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 .
Information Disclosure Statement
The Information Disclosure Statements filed on 5/12/2025, 11/4/2025, 11/17/2025, 1/17/2026, 8/4/2026 have been entered and considered. Initialed copies of the form PTO-1449 are enclosed with this action.
Status of claims
On 8/21/2025, a new specification was filed. The claim set was amended.
Claims 1-96 were canceled. New claims 97-116 were added.
In summary, claims 97-116 are pending and examined in the following Office action.
Priority
Instant 19205140, filed 05/12/2025, is a Continuation of 17078919, filed 10/23/2020, now U.S. Patent 12331330.
17078919 Claims Priority from Provisional Application 62925097, filed 10/23/2019.
62925097 disclosed the claimed subject matter, thus, the priority is recognized.
Objections to the Specification
In the specification, the claimed term “GCN4” (claim 103) is not provided the full name.
Appropriate correction is required.
Interpretation of “extended guide RNA”
The specification does not define “extended guide RNA”.
According to the specification (p30, 3rd para), “In some embodiments, an extended guide RNA may comprise, 5'-3', a spacer sequence, a repeat sequence, and an extended portion, the extended portion comprising, 5' to 3', a reverse transcriptase template and a primer binding site. In some embodiments, an extended guide RNA may comprise, 5'-3', a spacer sequence, a repeat sequence and an extended portion, the extended portion comprising, 5' to 3', a primer binding site and a reverse transcriptase template. In some embodiments, an extended guide RNA may comprise, 5'-3', an extended portion, a spacer sequence, and a repeat sequence, wherein the extended portion comprises, 5' to 3', a reverse transcriptase template and a primer binding site. In some embodiments, an extended guide RNA may comprise, 5'-3', an extended portion, a spacer sequence, and a repeat sequence, wherein the extended portion comprises, 5' to 3', a primer binding site and a reverse transcriptase template”.
According to the specification (p31, 1st para), a primer editing guide RNA (pegRNA) is an extend guide RNA.
Accordingly, by BRI, “an extended guide RNA” is interpreted as a guide RNA comprising any extension or addition, not limited to spacer(s) and/or template(s) and/or binding site(s).
"Recruit" in the specification
In the specification (p24, 3rd para), "Recruit," "recruiting" or "recruitment" as used herein refer to attracting one or more polypeptide(s) or polynucleotide(s) to another polypeptide or polynucleotide (e.g., to a particular location in a genome) using protein-protein interactions, RNA-protein interactions, and/or chemical interactions.
Claim Objections
Claim 103 is objected to because of the following informality:
The “GCN4” appears in a claim for the first time, the full name should be recited, followed by the abbreviation in a ().
Claim 104 is objected to because of the following informality:
The claim recites “first polynucleotide encoding a plant specific promoter”, which is scientifically incorrect. A promoter is a part of the polynucleotide/DNA sequence. It is suggested to recite --first polynucleotide comprising a plant specific promoter—instead.
The metes and bounds of the claim is clear, thus, the claim is not rejected for indefiniteness.
See the requirement of 37 CFR 1.71(a) for “full, clear, and exact terms”.
Appropriate correction is required.
Claim Rejections - 35 USC § 103
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 non-obviousness.
Claims 97-98, 100-116 are rejected under 35 U.S.C. 103 as being unpatentable over Anzalone et al (Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 1-37, published online 2019.10.21, see attached PDF for publication date), in view of Liu et al (WO 2020191234, priority date 5/11/2019), and Osakabe et al (Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants. Nature Scientific Reports. P1-10, 2016).
Claim 97 is drawn to a method comprising a step of contacting the target nucleic acid with:
a Cas9 nickase (nCas9);
a reverse transcriptase, wherein the reverse transcriptase is fused to the nCas9 or recruited to the nCas9; and
an extended guide nucleic acid,
For modifying a target nucleic acid in a plant cell (preamble), thereby modifying the target nucleic acid to provide a modified target nucleic acid in the plant cell (thereby clause).
Claim 98 limits claim 97, wherein the reverse transcriptase is fused to the nCas9.
Regarding claims 97-98
Anzalone et al teach making a complex construct comprising an extended peg RNA (primer editing guide RNA, a specific guide RNA, see p1, Abstract), a Cas9 nickase, and a reverse transcriptase (p4, 2nd to 3rd para).
Anzalone et al teach that the reverse transcriptase (RT) is fused to the C-terminus of the Cas9 nickase (p4, last para).
Anzalone et al teach contacting target nucleic acids in yeast and animal cells and demonstrated successful modifications in the genome of the cells (p3, last para to p8, 1st para; Extended Data in p20-39).
Accordingly, Anzalone et al teach exactly the same structure of claim 1 and demonstrated contacting cells and successful modifications in the genome of the cells,
Except does not teach the contacted cells are plant cells.
Liu et al teach a system comprising an extended peg RNA, a CRISPR Cas9 nuclease, and a reverse transcriptase ([0610]-[0613], fig 3A-3F).
According to the specification (p24, 3rd para), "Recruit," "recruiting" or "recruitment" as used herein refer to attracting one or more polypeptide(s) or polynucleotide(s) to another polypeptide or polynucleotide (e.g., to a particular location in a genome) using protein-protein interactions, RNA-protein interactions, and/or chemical interactions. Accordingly, the system of the fig 3A-F reads on that the reverse transcriptase is recruited to the Cas9 nuclease. Liu et al nevertheless suggest that the reverse transcriptase can be bind to RNA recruiting protein/domain ([0082], fig 3A-3F).
The difference between Liu and Anzalone is Cas9 nuclease vs Cas9 nickase. Liu et al teach that Cas9 nickase is a alternative of Cas9 nuclease ([0013]-[0014], [0060]). Liu et al also suggest that the reverse transcriptase is fused to a Cas9 nickase ([0069]).
Liu et al teach applying the system to plant cell and to yeast cell ([1121]). Thus, plant cells and yeast cells (Anzalone et al teach the subject matter of yeast cells as analyzed above) are alternatives. Liu et al additionally teach a method of applying the system to plant cells to make transgenic plants ([1014], [1504] in Example 17), and cite multiple references to support the application ([1509]).
As a support to Liu et al, Osakabe et al teach a detailed method of making a construct comprising genes encoding CRISPR-Cas9, guide RNA, gene of interest, and GFP marker, and transforming an Arabidopsis plant with the construct (p8, Methods). Please note that the mere difference of the construct of Osakabe from the construct of Anzalone is gene of interest and marker gene vs reverse transcriptase.
Osakabe et al demonstrated success of transformation and demonstrated success of gene editing in the plant cells (p2-5, Results; p3-4, figs 1-2).
Thus, Osakabe et al support Anzalone et al in view of Liu et al by providing high expectation of success.
Regarding dependent claims
Osakabe et al teach that the reverse transcriptase (RT) is fused to the C-terminus of Cas9 nickase (p4, last para), the limitation of claim 100.
As analyzed above, in view of the specification, Liu et al at least suggest that the reverse transcriptase is recruited to the Cas9 nickase, the limitation of claim 101.
Liu et al teach that the system comprises a peptide tag, including a GCN4 tag ([0108], Example 4, [1202]), the limitations of claims 102-103.
Osakabe et al teach that the expression cassette comprises AtU6-1 promoter, a plant-specific promoter, and CaMV35S promoter, a viral promoter that can be used in plants, to drive genes including the Cas9 gene (p3, fig 1), the limitations of claims 104-105.
Anzalone et al teach making targeted small insertions and deletions in the target sites (p7,5th para), the limitation of claim 106.
Liu et al teach that the guide RNA is linked to a Pol II promoter ([0648]-[0650]), the limitation of claim 107.
As analyzed above, Liu et al additionally teach a detailed method of applying the system to plant cells including the method of plant transformation. Liu et al further teach that the system comprises 5ʹ end DNA flap endonuclease, FEN1 ([0011], Example 1, [1168]). Thus, Liu et al at least suggest the limitations of claims 108-110.
As analyzed above, Osakabe et al editing Arabidopsis, a dicot plant, the limitation of claim 111.
Osakabe et al also teach editing rice (p1, 1st para), a monocot plant, the limitation of claim 112.
Osakabe et al teach that the transformed and edited plant cells grow up to T1 and T2 generations (p5, 1st to 4th para), reading on regenerating the modified plant, the limitation of claim 113.
Liu et al teach that the extended guide RNA comprises reverse transcriptase (RT) template of 51 nt in length (Fig 6, B) and that the extended guide RNA comprises primer binding site that is about 15 nucleotides in length (Fig 28B), the limitations of claims 114-115.
Liu et al also teach that the RT template is after the primer binding site ([0009], [0069], figs 1A-1F), and suggest that RT template sequence can be at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, and more ([0618]). Thus, Liu et al teach the limitation of claim 116.
An invention would have been obvious to one ordinary skill in the art if any teaching, suggestion or motivation in prior art leading the one to combine the teaching(s) or suggestion(s) of the cited references to arrive the claimed invention.
In this case, it would have been obvious to modify the invention of Anzalone et al, such that the method of Anzalone et al is applied to plant cells, as taught by Liu et al and demonstrated by Osakabe et al. One ordinary skill in the art would have been motivated to do so because Liu et al not only suggest to apply Liu’s method to yeast (Anzalone) and plant (Liu) cells, but also teach a method of such application in plant cells, which is further demonstrated by Osakabe et al. The expectation of success would have been high, because the only structural difference of the constructs between Anzalone and Liu is Cas9 nickase vs Cas9 nuclease, between Anzalone and Osakabe is gene encoding reverse transcriptase vs gene of interest and marker gene. Given that method of editing plant cells had been demonstrated, one ordinary skill in the art would have expected that a method of editing plant cells with a system comprising extended guide RNA, reverse transcriptase and Cas9 nickase would work the same way. Plant transformation had been a routine method as taught by Liu et al and demonstrated by Osakabe et al.
Therefore, the invention would have been obvious to one ordinary skill in the art.
Claim 99 is rejected under 35 U.S.C. 103 as being unpatentable over Anzalone et al in view of Liu et al and Osakabe et al, as applied to claims 97-98 above, and further in view of Dong et al (Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria. Nature Communication. 1-11, 2018).
Claims 97-98 have been analyzed above.
Claim 99 limits claim 98, wherein the reverse transcriptase is fused to the nCas9 via a peptide linker having a length of 10 to 20 amino acid residues.
Liu et al further teach that Cas9 fusion proteins comprises a peptide linker ([0201]), but are silent on the length of the linker.
Dong et al teach that CRISPR cas9 is recruited or fused to other protein(s) to form a fusion protein, and that the recruiting or fusing can be via a peptide linker so that the complex is flexible (p7, left and right cols; p8, left col, 1st to 2nd para).
Dong et al teach making flexible peptide linkers having the length of 2, 5, 10 and 20 amino acids, and tested each length, and observed that no significant difference in the
position of effective target sites (p8, left col, 2nd para). The length includes 10 and 20 amino acids as instantly claimed.
In this case, it would have been obvious to modify the invention rendered obvious by Anzalone et al in view of Liu et al and Osakabe et al, such that the linker in the recruited or fused protein complex comprising Cas9 of Liu et al have a length including 10-20 amino acids, as taught and demonstrated by Dong et al. One ordinary skill in the art would have been motivated to do so because Dong et al tested and proved such length for flexibility and targeting. The expectation of success would have been high, because Dong et al not only had tested the length, but also had taught to test and optimize the length of the peptide linkers.
Therefore, the dependent claim would have been obvious to one ordinary skill in the art.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the claims at issue are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the reference application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO internet Web site contains terminal disclaimer forms which may be used. Please visit http://www.uspto.gov/forms/. The filing date of the application will determine what form should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to http://www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
2 rejections are made. The US Patents and instant application share multiple inventors and applicant Pairwise Plant Services.
Claims 97-116 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12, 16-28 of US Patent 12331330.
The USP (reference) claims:
Claim 1. A method of modifying a target nucleic acid in a cell, the method comprising:
contacting the target nucleic acid with
a DNA binding polypeptide;
a DNA endonuclease;
a guide nucleic acid that comprises an RNA recruiting motif and a first spacer that has substantial complementarity to a first site on a first strand of the target nucleic acid, wherein the guide nucleic acid is devoid of a primer binding site, and wherein the guide nucleic acid binds to the first strand;
an extended guide nucleic acid, wherein the extended guide nucleic acid comprises (a) a second spacer having substantial complementarity to a second site on a second strand of the target nucleic acid and (b) an extended portion that comprises a primer binding site and a reverse transcriptase template encoding a modification to be incorporated into the target nucleic acid, wherein the extended guide nucleic acid binds to the second strand; and
a reverse transcriptase that binds to the RNA recruiting motif, thereby modifying the target nucleic acid in the cell,
wherein the target nucleic acid comprises the first strand and the second strand that are opposite strands of the target nucleic acid;
wherein the DNA binding polypeptide and the DNA endonuclease bind to the guide nucleic acid on the first strand;
wherein the reverse transcriptase is recruited to the second strand of the target nucleic acid by the RNA recruiting motif of the guide nucleic acid, and
wherein the reverse transcriptase polymerizes a first polynucleotide from one end of the second strand.
Claim 3. The method of claim 1, wherein the DNA binding polypeptide and the DNA endonuclease are comprised in a CRISPR-Cas nuclease.
Claim 4. The method of claim 1, wherein the DNA binding polypeptide is a CRISPR-Cas nuclease domain and the CRISPR-Cas nuclease domain is a Cas9 nickase (nCas9) domain or Cas12a domain.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Reference claims 1 and 3-4 claim the subject matter of contacting the target nucleic acid with a Cas9 nickase (nCas9); a reverse transcriptase, wherein the reverse transcriptase is fused to the nCas9 or recruited to the nCas9; and an extended guide nucleic acid, and teach instant claim 97 in a narrow and more specific manner (including specific structure of the extended guide RNA and more). Thus, the reference US patent recites a species of the genus recited in the instant application. Claims directed to a genus are prima facie obvious over claims directed to species of that genus.
Regarding dependent claims, reference claims 2-4 teach instant claim 98.
Reference claims 5-12, 16-28 teach or suggest the limitations of instant claims 99-116.
In addition, in view of Anzalone et al, Liu et al and Osakabe et al as analyzed above, instant dependent claims are deemed obvious.
Therefore, the reference and instant claims are obvious over each other.
Claims 97-116 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of US Patent 11926834.
The USP (reference) claims:
Claim 1. A method of modifying a target nucleic acid, the method comprising:
contacting the target nucleic acid with
(a) a Type V CRISPR-Cas effector protein;
(b) a reverse transcriptase; and
(c) an extended guide nucleic acid, wherein the extended guide nucleic acid comprises:
(i) a Type V CRISPR nucleic acid; and
(ii) an extended portion comprising a primer binding site and a reverse transcriptase template (RT template),
wherein the extended portion of the extended guide nucleic acid comprises an RT template and a primer binding site, optionally wherein the extended portion is fused to either the 5′ end or 3′ end of the Type V CRISPR nucleic acid and/or the RT template of the extended portion is 5′ of the primer binding site, and
wherein the target nucleic acid is double stranded comprising a first strand and a second strand, the Type V CRISPR-Cas effector protein is a double stranded nuclease that cuts the first strand and the second strand of the target nucleic acid resulting in a double stranded break, and the primer binding site binds to the first strand of the target nucleic acid, which is the target strand and same strand to which the Type V CRISPR-Cas effector protein is recruited, thereby modifying the target nucleic acid.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Reference claim 1 claims contacting the target nucleic acid with a Type V CRISPR-Cas effector protein; a reverse transcriptase; and a very specific extended guide nucleic acid, thus, teach instant claim 97 in a narrow and more specific manner,
except do not directly claim that CRISPR-Cas effector protein is a Cas9 nickase (nCas9).
However, in view of Anzalone et al, Liu et al and Osakabe et al as analyzed above, the subject matter of Cas9 nickase is deemed obvious, and Cas9 nickase is a CRISPR-Cas effector protein.
Reference claims 2-15 teach or suggest the limitations of instant claims 98-116.
In addition, in view of Anzalone et al, Liu et al and Osakabe et al as analyzed above, instant dependent claims are deemed obvious.
Therefore, the reference and instant claims are obvious over each other.
Conclusion
No claim is allowed.
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/Wayne Zhong/
Primary Examiner, Art Unit 1662
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