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 .
Claim Status Summary
Claims 1- 22 are pending.
Claims 1- 7, and 14- 22 are considered on the merits.
Claims 8- 13 are withdrawn.
Claims 1- 7, and 14- 22 are rejected.
No Claims are allowed.
Application Status
Applicant’s election without traverse of the promoter “At. UBQ10 ubiquitous” of Species Group A in the reply filed on 2026 June 2 is acknowledged.
Claims 8-13 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 2026 June 2.
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- 7, 14, and 18- 22 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.
Those claims included in the statement of rejection but not otherwise discussed (claims 2-4, 7, 14, 21, and 22) are rejected for depending from a rejected claim but failing to remedy the indefiniteness therein.
Claim 1 recites:
1. A homologous recombination system for detecting an accurate homologous recombination event in a gene of interest in a cell, the recombination system comprising:
a. an expression construct for expressing a programmable RNA-guided nuclease transcription regulator, the expression construct comprising a promoter operably linked to a nucleic acid sequence encoding the programmable RNA-guided nuclease transcription regulator;
b. one or more expression constructs for expressing a guide RNA (gRNA) and a deadRNA (dRNA), the one or more expression constructs comprising a promoter operably linked to a nucleic acid sequence comprising the gRNA, a promoter operably linked to a nucleic acid sequence comprising the dRNA [comma and/or word(s) missing] an expression construct comprising a promoter operably linked to a dRNA, or a promoter operably linked to a nucleic acid sequence comprising the gRNA and a nucleic acid sequence comprising the dRNA, wherein the gRNA targets the programmable RNA-guided nuclease transcription regulator to a first nucleic acid sequence at a homologous recombination site in a gene of interest and the dRNA targets the programmable RNA-guided nuclease transcription regulator to a second nucleic acid sequence in a regulatory sequence of the gene of interest; and
c. a donor polynucleotide comprising a nucleic acid sequence encoding a reporter flanked by regions homologous to nucleic acid sequences at the homologous recombination site;
wherein a programmable RNA-guided nuclease transcription regulator targeted by the gRNA induces a homologous recombination event at the homologous recombination site and a programmable RNA-guided nuclease transcription regulator targeted by the dRNA regulates expression of the gene of interest.
There appears to be a missing comma and/or word(s) in line 5 of clause (b) (line 4 from above). See the bracket insert above for location. This is a grammatical error that makes the claim uninterpretable.
Claim 1 recites the limitations "expression construct" in multiple lines. There is insufficient antecedent basis for these limitations in the claim.
The claim recites multiple expression constructs. The claim recites “an expression construct” twice (line 4 and line 12) and “one or more expression constructs” (line 8 and line 9). It is unclear whether the two “an expression constructs” are the same or different. The claim further recites “one or more expression constructs” twice (line 8 and line 9). The claim then recites “the expression construct” in line 5. The recitation of the latter “an expression construct” and the “one or more expression constructs” makes the identity of “the expression construct” of line 5 unclear.
Furthermore, the claim is written such that the multiple expression constructs in clause (b) are not clearly claimed in the alternative.
Claim 1 recites the limitations "gRNA" in multiple lines. There is insufficient antecedent basis for these limitations in the claim.
There are numerous antecedent basis issues directed toward the claim limitation “gRNA.” The claim recites “a gRNA” (line 8) in the first line of clause (b). The claim continues to recite “the gRNA” four times (line 11, line 14, and line 15, line 25), where it is unclear whether “the gRNAs” are the same as “a gRNA” of line 8 because it appears that each of “the gRNA” belong to a different expression construct. Furthermore, the claim’s recitation of multiple expression constructs (as noted above) is such that it is unclear what gRNA is associated with which particular expression construct.
Claim 1 recites the limitations "dRNA" in multiple lines. There is insufficient antecedent basis for these limitations in the claim.
There are numerous antecedent basis issues directed toward the claim limitations “dRNA.” The claim recites “a dRNA” (line9) in the first line of clause (b) and another “a dRNA” (line 13). The claim further recites four “the dRNA” (line 12, line 15, line 17, and line 27) where it is unclear whether any of the “the dRNA” are the same as “a dRNA” of line 9, “a dRNA” of line 13, or some combination of the two. Furthermore, the claim’s recitation of multiple expression constructs (as noted above) is such that it is unclear what dRNA is associated with which particular expression construct.
Claims 5, 6, and 18- 20 contains the trademark/trade name “Act3.0.” Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe the “transcriptional activator” and, accordingly, the identification/description is indefinite.
Claim 20 recites the limitations " wherein the zCas9-Act3.0 transcriptional activator is encoded by a nucleic acid sequence comprising at least about 75% or more, at least about 85% or more, at least about 95% or more, or 100% sequence identity with base 1 to base 6,250 of SEQ ID NO: 14." In particular, line 4 recites “… base 1 to base 6,250 of SEQ ID NO: 14.” This is unclear because SEQ ID NO 14 only has 4687 bases not 6250 as the instant claim recites. The ambiguity of the sequence length renders sequence identity matching impossible.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 22 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
The “kit” limitation of the instant claim is not further limiting because the limitation clause of a “for detecting one or more accurate homologous recombination events in a cell” is identical to claim 1 and merely intended use that provides no structural limitation. Similarly, the limitation clause “the kit comprising a homologous recombination system of claim 1” is not further limiting because it is also simply the identical system of claim 1.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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, 2, 3, 14, 15, 16, 17, 22 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zhang (Zhang. WO 2022087451 A1, effectively filed Oct. 23, 2020). Claim 3 is further evidenced by Vector Builder (Vector Builder. So Many Promoters, So Little Time: Selecting Ubiquitous Promoters for Effective Gene Delivery. 2024. https://en.vectorbuilder.com/).
Regarding claim 1, Zhang teaches “Systems, methods, and compositions for targeting polynucleotides” [Abstract]; and “compositions induce a double strand break for the purpose of inducing HDR-mediated correction.” In the section titled “APPLICATIONS AND USES IN GENERAL” [0368]; and “The reporter construct [template] may include a detectable marker” is described in an embodiment in their section titled “Saturating Mutagenesis” [0429]. Furthermore, regarding the limitation “detecting an accurate homologous recombination event,” Zhang teaches their detection system is accurate, “’recognition’ of an (off-)target site by a gRNA presupposes composition, system, functionality” [0621]; and “in a cell” [0259].
Zhang further teaches their methods and compositions are expression constructs useful for transcriptional regulation which map to clause (a) of the instant claim, “a single promoter drives expression of a transcript encoding a nucleic acid-targeting effector protein and a guide RNA [including dRNA, see [0117]]” [0249]; and “Targeting of known control elements can be used to activate or repress the gene of interest” [0132].
Zhang further teaches embodiments of their expression constructs that map to clause (b) of the instant claim. Zhang teaches their promoters are linked to gRNA and dRNA as recited in paragraph [0249] and [0117] above. Zhang teaches a first RNA guided nuclease is directed toward HDR and a second RNA guided nuclease is directed toward a regulatory sequence, “a break … is introduced into the DNA or RNA sequence by the nucleic acid-targeting, the break is repaired via homologous recombination” [0366]; and “nucleic acid-guided nuclease may be fused to a transcriptional repression [and or activation] domain and recruited to the promoter region of a gene” [0380]. Zhang further teaches the first RNA guided nuclease is directed by the gRNA and the second RNA guided nuclease is directed by the dRNA by teaching the functionality of the expression products, “a dRNA complex with active Nucleic acid-guided nuclease directs gene regulation by a functional domain at on gene locus while an gRNA directs DNA cleavage by the active Nucleic acid-guided nuclease at another locus” [0117].
Zhang further teaches their donor nucleotide which maps to clause (c) of the instant claim, “A recombination template nucleic acid comprises the following components: [5' homology arm]-[replacement sequence]-[3' homology arm]. The homology arms provide for recombination into the chromosome,” [0377]; and “the recombination template may further comprise a marker… Examples of suitable markers include… fluorescent proteins… the break is repaired via homologous recombination with a recombination template such that the template is integrated into the target.” [0366].
Zhang further teaches the final clause, “compositions [programmable RNA-guided nuclease transcription regulator targeted by the gRNA] induce a double strand break for the purpose of inducing HDR-mediated correction.” [0368]; and “nucleic acid-guided nuclease may be fused to a transcriptional repression [and/or activation] domain and recruited to the promoter region of a gene” [0380]; this invention provides a method of modifying expression of a RNA [regulates expression of the gene of interest]” [0366].
It would have been obvious for a person having ordinary skill in the art (PHOSITA) at the time of filing to have combined variants of the embodiments of Zhang and arrived at the instant claimed “homologous recombination system” because it is simply combining prior art elements according to known methods to yield predictable results. . Zhang teaches a homologous recombination System. Zhang further teaches the system for detecting HDR events. Zhang teaches all of the elements of the claimed homologous recombination System. Zhang further teaches the elements are interchangeable within embodiments. Therefore a PHOSITA would have recognized all of the claimed elements within the variants of Zhang’s embodiments and predicted they could be combined according to the instant claim.
Regarding claim 2, Zhang teaches “the nucleic acid-guided nucleases are Cas proteins” [0095]; and “the single guide molecule capable of forming a complex with the nucleic acid-guided nuclease …” [0147]; and “the nucleic acid-guided nuclease is associated with one or more functional domains. The association can be by … association with the crRNA. … the crRNA comprises an added or inserted sequence that can be associated with a functional domain of interest, including, for example, an aptamer” [0113]; and “the one or more heterologous functional domains to have one or more of the following activities: …transcription activation activity” [0114].
Regarding claim 3, Zhang teaches “the plant promoter is a regulated promoter, which directs gene expression not constitutively, but in a temporally- and/or spatially-regulated manner, and includes tissue-specific…promoters” [0677]; and “Elements of these systems may be engineered to work within the context of the invention.” [0235]; and “the polynucleotide may comprise … a pol3 promoter” [0242]. Vector Builder provides the evidence Pol III are ubiquitous promoters “This article provides an overview of commonly used ubiquitous promoters and guidance on incorporating them into vector design to achieve successful gene delivery. Pol III promoters, such as U6 and H1, are commonly used…” (1st paragraph, section (4)).
Regarding claim 14, Zhang teaches “the polynucleotide molecules that encode one or more components of one or more systems as described in any of the embodiments herein are optimized for expression in … a plant cell” [0282].
Regarding claim 15, Zhang teaches all of the elements of claim 1 described above, which correspond to all of the limitations of the instant claim 15 except “stably integrated” expression construct. Zhang further teaches their methods and compositions are stably integrated in the section titled “Stable integration in the genome of plants” page 242, [0681]; and “polynucleotides encoding the components of the compositions and systems may be introduced for stable integration” [0681].
Regarding claim 16, Zhang teaches all of the elements of claims 1 and 15 described above. Furthermore, Zhang teaches the instant limitation of claim 16 as described in claim 1 above.
Regarding claim 17, Zhang teaches all of the elements of claims 1 and 15 described above. Furthermore, Zhang teaches the instant limitation of claim 17 as described in claim 2 above.
Regarding claim 22, Zhang teaches all of the elements of claim 1 described above. Furthermore, Zhang teaches “the invention provides kits containing any one or more of the elements disclosed in the above methods and compositions” [0761].
Claim(s) 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zhang (Zhang. WO 2022087451 A1, effectively filed Oct. 23, 2020) as applied to claim 1 above, and further in view of Voytas (Voytas US 20160237451 A1), and Aharoni (Aharoni US 20190048330 A1).
Regarding claim 4, applicant is reminded their elected species is At. UBQ10 ubiquitous promoter. Zhang teaches all of the elements of claims 1 and 3 described above.
Zhang does not teach the limitation “wherein the ubiquitous promoter or tissue-specific promoter is At. UBQ10 ubiquitous promoter.”
However, Zhang teaches their methods and compositions are useful in plants in the section titled “Stable integration in the genome of plants” page 242, [0681].
Voytas teaches “methods for using CRISPR/Cas systems to confer resistance to gemini viruses to plants” [Abstract]. Voytas further teaches “The tracrRNA sequence and the one or more crRNA sequences can be operably linked to a constitutive promoter (e.g., an RNA polymerase III promoter or an RNA polymerase II promoter), an inducible promoter, or a plant tissue specific promoter.” [0007]. Voytas further teaches “Transcription of the gRNA is controlled either by a … a constitutive RNA pol II promoter (e.g. … Ubq10)” [0048]. Voytas further teaches “Downstream of Cas9 is an Arabidopsis thaliana RNA pol III promoter (AtU6 or At7SL) followed by gRNA sequence.” [0015].
Voytas does not teach their UBQ10 promoter operably linked to a gRNA is an At. UBQ10 promoter.
Aharoni teaches “Disclosed herein are compositions and methods for regulating gene expression for gene targeting in eukaryotes, including plants and algae.” [0002]. Aharoni further teaches “A skilled artisan would appreciate that … CRISPR associated protein (Cas) system comprises genome engineering tools ... This RNA-based technology … allows targeted cleavage of genomic DNA …, resulting in gene modifications by … homology-directed repair (HDR) mechanisms” [0065]. Aharoni further teaches in their Fig. 2 “Agrobacterium containing a plasmid that harbor the RFP gene under the control of various promoters … AtUBIQ10: POLYUBIQUITIN10 of Arabidopsis (AT4G05320—AtUBIQ10long promoter” [0023].
It would have been obvious to a person having ordinary skill in the art (PHOSITA) at the time of filing to have substituted the ubiquitous Pol3 promoter of Zhang with the At.UBQ10 ubiquitous promoter of Aharoni because it is a simple substitution of one known element for another to obtain predictable results. Zhang disclosed plant-compatible ubiquitous promoters operably linked to gRNA. Similarly, Voytas disclosed the particular and similar ubiquitous promoter UBQ10 operably linked to gRNA and simultaneously taught a list of their promoters, demonstrating the promoters were interchangeable. Aharoni disclosed the Arabidopsis thaliana specific UBQ10 promoter operated similarly in RNA guided nuclease genome editing. Therefore, a PHOSITA would have predicted the substitution of Aharoni’s At.UBQ10 promoter for Zhang’s Pol3 promoter would have been successful.
Claim(s) 5 and 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zhang (Zhang. WO 2022087451 A1, effectively filed Oct. 23, 2020) as applied to claims 1 and 15 above, and further in view of Qi (Qi US 20230374528 A1).
Regarding claim 5 and 18, Zhang teaches all of the elements of claims 1 and 15 described above.
Zhang does not teach the limitation “wherein the programmable RNA-guided nuclease transcription regulator is zCas9-Act3.0 transcriptional activator.”
However, Zhang teaches their methods and compositions are useful in plants “The compositions, systems, and methods described herein can be used to perform gene or genome interrogation or editing or manipulation in plants” [0663] and goes further to provide motivation describing its stable properties in the section titled “Stable integration in the genome of plants” page 242, [0681].
Qi teaches “A potent CRISPR transcriptional activation system in plants, termed CRISPR-Act3.0, is provided. The system provides higher levels of gene activation than all other gene activation systems reported in plants to date… which allows for simultaneous and combinational gene activation, editing, and repression… The gene editing may include … homology-based repair (HDR).” [0008]. In their Example 2, Qi further teaches “The dzCas9 based CRISPR-Act3.0 system induced a comparable activation efficiency … consistent with previous reports that … zCas9 proteins were efficient for genome editing” [0269].
It would have been obvious for a PHOSITA at the time of filing to have used Qi’s zCas9-Act3.0 RNA-guided nuclease transcription regulator in Zhang’s system because there was some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. Zhang and Qi are in the same field of endeavor (genome editing) and Zhang further teaches their method is useful in plants. Zhang and Qi both showed their methods using RNA-guided nuclease transcription regulator were successful. Therefore, a PHOSITA would also have had a reasonable expectation of success using Qi’s zCas9-Act3.0 RNA-guided nuclease transcription regulator in Zhang’s system.
Claim(s) 21 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zhang (Zhang. WO 2022087451 A1, effectively filed Oct. 23, 2020) as applied to claims 1, 3, and 15 above, and further in view of Qi (Qi US 20230374528 A1) as applied to claim 18 above, and further in view of and Voytas (Voytas US 20160237451 A1), and further in view of Aharoni (Aharoni US 20190048330 A1) as applied to claim 4 above.
Regarding claim 21, applicant is reminded their elected species is At. UBQ10 ubiquitous promoter.
Zhang teaches all of the elements of claims 1 and 3 described above.
Zhang and Qi teaches all of the elements of claims 15 and 18 described above.
Zhang, Voytas , and Aharoni, teach all of the elements of claims 4 described above.
Zhang alone does not teach the limitation “wherein zCas9-Act3.0 transcriptional activator is under control of the At. UBQ10 ubiquitous promoter, egg-cell specific promoter At. EC1.2e1.1p, or embryo specific promoter At.YAO.”
However, as described above, Zhang, Qi, Voytas , and Aharoni, teach the similar cell-based homologous recombination system wherein the RNA-guided nuclease transcription regulator is a zCas9-Act3.0 transcriptional activator, and the promoter is At. UBQ10 ubiquitous promoter.
Likewise, as described above, Zhang and Qi teaches the nearly identical genetically modified cell wherein the RNA-guided nuclease transcription regulator is a zCas9-Act3.0 transcriptional activator, and the regulator/activator is operably linked to a promoter.
Zhang-Qi showed their cellular methods using RNA-guided nuclease transcription regulator were successful with the zCas9-Act3.0 RNA-guided nuclease transcription regulator. It has been shown Zhang- Voytas-Aharoni’s substitution of At.UBQ10 promoter for Pol3 promoter would have been successful. Therefore, a PHOSITA would have predicted the substitution of Zhang- Voytas-Aharoni’s At.UBQ10 promoter for Zhang-Qi’s Pol3 promoter would have been successful.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Regarding claims 6 and 19, this examiner was not able to find prior art that reads on the claim limitation “wherein the zCas9-Act3.0 transcriptional activator is encoded by a nucleic acid sequence comprising at least about 75% or more, at least about 85% or more, at least about 95% or more, or 100% sequence identity with base 1 to base 6,250 of SEQ ID NO: 13.” The closest prior art found was Gao (Gao US 20200340002 A1). Gao’s SEQ ID NO 10 is 5406 bases and matches 66.6% to bases 1- 6250 of instant SEQ ID No 13. Gao teaches “a method for base editing in plant is provided. … by a guide RNA-directed CRISPR-adenine deaminase fusion protein” [Abstract[.
Regarding claim 7, the claim limitation has similar language to claim 21 and would therefore be rejected for similar reasons as claim 21. However, claim 7 depends from claim 6 and as noted above, is currently free of the prior art and therefore claim 7 is currently immune to a prior art rejection.
Regarding claim 20, the instant SEQ ID NO 14 is only 4687 bases long but the claim recites “base 1 to base 6,250.” The full length of the sequence was used to search for prior art against the instant claim. This examiner was not able to find prior art that reads on the claim limitation “wherein the zCas9-Act3.0 transcriptional activator is encoded by a nucleic acid sequence comprising at least about 75% or more, at least about 85% or more, at least about 95% or more, or 100% sequence identity with base 1 to base 6,250 of SEQ ID NO: 14.” The closest prior art found was Shultz (Shultz US 20190264218 A1). Shultz’s SEQ ID NO 50 is 3493 bases and matches 39.4% instant SEQ ID No 14. Shultz teaches “Disclosed herein are compositions and methods for effecting alterations at a defined location in the genome of a non-epidermal plant cell” [Abstract[.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AARON DUREL WARD whose telephone number is (571)272-8495. The examiner can normally be reached Monday to Thursday 8:00AM 6:00PM.
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/AARON DUREL WARD/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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