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 24 February 2026. Claims 1-9 and 12-22 are currently pending. Claims 19-22 are newly added. Accordingly, claims 1-9 and 12-22 are examined herein.
Applicant’s arguments regarding the previously utilized Lee reference, see pg. 9-11, filed 24 February 2026, with respect to the rejection(s) of claim(s) 1-6, 8-9, 12-13, and 15-17 under 35 USC 103 have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Verwaal. Accordingly, 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) 1-9 and 12-22 is/are rejected under 35 U.S.C. 103 as being unpatentable over Verwaal (PG Pub No. WO 2016/110512 A1).
Regarding claim 1, Verwaal is drawn towards an invention concerned with a CRISPR-Cas system for a yeast host cell (Abstract). Verwaal teaches the use of a linear ADE2.Y guide RNA cassette (i.e., a guide-RNA expression cassette that is specific for an ADE2 target sequence) that is adjacent to a donor sequence (i.e., an additional polynucleotide element) (i.e., a CTEC), wherein the sequence of the donor has sequence identity to sequences that flank the target ADE2 locus in a target’s genome (i.e., a method of introducing into a host cell a linear construct comprising adjacent guide RNA expression cassettes and a donor DNA) (pg. 5, lines 6-13; pg. 81, lines 10-29; see Figure 16).
Verwaal does not explicitly teach that the adjacent ADE2.Y guide RNA cassette/donor construct comprises two or more polynucleotide sequences capable of recombining with a vector that is linear and present in the host cell, to in vivo yield the CTEC integrated into the vector (Claim 1).
However, Verwaal further teaches that in a different embodiment a guide RNA expression cassette may comprise flanking homology arms to enable in vivo recombination into a linear vector (pg. 93, lines 21-31). Verwaal explicitly teaches that “in a composition according to the invention, the polynucleotide encoding a guide-polynucleotide has sequence identity with a vector such that recombination of the polynucleotide encoding the guide-polynucleotide and said vector is facilitated, wherein the recombination preferably is in vivo recombination in the host cell and wherein the vector is preferably linear” (pg. 28, lines 24-35 to pg. 29, lines 1-4; see Figure 25). Verwaal also teaches that, in a different embodiment, the ADE2.Y guide RNA expression cassette itself may comprise a 56-58 bp overhang with a digested vector pCSN049 such that it allows in vivo recombination of the PCR fragment and the digested pCSN049 vector upon transformation of the PCR fragment and the digested vector to yeast (pg. 72, lines 12-19; see Figure 9).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the linear ADE2.Y guide RNA cassette that was adjacent to a donor sequence via the inclusion of two or more polynucleotide sequences capable of recombining with a linear vector in vivo, in order to yield the CTEC integrated into the linear vector in vivo, because it would have merely amounted to a combination of prior art elements according to known methods to yield predictable results. Because Verwaal already teaches that a guide RNA expression cassette, including the same guide RNA expression cassette that is fused to the donor DNA molecule, may be flanked by linearized vector-specific homology arms in order to integrate the expression cassette into the vector, then one of ordinary skill in the art would have expected utilizing linearized vector-specific homology arms that flank the ADE2.Y guide RNA/donor construct to have similarly and predictably allowed for the integration of the ADE2.Y guide RNA/donor construct into a linearized vector in vivo. Additionally, because Verwaal provides evidence that the same ADE2.Y guide RNA may itself comprise flanking vector-specific homology arms, one of ordinary skill in the art would have expected the inclusion of the homology arms into the ADE2.Y guide RNA/donor construct would have predictably resulted in a functional construct when expressed in the cell.
Regarding claim 2, the embodiments of Verwaal do not teach that the guide RNA is expressed from any other nucleic acid than the introduced guide RNA expression cassettes (i.e. the guide RNA is exclusively expressed from the system in order to guide the system to the target genome).
Regarding claim 3, Verwaal teaches that the ADE2.Y guide-RNA sequence may be directly fused to the donor DNA sequence or it can be separated by the 20 bp ADE2.Y guide sequence and a PAM sequence, wherein the latter approach results in cleaving off the donor DNA sequence from the ADE2.Y guide-RNA sequence (pg. 81, lines 22-29; see Figure 16).
Regarding claims 4-5, Verwaal teaches that the ADE2.Y guide expression cassette may comprise an RNA polymerase III promoter (i.e., a eukaryotic promoter) (pg. 69, lines 4-8).
Regarding claim 6, Verwaal does not specifically teach that the guide expression cassette eukaryotic promoter is a K11 promoter (Claim 6).
However, Verwaal further teaches that the K/11 promoter from Kluyveromyces lactis (i.e. a eukaryotic K11 promoter) may be utilized by, and operably linked to, nucleic acids encoding the CRISPR Cas9 nuclease such that the nuclease is expressed in the host cell (pg. 67, lines 27-30).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the RNA polymerase III promoter present in the guide RNA expression cassette for a K11 promoter because it would have merely amounted to a simple substitution of one known element for another to obtain predictable results. Because Verwaal already teaches the expression of components of the gene editing system from a K11 promoter (i.e., a eukaryotic promoter utilized for the same purpose of expressing components of the gene editing system when compared to the eukaryotic RNA polymerase II promoter), then one of ordinary skill in the art would have expected expressing the guide RNA cassette via the use of a K11 promoter to have similarly and predictably have resulted in the expression of the guide RNA.
Regarding claim 7, Verwaal teaches that the guide RNA cassette and the donor molecule may be linked via a linker that encodes for or represents the guide RNA cassette’s 5’ sequence (i.e., the guide RNA cassette may be 3’ of the donor molecule) (pg. 45, line 24 to pg. 46, line 17).
Regarding claim 8, Verwaal teaches that the nucleic acid encoding the gRNA that is adjacent to the donor polynucleotide can be generated via a library synthesis in order to facilitate the generation of multiplex systems (pg. 45, lines 24-35).
Verwaal does not explicitly teach that the library of CTEC molecules were delivered to a population of cells (Claim 8).
However, Verwaal further teaches that in a different embodiment multiple cells (i.e., a population of cells) can be transformed with nucleic acids encoding the gRNA cassettes and donor nucleic acids in order to use the nucleic acids in method of multiplexed editing (pg. 7, lines 4-13; see Figure 27).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized the CTECs in a method of multiplexed editing through the administration of a library of the CTECs to a population of cells because it would have merely amounted to a combination of prior art elements according to known methods to yield predictable results. Because Verwaal teaches that nucleic acids encoding the individual gRNA and donor molecule could successfully be expressed in multiple cells, then one would have expected delivering a library of CTECs encoding the same components to have performed the same function of multiplexed editing. Further, because Verwaal explicitly teaches that the nucleic acid encoding the gRNA expression cassette and donor molecule could be used in a multiplex system, it would have been predictable that using the constructs in a multiplexed method would have predictably worked.
Regarding claims 9 and 16, Verwaal teaches that a plasmid encoding a CRISPR-Cas9 system comprising Cas9 can be introduced alongside the ADE2.Y guide RNA cassette that was fused to the donor DNA sequence (pg. 5, lines 6-13; pg. 81, lines 10-29; see Figure 16).
Regarding claims 12-13, Verwaal teaches that the donor DNA molecule may encode carotenoids (pg. 88, lines 26-35). Verwaal teaches that an easy readout of successful integration of the donor DNA molecule into the target organism can be detected by the detection of produced carotenoids which are colored compounds (i.e., gene products may be analyzed to determine successful integration of the CTEC) (pg. 87, lines 10-23).
Regarding claim 14, Verwaal teaches that preferably the host cell of the disclosure is deficient in non-homologous end joining (pg. 46, lines 25-28).
Regarding claim 15, Verwaal only teaches that the donor molecule comprises homology arms that allow for the integration of only the donor molecule into the genomic target region of interest, while the guide RNA expression cassette does not comprise homology arms that allow for integration into the host genome (i.e., the guide RNA expression cassette does not integrate into the genome of the host cell) (pg. 5, lines 6-13; pg. 81, lines 10-29; see Figure 16).
Regarding claim 17, Verwaal teaches that the pCSN049 vector into which the pCSN049 vector-specific homology arms allow for the insertion of the guide RNA expression cassette is a plasmid (pg. 72, lines 12-19; see Figure 9).
Regarding claims 18 and 20, Verwaal teaches that the vectors of the disclosure may comprise a selectable marker to permit easy selection of transformed cells and that the selectable marker may produce gene products that confer biocide or viral resistance (pg. 35, lines 10-17).
Regarding claim 19, Verwaal teaches that the PCR product containing the ADE2.Y guide RNA cassette was generated via the use of forward and reverse primers (i.e., the ADE2.Y guide RNA cassette is double stranded) (pg. 72, lines 12-32). Verwaal also teaches that the donor molecule is a double stranded oligonucleotide (pg. 3, lines 16-26; see Figure 7).
Regarding claim 21, Verwaal teaches that the host cell may be a yeast cell (i.e., a fungal cell).
Regarding claim 22, Verwaal teaches that the ADE2.Y gRNA cassette consists of a SNR52p RNA polymerase III promoter, the guide-sequence, the gRNA structural component, and the SUP4 3' flanking region (pg. 9; lines 21-25). Verwaal teaches that the SUP4 gene comprises a terminator from the 3’ region of the yeast SUP4 gene (pg. 4, line 33 to pg. 5, line 4; see Figure 15).
Response to Arguments
Applicant’s arguments regarding the previously utilized Lee reference, see pg. 9-11, filed 24 February 2026, with respect to the rejection(s) of claim(s) 1-6, 8-9, 12-13, and 15-17 under 35 USC 103 have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Verwaal above.
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).
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.
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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