DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Application Status
This action is written in response to applicant’s correspondence received 14 April 2026. Claims 12-13 and 43 are currently pending. Accordingly, claims 12-13 and 43 are examined herein.
Any rejection or objection not reiterated herein has been overcome by amendment.
Applicant' s arguments have been thoroughly reviewed, but are not persuasive to place the
claims in condition for allowance for the reasons that follow.
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 and induce at least some degree of double-stranded cleavage activity.
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. This rejection is maintained.
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).
Additionally, 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).
Response to Arguments - 35 USC § 112
Applicant's arguments filed 14 April 2026 have been fully considered but they are not persuasive.
Applicant alleges that the present specification demonstrates possession of the claimed subject matter at the time of filing (Remarks; pg. 2). Applicant alleges that because the specification describes the steps of the method (i.e., Examples 3, 4, 7, and 8, and Figures 1-3, which detail how variant recognition sites are identified by contacting genomic DNA with a rare-cutting engineered double-strand-break-inducing agent, capturing the resulting cleavage products, and sequencing and aligning those products to a reference genome), there is adequate written description support for the claimed method (Remarks; pg. 2). Applicant alleges that the disclosed methods also enable determination of whether a variant recognition site exhibits increased activity relative to an intended recognition site (i.e., See Examples 9-10 and Figures 4-6) (Remarks; pg. 2). Applicant alleges that the specification also discloses multiple independent assays by which increased activity may be assessed, including percent cleavage of genomic DNA (i.e., Example 3), percent cleavage of plasmid DNA (i.e., Examples 9 and 10; Figures 5 and 6), and yeast-based recombination or sectoring assays (i.e., Example 16; Figures 8 and 9) (Remarks; pg. 2).
These arguments are not found persuasive because Applicant has not addressed the grounds of rejection addressed in the 35 USC 112(a) rejection of record. It is noted that claim 12 is not merely directed to the method step of screening for a variant recognition site present in step a) of the claim; rather, claim 12 requires knowledge of the genus of variant recognition sites such that a donor DNA comprising the sites could be provided (see step b) of claim 12). Accordingly, knowledge of the complete genus of structures of the variant recognition sites that have increased activity for a rare-cutting agent is required to practice claim 12, which the instant specification has not adequately provided (see above 35 USC 112(a) rejection of record). The method requires the knowledge of the structure of the complete genus of variant recognition sites that is not adequately described in the instant specification (see above 35 USC 112(a) rejection of record).
Additionally, the claimed invention is not solely limited to the LIG3-4 or MHP14+ meganucleases disclosed in the specification, and the art provides evidence that the determination of a variant recognition site’s activity compared to an intended recognition site is unpredictable and requires testing (see maintained 35 USC 112(a) rejection of record above).
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). This rejection is maintained.
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).
Response to Arguments - 35 USC § 103
Applicant's arguments filed 14 April 2026 have been fully considered but they are not persuasive.
Applicant alleges that the combination of Molina and Yang do not teach or suggest steps (a)-(b) present in the instantly claimed method (Remarks; pg. 3-4). Applicant alleges that Molina describes cleavage/recombination screening in yeast in which I-Crel endonuclease is tested against a panel of predefined I-Crel target-site sequence variants and determines which I-Crel target-site sequence variants are cleaved and which are not for purposes of understanding I-Crel endonuclease specificity. See, Molina, p. 6937 (Fig. 1). To accomplish that objective, Molina constructs and tests a panel of I-Crel target-site sequence variants. See, Molina, p. 6937 (Fig. 1) (Remarks; pg. 4). Applicant alleges that the instantly claimed method steps (a)-(b) differ from this disclosure of Molina (Remarks; pg. 4).
Regarding step (a), this argument is not found persuasive because it is noted that even though Molina’s I-Crel target-site sequence variants are predefined, the study nonetheless a) identifies which 4 base pair target-site sequence variants are cleaved with a similar or higher cleavage efficiency when compared to other 4 base pair combinations (i.e., resulting in an increased activity for I-Crel: a rare-cutting engineered double-strand-break-inducing agent) (see Supplementary Fig. 1). As discussed above in the “Claim Interpretation”, the claimed intended recognition site is not limited to a wild-type recognition site. Rather, 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). Accordingly, any 4 base pair combination of Molina that exhibits double-stranded breakage is encompassed by the claimed intended recognition site. Therefore, Molina does teach step (a) of the instantly claimed method because Molina tests the cleavage activity of all possible 4 base pair recognition sequences and found that some variants (i.e., variant recognition sites) had higher cleavage activity than other recognition sites (i.e., intended recognition sites) (see Supplementary Fig. 1).
Regarding step (b), Molina provides a reporter plasmid (i.e., a donor DNA) that comprises the claimed variant recognition sites in order to determine the cleavage activity of I-Crel in vivo (pg. 6938; see Supplementary Fig. 1). Accordingly, Molina teaches step (b) of the claimed method.
Applicant alleges that if Molina were modified to first identify whether a I-Crel target-site sequence variant results in increased activity for I-Crel and then provide the I-Crel target-site sequence variant with increased activity, Molina would not be able to evaluate the non-permissive substitutions that abolish cleavage and therefore could not map I-Crel substrate discrimination and sequence tolerance (Remarks; pg. 5). Applicant alleges that Yang does not cure these deficiencies because Yang uses a fixed, intended recognition site and does not disclose variant recognition sites or identifying whether a variant recognition site has increased activity compared to an intended recognition site. (Yang, p. 671, Fig. 1) (Remarks; pg. 6).
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). It is the combination of Molina and Yang that renders the claimed invention obvious because Molina teaches the identification of the claimed rare-cutting engineered double-strand-break-inducing agent variant recognition sites, and their use on donor DNA reporter plasmids, while Yang teaches the integration of rare-cutting engineered double-strand-break-inducing agent recognition sites into plant genomes through the use of donor DNA molecules. Therefore, as discussed above in the maintained 35 USC 103 rejection of record, one would have been motivated to have utilized a variant recognition site as described in Molina within the plant cell of Yang in order to similarly target chromosomal sites with the use of variant I-Crel recognition sites that had demonstrated higher cleavage activity when compared to other (i.e., intended) recognition sites.
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning (Remarks; pg. 5), it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
Conclusion
THIS ACTION IS MADE FINAL. 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.
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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