the cell.
Stanley teaches that aca proteins (anti-CRISPR-associated proteins) promote CRISPR activity.
Regarding claim 28, Stanley teaches that aca proteins inhibit the inhibitory function of bacteriophage Acr proteins (anti-CRISPR proteins), allowing for CRISPR activity in infected cells (see summary). It would have been obvious to a person of ordinary skill in the art at the time of filing that in order to increase the genome editing efficiency of the invention of Gersbach in cells already infected by a bacteriophage carrying anti-CRISPR genes, an aca protein or gene should be added to counteract the inhibitory activity of the anti-CRISPR genes on the CRISPR system of the invention.
Claim(s) 1, 20, and 54 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gersbach (US 20180334688 A1), in view of Beisel (US 20170028083 A1).
Regarding claim 1, Gersbach teaches a crRNA for use with a Type I-C CRISPR-Cas3 system (claims 1-2), used for generating deletions in a cell (claim 58) or inducing HDR (claim 59). The crRNA comprises a first repeat of 20-40 nucleotides comprising a first stem and a first loop, a second repeat of 20-40 nucleotides comprising a second stem and a second loop, and a spacer of 30-40 nucleotides located between the first and second repeats and which targets a genomic locus within a cell, and wherein the first and second repeats differ in nucleotide sequences (see Fig. 11 for an example of a Type I-C crRNA, wherein the repeat sequences and spacer sequences are 30-40 nucleotides long; see paragraphs [0129] and [0232], teaching that a crRNA (also a CRISPR array) comprises at least one repeat sequence or portion thereof and a second repeat sequence or portion thereof; see paragraph [0140], a “portion” is a sequence whose length is reduced by at least 1 nucleotide, thus differing by at least one nucleotide).
Regarding claim 20, Gersbach teaches a method of inducing a deletion in the genome of a cell comprising a type I-C CRISPR-Cas3 system, the method comprising introducing into the cell the I-C CRISPR-Cas3 crRNA, thereby resulting in a deletion in the genome of the cell at the target genomic locus (claims 69-70 and 98).
However, Gersbach does not teach that the crRNA induces deletions at an efficiency of at least 70%, as required by claim 54.
Beisel teaches that crRNAs in a I-C CRISPR system can exhibit varying deletion efficiencies.
Regarding claim 54, Beisel teaches that crRNAs targeting different sequences of a plasmid exhibit different efficiencies of deletion of the genes within the plasmid (Figs. 1-2), including crRNAs that exhibit greater than 70% deletion efficiency.
Beisel teaches that the efficiency of a Type I-C CRISPR system crRNA to produce a deletion in a nucleic acid molecule can depend on the target sequence itself, as seen in Fig. 2. While the crRNAs of Gersbach do not exhibit greater than 70% deletion efficiencies, the teachings of Beisel render obvious that changing the target sequence can significantly affect the efficiency of a crRNA to induce a deletion in a genome. Therefore, it would have been obvious to a person of ordinary skill in the art that in order for the invention of Gersbach to exhibit at least 70% deletion efficiency in the genome of the cell, the specific sequence targeted by the crRNA should be changed, as taught by Beisel.
Response to Arguments
Applicant's arguments filed 08/08/2025 have been fully considered but they are not persuasive. Applicant argues that Gersbach does not “teach or suggest a crRNA as claimed that has repeats that differ at 5-11 [nucleotides] and wherein the differences maintain base pairing” (page 8). However, Gersbach does teach 3’ truncations of 5-11 nucleotides of direct repeat sequences, and a 3’ truncation of up to 11 nucleotides would not affect base pairing, as evidenced by the direct repeat structure shown in Gersbach Fig. 11. Applicant further argues that paragraph [0016] of the specification describes that the lack of perfect homology between repeat sequences prevents or reduces recombination events between the repeat sequences. This is found in paragraph [0046]. The language of this excerpt makes clear that this is a quality that is “believed” to be true (“it is believed that…”). Applicant has not provided evidence that this is a quality of the claimed invention commensurate with the scope of the claimed invention (i.e., that the full scope of the claimed invention does, in fact, prevent or reduce recombination events between repeat sequences), nor that this quality is an unexpected result.
Regarding rejections of other claims (not claims 1 and 2) under 35 USC 103, Applicant has merely argued that the “rejections be withdrawn as the cited art does not teach or suggest all of the elements of the claims”. As described in the rejections of claim 1 under 35 USC 102 and 103, and of claim 2 under 35 USC 103, the cited art does teach or suggest all the elements of claims 1-2. The rejections of the claims under 35 USC 103 are maintained.
Conclusion
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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/AFRICA M MCLEOD/ Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635