DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 17 September 2025 has been entered.
Withdrawn Claim Rejections
Applicant’s arguments, filed 17 September 2025 have been fully considered and are deemed persuasive.
Applicant alleged that Gao did not disclose the claimed step a) of claim 12: “identifying whether a variant recognition site results in increased activity for a rare-cutting engineered double-strand-break-inducing agent as compared to the activity at an intended recognition site”. Applicant alleged that the Lig34-site of Gao was a pre-selected target and not a variant recognition site, as claimed in the instant specification.
These arguments are found persuasive. Accordingly, the previously pending objections and 102 rejection of record, filed 17 April 2025, have been withdrawn.
Claim Objections
Claim 12 objected to because of the following informalities: the currently pending claim amendments recite “a)[[.]” in line 5 of the claim. The lack of a double bracket on either side of the period in claim 12 is not sufficient to delete the period from the claim. Examiner suggests amending the claim to recite “a)[[.]]” such that the period is flanked on either side by a double bracket. Appropriate correction is required.
Claim Interpretation
Regarding the phrase “an intended recognition site” in lines 3-4 of claim 12, it is noted that the specification defines an intended recognition site as “a recognition sequence to which an engineered rare-cutting double-strand-break-inducing agent, such as an engineered meganuclease, was directed to specifically recognize and induce a double-strand break” (Instant specification; pg. 14).
Regarding the phrase “a variant recognition site” in lines 1-2 of claim 12, it is noted that the specification defines a variant recognition site as “a variant nucleotide sequence that comprises at least one base nucleotide alteration when compared to the intended recognition site to which an engineered rare-cutting double-strand-break-inducing agent such as a meganuclease, was directed to specifically recognize and induce a double-strand break” (Instant specification; pg. 15).
Therefore, it is noted that the claimed intended recognition site is not solely limited to a wild-type recognition site of a rare-cutting engineered double-strand-break-inducing agent. Rather, the intended recognition site encompasses recognition sites that the double-strand-break-inducing agent was engineered to recognize.
Claim Rejections - 35 USC § 112
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 12-13 and 43 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.
Regarding claim 12, it is noted that the claim is not limited to a particular rare-cutting engineered double-strand-break-inducing agent nor a specific sequence of a variant recognition site. Thus, a donor DNA molecule comprising a large genus of variant recognition sites that results in increased activity for a large genus rare-cutting engineered double-strand-break-inducing agents when compared to the activity at an intended recognition site is required to practice the invention.
Working Examples
The instant specification does not describe the complete claimed structure of a donor DNA comprising the claimed genus of variant recognition sites. Further, the specification does not describe any correlation between the claimed genus of variant recognition sites sequences and the function of a genus of rare-cutting engineered double-strand-break-inducing agent having increased activity.
The specification teaches that DNA base compositions at each of the nucleotides present within the LIG3-4 and MHP14+ meganucleases were screened for in order to determine nucleotides that were preferred variants within the intended recognition sites of the meganucleases (pg. 4; see Figure 3). The specification also describes a method of screening for variant recognition sites having increased cleavage activities for LIG3-4 and MHP14+ meganucleases via the modification of nucleotides present within intended recognition sites of the meganucleases (pg. 53-55; see Example 10). The specification also teaches that non-preferred variants of nucleotides within the intended recognition sites were not cleaved at a rate higher than the intended recognition site and that only specific variant recognition sites resulted in a higher cleavage activity for LIG3-4 and MHP14+ meganucleases (pg. 53-55; see Example 10 and Figures 5A-5B).
However, the claimed invention is not solely limited to a LIG3-4 or MHP14+ meganucleases. Rather, as discussed above, the claim is not limited to a particular rare-cutting engineered double-strand-break-inducing agent nor a specific sequence of a variant recognition site. Thus, the instant specification teaches that a large amount of experimentation is required in order to identify a variant recognition site and does not allow one of skill in the art to visualize or recognize the structure of the genus of claimed variant recognition sites that result in higher cleavage activity for the genus of claimed rare-cutting engineered double-strand-break-inducing agents required to practice the claimed method.
Prior Art
The level of skill and knowledge in the art is that there is not a pre-determined and known structural component of a variant recognition site that does not require screening prior to the identification of an increased activity level of a rare-cutting engineered double-strand-break-inducing agent.
Molina is drawn towards a study concerned with the analysis of I-CreI (i.e., a rare-cutting engineered double-strand-break-inducing agent) cleavage patterns and substrate discrimination (Abstract). Molina teaches that I-CreI is a homing meganuclease that can generate double-stranded breaks at a central target site comprising 4 nucleotides (pg. 6937-6938; see Figure 1). Molina teaches that variant recognition sites for the I-CreI can be generated and the increased cleavage activity of the I-CreI at the variant recognition sites can be identified via the use of a reporter plasmid (pg. 6937, 6938; see Figure 1 and Supplementary Figure 1).
However, Molina further teaches that all 256 possible four base-pair combinations needed to be tested for cleavage activity and compared to every other iteration of the central base pairs in order to determine what central base pairs resulted in increased cleavage activity by the I-CreI (pg. 6937; see Figure 1 and Supplementary Figure 1).
Thus, the prior art does not teach or suggest the use of a predetermined variant recognition site that a rare-cutting engineered double-strand-break-inducing agent has increased cleavage activity at. Rather, the prior art demonstrates that the variant recognition sites had to be screened and individually tested in order to determine if the rare-cutting engineered double-strand-break-inducing agent has increased cleavage activity at the variant recognition sites.
Conclusion
The specification does not allow one of skill in the art to visualize or recognize the structure of the genus of claimed variant recognition sites that result in higher cleavage activity for the genus of claimed rare-cutting engineered double-strand-break-inducing agents required to practice the claimed method. Further, the prior art teaches that identifying variant recognition sites for rare-cutting engineered double-strand-break-inducing agents requires a lot of experimentation and that the sequence of the variant recognition sites were not known prior to the experimentation. Therefore, the specification fails to satisfy the written description requirement of 35 USC 112(a) with respect to claim 1.
Regarding claim 13, the claim further limits the rare-cutting engineered double-strand-break-inducing agent. However, the rare-cutting engineered double-strand-break-inducing agents recited in claim 13 are drawn to a large genera of rare-cutting engineered double-strand-break-inducing agents that are not adequately described in the instant specification, as discussed above. Accordingly, the claim is also rejected under 35 USC 112(a).
Regarding claim 43, as the claim is ultimately dependent on claim 12 and does not rectify the 35 USC 112(a) rejection above, the claim is also rejected under 35 USC 112(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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 pre-AIA 35 U.S.C. 103(a) 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claim 12-13 and 43 is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Molina (Nucleic acids research 40.14 (11 April 2012): 6936-6945) in view of Yang (Plant molecular biology 70.6 (2009): 669-679).
Regarding claim 12, Molina is drawn towards a study concerned with the analysis of I-CreI (i.e., a rare-cutting engineered double-strand-break-inducing agent) cleavage patterns and substrate discrimination (Abstract). Molina teaches that I-CreI is a homing meganuclease that can generate double-stranded breaks at a central target site comprising 4 nucleotides (pg. 6937-6938; see Figure 1). Molina teaches the use of a method comprising a) identifying whether a variant I-CreI recognition site results in increased activity as compared to the activity at an intended I-CreI recognition site (pg. 6937; see Figure 1 and Supplementary Figure 1). Molina teaches the use of b) a reporter plasmid (i.e., a donor DNA) comprising the variant recognition site that the I-CreI can cleave (pg. 6938). Molina teaches that c)-d) yeast cells were contacted with the reporter plasmid and an I-CreI expression vector and that e) the variant recognition sites that the I-CreI were able to cleave were identified via the differential expression of a gene on the reporter plasmid (pg. 6938).
Molina does not teach or suggest that the variant recognition site is introduced into the genome of a cell (Claim 12). Molina does not teach or suggest that the cell is a plant cell (Claim 12).
However, one of ordinary skill in the art would have considered the teachings of Yang as both references are common fields of endeavor pertaining to the use of homing nucleases and their target sites in cells of interest.
Yang is drawn towards a study concerned with targeted mutagenesis in maize transgenic plants (Abstract). Yang teaches the use of c)-d) an artificial homing endonuclease, termed I-SceI (i.e., a rare-cutting engineered double-strand-break-inducing agent), that is able to induce double-stranded breaks at artificial I-SceI target sites present within a plant cell’s genome (pg. 670-671; see Fig. 1). Yang teaches the use of genetic elements (i.e., donor DNA molecules) comprising the artificial I-SceI target sites that were able to be randomly integrated into parental plant cells (pg. 671; see Fig. 1). Yang teaches that the PCR was able to be utilized in order to determine if the I-SceI successfully induced a double-stranded break at the artificial target site (pg. 672). Yang teaches that the system allows for targeted mutagenesis of specific chromosomal sites marked by the artificial I-SceI target sites (pg. 670).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Molina such that the variant recognition site is introduced into the genome of a plant cell, as described by Yang. A person of ordinary skill in the art would have been motivated to do so in order to target chromosomal sites within a plant gene via the use of artificial I-CreI target sites. A person of ordinary skill in the art would have had a reasonable expectation of success because both Molina and Yang teach the use of homing endonucleases that can recognize and cleave artificial target sites within target DNA while Yang further teaches that artificial target sites for homing endonucleases can be introduced into the genome of a plant cell via a donor DNA molecule.
Regarding claim 13, Molina teaches that the rare-cutting engineered double-strand-break-inducing agent is a meganuclease (pg. 6938).
Regarding claim 43, Molina teaches that the cleavage activity of different I-CreI target sites were compared to one other and were quantified by the degree of cleavage (i.e., the percentage of cleavage at a specific target site) (see Supplementary Fig. 1). Molina teaches that the target sites were present on a reporter plasmid (i.e., plasmid DNA) (pg. 6938).
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.
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.
/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636