DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Application Status and Election
The amendments and remarks filed 8/18/25 in response to the office action 5/19/25 are acknowledge and have been entered. Claims 4, 7, 12, 14, 16, 19, 23, 25, 28, 30, 34, 37, 41, 46, 50, and 51-58 are pending.
Claims 4, 7, 19, 23, 28, 30, 34, 37, 41, and 50 are amended.
New claims 51-58 are added.
Applicant’s election without traverse of group 1 (claims 4, 7, 12, 14, 16, 19, 23, 25, 28, 30, 34, 37, and 41) remains acknowledged.
Applicant elected the following species without traverse in the Remarks file 3/28/25.
Species 1: The gene encoding or processed into the RNA silencing molecule is positioned in a non-coding gene (claim 7).
Species 2: The RNAi type is miRNA (claim 19).
Species 3: The presence of an endonuclease, specifically Cas9 (claim 30).
Species 4: The editing enzyme is a DNA methyltransferase (claim 34).
Species 5: The organism is a plant, and the gene is a gene associated with apoptosis, specifically the BAX gene (claim 41).
Claims 46 and 50 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention or species, there being no allowable generic or linking claim.
New claim 51 is drawn to a non-elected species, i.e. “positioned in a coding gene” as opposed to the elected species of “non-coding gene “ therefore, claim 51 is withdrawn.
Examination on the merits commences on claims 4, 7, 12, 14, 16, 19, 23, 25, 28, 30, 34, 37, 41, and 52-58.
35 USC §§ 103 and 112b rejections and NSDP rejections of record for claims 4, 7, 12, 14, 16, 19, 23, 25, 28, 30, 34, 37, 41, and 52-58 are maintained.
Applicants are informed that the rejections and/or objections of the previous Office action not stated below have been withdrawn from consideration in view of the Applicant' s arguments and/or amendments. Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Terminal Disclaimer
The terminal disclaimer filed on 8/18/25 filed over patent # 11555199 disclaiming the terminal portion of the patent being reexamined which would extend beyond the expiration date of 10/01/2038 has been reviewed and is accepted. The terminal disclaimer has been recorded.
Claim Rejections - 35 USC § 112(b) - Maintained
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 4, 7, 12, 14, 16, 19, 23, 25, 28, 30, 34, 37, and 41 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.
Claim 4 recites, “said target RNA and said second target RNA being distinct”. It is unclear what is meant by distinct and how the required distinctness may be determined.
Claims 7, 12, 14, 16, 19, 23, 25, 28, 30, 34, 37, 41, and 52-58 are also rejected under 35 USC 112 (b) by virtue of their dependency on claim 4 without remedying the indefiniteness.
Claim Rejections - 35 USC § 103 - Maintained
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.
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.
Claims 4, 7, 12, 14, 16, 19, 23, 25, 28, 37, 52-55, and 57 are rejected under 35 U.S.C. 103 as being unpatentable over Zhou (Zhou, Jianping, et al. "CRISPR-Cas9 based genome editing reveals new insights into microRNA function and regulation in rice." Frontiers in Plant Science 8 (2017): 1598.) in view of Kawahara (Kawahara, Yukio, et al. "Redirection of silencing targets by adenosine-to-inosine editing of miRNAs." Science 315.5815 (2007): 1137-1140.) and and Bhattacharya (Bhattacharya, Anindya, and Yan Cui. "Systematic prediction of the impacts of mutations in MicroRNA seed sequences." Journal of Integrative Bioinformatics 14.1 (2017): 20170001.).
Regarding claim 4, Zhou teaches CRISPR-Cas9 base editing to directly generate miRNA mutants in plants and where the mutant miRNA are superior for carrying out reverse genetic research strategies (pg 2 col 2 para 1), i.e. employing genetic base editing to modify a non-coding gene processed into a RNA silencing molecule with a targeting specificity directed to a target RNA in a eukaryotic cell. Zhou teaches knocking out a single miRNA can result in expression profile changes of many other seemingly unrelated miRNAs (abstract).
Although Zhou does not specifically teach redirection of target RNA such as miRNA towards an alternative target, Zhou does teach guide RNAs with CRISPR-Cas9 endonuclease as a DNA editing agent (abstract).Zhou does not teach the method comprising introducing into the eukaryotic cell a DNA editing agent which redirects a silencing specificity of said RNA silencing molecule towards a second target RNA.
Kawahara teaches that the editing of miRNA molecules from an A to I changes the target selection of miRNAs, therefore redirecting the miRNA to a second target (see throughout and figures), thus establishing that it was known as of 2007 that editing miRNAs in specific positions with specific bases would change the target site for the miRNA (pg 1139 col 3 para 1). Kawahara teaches the edited miR-376 RNA silences specifically a different set of genes (Fig. 3).
Bhattacharya teaches the systematic prediction of the impacts of mutations in miRNA sequences including changed target sites (pg 1 para 3 and Fig. 4). Bhattacharya teaches mutations in microRNA seed regions may disrupt the binding of microRNAs to their original target genes and make them bind to new target genes (abstract). Bhattacharya teaches knowledge based computational method to systematically predict the functional effects of all the possible single nucleotide mutations in human microRNA seed regions (abstract).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have modified Zhou’s method of nucleic acid base editing to directly generate miRNA mutants which can selectively target alternative target nucleic acids. It would have merely amounted to a simple combination of prior art elements according to known methods to yield predictable results. The skilled artisan would have had a reasonable expectation that edited miRNA as performed by DNA editing agents in Zhou’s method of base editing could create mutated miRNA which could target alternative sets of genes because Kawahara teaches editing miRNAs in specific positions with specific bases would change the target site for the miRNA to target alternative genes. It would have been predictable that specific mutations could redirect targeting to anticipated alternative sites because Bhattacharya teaches the systematic prediction of the impacts of mutations in miRNA sequences including changed target sites. Thus, the skilled artisan would be motivated to employ the controlled redirection of anticipated new targets by known base editing techniques as an improved means of genetic control.
Additionally, given the state of the art at the time of filing and the disclosures by Zhou, Kawahara, and Bhattacharya it would further have been obvious to at least test the impact of the mutated miRNA sequences taught by Zhou in assessing possible target sites for the mutated miRNA sequences. Given the technology available at the time of filing, it would have been obvious to use the methods taught by Bhattacharya to assess which mutations would alter target sites and further assess the impact of changing those target sites. One of ordinary skill in the art would have been motivated to do so given the teachings of Zhou on using miRNA mutations to impact processes in plants.
Regarding claim 7, Zhou teaches CRISPR-Cas9 base editing to directly generate miRNA mutants in plants and where the mutant miRNA are superior for carrying out reverse genetic research strategies (pg 2 col 2 para 1), i.e. employing genetic base editing to modify a non-coding gene processed into a RNA silencing molecule with a targeting specificity directed to a target RNA in a eukaryotic cell.
Regarding claim 12, Zhou teaches in Figure 1 the targeting of rice (eukaryotic) microRNA endogenous genes with CRISPR-Cas9 in the method.
Regarding claim 14, Zhou teaches in plants, miRNAs recognize target mRNAs by highly specific complementary base-pairing mechanisms and regulate many processes (pg 2 col 1 para 1). Examiner interprets highly specific miRNA complementary base-pairing is equivalent to at least 45% complementarity to any target including the second target as deemed obvious in the obviousness rejection applied above to claim 4.
Regarding claims 16, Zhou teaches genotypic assays and phenotypic assays (Fig. 3-5).
Regarding claim 19, Zhou teaches edited miRNA silencing molecules where the miRNAs starts with processing of RNA Polymerase II promoter driven precursor primary miRNA (pri-miRNA) transcripts that fold back to form hairpin structures (pg 2 col 1 para 1).
Regarding claim 23 and 25, Zhou teaches modification of the miRNA by single base pair insertion or deletion mutations (abstract), i.e. a point mutation which is less than 200 nucleotides.
Regarding claim 28, 30, and 55, Zhou teaches guide RNAs with CRISPR-Cas9 endonuclease as the DNA editing agent (abstract).
Regarding claim 37, Zhou teaches a guide RNA sequence delivered to rice plant cell lines selected for a target nucleic acid sequence (abstract) i.e. DNA editing agent applied to the cell as DNA or RNA.
Regarding claims 52 and 53, Zhou teaches CRISPR-Cas9 base editing to directly generate miRNA mutants in plants and where the mutant miRNA are superior for carrying out reverse genetic research strategies (pg 2 col 2 para 1), i.e. employing genetic base editing to modify a non-coding gene processed into a RNA silencing molecule with a targeting specificity directed to a target RNA in a eukaryotic cell. Zhou teaches knocking out a single miRNA can result in expression profile changes of many other seemingly unrelated miRNAs (abstract).
Regarding claim 54, Zhou teaches wherein said one or more point mutations are in a stem region of said RNA silencing molecule (Fig 1a).
Claim 34 and 57 is rejected under 35 U.S.C. 103 as being unpatentable over Zhou (Zhou, Jianping, et al. "CRISPR-Cas9 based genome editing reveals new insights into microRNA function and regulation in rice." Frontiers in Plant Science 8 (2017): 1598.) in view of Kawahara (Kawahara, Yukio, et al. "Redirection of silencing targets by adenosine-to-inosine editing of miRNAs." Science 315.5815 (2007): 1137-1140.) and Bhattacharya (Bhattacharya, Anindya, and Yan Cui. "Systematic prediction of the impacts of mutations in MicroRNA seed sequences." Journal of Integrative Bioinformatics 14.1 (2017): 20170001.) as applied to claim 4, and in further view of Abu (Abudayyeh, O., WO2019005884A1).
Regarding claim 34, the teachings of Zhou, Kawahara, and Bhattacharya as applied above to claim 4 are incorporated here.
Zhou does not teach the editing agent to be capable of epigenetic editing.
However, in a similar method of Cas mediated editing of regulatory sequences, Abu teaches epigenetic base editing by introducing into a cell containing said target nucleic acids directed editing techniques comprising a targeting domain and an adenosine deaminase [0038]. Abu teaches the method of modifying an Adenine in a target RNA sequence of interest by delivering to said target RNA: (a) a catalytically inactive (dead) Casl3 protein; (b) a guide molecule which comprises a guide sequence linked to a direct repeat sequence; and (c) an adenosine deaminase protein in order to alter the target nucleic acid [0008].
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have applied Abu’s epigenetic nucleic acid editing method to specifically alter miRNA in Zhou’s method of editing miRNA. The skilled artisan would have had a reasonable expectation of success at applying RNA base editing to modify and redirect miRNA towards alternative targets given the obviousness rational applied above for claim 4 and because Abu teaches the effective method of Cas mediated editing of regulatory sequences in modulation of transcriptional activity. The skilled artisan would be motivated to employ Abu’s epigenetic editing method for enhanced transcriptional control.
Regarding claim 57, Abu further teaches additional modifications of the CRISPR-Cas protein for altered functionality where such different modifications may be combined such as mutated nuclease which is catalytically inactive and which further is fused to a functional domain, such as for instance to induce DNA methylation with heterologous domains including a methyltransferase [0592].
Claim 41 and 58 is rejected under 35 U.S.C. 103 as being unpatentable over Zhou (Zhou, Jianping, et al. "CRISPR-Cas9 based genome editing reveals new insights into microRNA function and regulation in rice." Frontiers in Plant Science 8 (2017): 1598.) in view of Kawahara (Kawahara, Yukio, et al. "Redirection of silencing targets by adenosine-to-inosine editing of miRNAs." Science 315.5815 (2007): 1137-1140.) and Bhattacharya (Bhattacharya, Anindya, and Yan Cui. "Systematic prediction of the impacts of mutations in MicroRNA seed sequences." Journal of Integrative Bioinformatics 14.1 (2017): 20170001.) and Abu (Abudayyeh, O., WO2019005884A1), as applied to claim 4, and in further view of Li (Li, Shize, et al. "MicroRNA-7 inhibits neuronal apoptosis in a cellular Parkinson’s disease model by targeting Bax and Sirt2." American journal of translational research 8.2 (2016): 993.)
Regarding claim 41 and 58, the teachings of Zhou, Kawahara, and Bhattacharya as applied above to claim 4 are incorporated here.
Zhou does not teach wherein said second target RNA is a transcript of a gene associated with cell apoptosis.
However, Li teaches the MicroRNA-7 (miR-7) displays neuroprotective properties in treating Parkinson’s Disease where miR-7 targets the Bax gene involved in the regulation of neuronal apoptosis (abstract).
Given that it is well known in the art that miRNAs with specific targets can be utilized for therapeutic interventions such as miR-7 targeting apoptotic BAX genes in the treatment of Parkinson’s Disease, It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have employed the miRNA redirection method as described in the obviousness rational applied above for claim 4 towards redirecting the miRNA to specific targets like targets of the well characterized miR-7 miRNA. It would have merely amounted to a simple combination of prior art elements according to known methods to yield predictable results. The skilled artisan would have had a reasonable expectation that miRNA could be genetically redirected to BAX targeting miR-7 miRNA to influence apoptosis because Li teaches miR-7 targets the Bax gene involved in the regulation of neuronal apoptosis and because Zhou, Kawahara, and Bhattacharya combine to demonstrate the miRNA redirection technique which could be predictably applied with computational models and endonuclease editing techniques described in the obviousness rationale provided above for claim 4. The skilled artisan would be motivated to apply the silencing molecule redirection technique to arrive at miR-7 for an alternative treatment of Parkinson’s Disease.
Claims 4 and 56 are rejected under 35 U.S.C. 103 as being unpatentable over Zhou (Zhou, Jianping, et al. "CRISPR-Cas9 based genome editing reveals new insights into microRNA function and regulation in rice." Frontiers in Plant Science 8 (2017): 1598.) in view of Kawahara (Kawahara, Yukio, et al. "Redirection of silencing targets by adenosine-to-inosine editing of miRNAs." Science 315.5815 (2007): 1137-1140.) and Bhattacharya (Bhattacharya, Anindya, and Yan Cui. "Systematic prediction of the impacts of mutations in MicroRNA seed sequences." Journal of Integrative Bioinformatics 14.1 (2017): 20170001.) as applied to claim 4, and in further view of Shalem (Shalem, Ophir, Neville E. Sanjana, and Feng Zhang. "High-throughput functional genomics using CRISPR–Cas9." Nature Reviews Genetics 16.5 (2015): 299-311. (Year: 2015).).
Regarding claim 56, the teachings of Zhou, Kawahara, and Bhattacharya as applied above to claim 4 are incorporated here.
Zhou does not teach wherein said endonuclease comprises a catalytically inactive endonuclease.
However, Shalem teaches catalytically inactive Cas9 (dCas9) fusions used to synthetically repress (CRISPRi) or activate (CRISPRa) expression, showing, advances using Cas9 for genome-scale screens, including arrayed and pooled screens, knockout approaches that inactivate genomic loci and strategies that modulate transcriptional activity (Figure 1d, pg 301 col 2 para 2).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have applied Shalem’s method of employing catalytically inactive Cas9 method to specifically alter miRNA in Zhou’s method of editing miRNA. The skilled artisan would have had a reasonable expectation of success at applying base editing to modify and redirect miRNA towards alternative targets given the obviousness rational applied above for claim 4 and because Shalem teaches effective use of inactive cas9 as an advantage in modulation of transcriptional activity. The skilled artisan would be motivated to employ Shalem’s inactive Cas9 for enhanced transcriptional control.
Double Patenting - Maintained
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 conflicting claims 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); 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 nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) 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 www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 4, 7, 12, 14, 16, 19, 23, 25, 28, 30, 34, 37, 41 and 52-58 are provisionally rejected on the grounds of nonstatutory double patenting as being unpatentable over Claims 1-2, 6, 8-10, 12, 18-19, 23, 31, 37-38 and 49, of co-pending Application No. 17439344 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because the co-pending claims anticipate the instant claims.
Regarding instant claim 4, the co-pending claims teach:
1. (Previously Presented) A method of producing a long dsRNA molecule in a plant cell that is capable of silencing a pest gene, the method comprising:(a) selecting in a genome of a plant a nucleic acid sequence encoding a silencing molecule having a plant gene as a target, said silencing molecule being capable of recruiting RNA-dependent RNA Polymerase (RdRp); and(b) modifying a nucleic acid sequence of the plant gene so as to impart a silencing specificity towards the pest gene, such that a transcript of said modified plant gene comprising said silencing specificity forms base complementation with said silencing molecule capable of recruiting said RdRp to produce the long dsRNA molecule capable of silencing the pest gene, thereby producing the long dsRNA molecule in the plant cell that is capable of silencing the pest gene.
2. (Previously Presented) The method of claim 1, wherein said silencing molecule capable of recruiting said RdRp comprises 21-24 nucleotides, and/or wherein said silencing molecule is selected from the group consisting of: trans-acting siRNA (tasiRNA), phased small interfering RNA (phasiRNA), microRNA (miRNA), small interfering RNA (siRNA), short hairpin RNA (shRNA), Piwi-interacting RNA (piRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), ribosomal RNA (rRNA), small nucleolar RNA (snoRNA), extracellular RNA (exRNA), repeat-derived RNA, autonomous transposable RNA, and non-autonomous transposable RNA, optionally wherein:(i) said miRNA comprises a 22 nucleotides mature small RNA, and/or (ii) said miRNA is selected from the group consisting of: miR-156a, miR-156c, miR-162a, miR-162b, miR-167d, miR-169b, miR-173, miR-393a, miR-393b, miR-402, miR-403, miR-447a, miR-447b, miR-447c, miR-472, miR-771, miR-777, miR-828, miR-830, miR-831, miR-831, miR- 833a, miR-833a, miR-840, miR-845b, miR-848, miR-850, miR-853, miR-855, miR-856, miR-864, miR-2933a, miR-2933b, miR-2936, miR-4221, miR-5024, miR-5629, miR-5648, miR-5996, miR- 8166, miR-8167a, miR-8167b, miR-8167c, miR-8167d, miR-8167e, miR-8167f, miR-8177, and miR-8182.
6. (Previously Presented) The method of claim 1, wherein said plant gene is a non-protein coding gene, and/or wherein the plant gene encodes a molecule having an intrinsic silencing activity towards a native plant gene.
8. (Previously Presented) The method of claim 1, wherein said modifying of step (b) comprises introducing into the plant cell a DNA editing agent which redirects a silencing specificity of said plant gene towards said pest gene, said pest gene and a native plant gene being distinct.
9. (Previously Presented) The method of claim 6, wherein said plant gene having said intrinsic silencing activity is selected from the group consisting of trans-acting siRNA (tasiRNA), phased small interfering RNA (phasiRNA), microRNA (miRNA), small interfering RNA (siRNA), short hairpin RNA (shRNA), Piwi-interacting RNA (piRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), ribosomal RNA (rRNA), small nucleolar RNA (snoRNA), extracellular RNA (exRNA), autonomous transposable RNA, and non-autonomous transposable RNA.
10. (Previously Presented) The method of claim 6, wherein said plant gene having said intrinsic silencing activity encodes for a phased secondary siRNA-producing molecule, optionally wherein:(i) modifying said plant gene comprises modifying at least one secondary silencing RNA molecule formed by processing of said phased secondary siRNA-producing molecule; or (ii) modifying said plant gene comprises modifying all the secondary silencing RNA molecules formed by processing of said phased secondary siRNA-producing molecule; or wherein said plant gene having said intrinsic silencing activity is a trans-acting-siRNA- producing (TAS) molecule.
12. (Previously Presented) The method of claim 1, wherein:(i) said silencing specificity of said plant gene is determined by measuring a transcript level of said pest gene, and/or(ii) said silencing specificity of said plant gene is determined phenotypically, optionally by determination of pest resistance of said plant; and/or (iii) said silencing specificity of said plant gene is determined genotypically, optionally wherein a plant phenotype is determined prior to a plant genotype, or wherein a plant genotype is determined prior to a plant phenotype.
18. (Previously Presented) A method of producing a long dsRNA molecule in a plant cell that is capable of silencing a pest gene, the method comprising:(a) selecting a nucleic acid sequence of a plant gene exhibiting a predetermined sequence homology to a nucleic acid sequence of the pest gene; and(b) modifying a plant endogenous nucleic acid sequence encoding an RNA molecule so as to impart silencing specificity towards said plant gene, such that small RNA molecules capable of recruiting RNA-dependent RNA Polymerase (RdRp) processed from said RNA molecule form base complementation with a transcript of said plant gene to produce the long dsRNA molecule capable of silencing the pest gene, thereby producing the long dsRNA molecule in the plant cell that is capable of silencing the pest gene.
19. (Previously Presented) The method of claim 18, wherein:(i) said predetermined sequence homology comprises 75-100 % identity; and/or (ii) said small RNA molecules capable of recruiting said RdRp comprise 21-24 nucleotides; and/or (iii) said small RNA molecules capable of recruiting said RdRp are selected from the group consisting of microRNA (miRNA), small interfering RNA (siRNA), short hairpin RNA (shRNA), Piwi-interacting RNA (piRNA), trans-acting siRNA (tasiRNA), phased small interfering RNA (phasiRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), ribosomal RNA (rRNA), small nucleolar RNA (snoRNA), extracellular RNA (exRNA), repeat-derived RNA, autonomous transposable RNA, and non-autonomous transposable RNA; and/or (iv) said RNA molecule has an intrinsic silencing activity towards a native plant gene.
23. (Previously Presented) The method of claim 18, wherein:(i) said modifying of step (b) comprises introducing into the plant cell a DNA editing agent which redirects a silencing specificity of said RNA molecule towards said plant gene, said plant gene and a native plant gene being distinct; and/or (ii) said plant gene exhibiting said predetermined sequence homology to said nucleic acid sequence of the pest gene does not encode a silencing molecule; and/or (iii) said silencing specificity of said RNA molecule is determined by measuring a transcript level of said plant gene or said pest gene; and/or (iv) said silencing specificity of the RNA molecule is determined phenotypically, optionally by determination of pest resistance of said plant; and/or (v) said silencing specificity of the RNA molecule is determined genotypically, optionally wherein a plant phenotype is determined prior to a plant genotype or wherein a plant genotype is determined prior to a plant phenotype.
31. (Previously Presented) The method of claim 8, wherein:(i) said DNA editing agent comprises at least one sgRNA, optionally wherein said DNA editing agent comprises an endonuclease, optionally wherein said DNA editing agent is of a DNA editing system selected from the group consisting of a meganuclease, a zinc finger nuclease (ZFN), a transcription-activator like effector nuclease (TALEN), a CRISPR-endonuclease, a dCRISPR- endonuclease, and a homing endonuclease, optionally wherein said endonuclease comprises Cas9;or (ii) said DNA editing agent does not comprise an endonuclease; and/or said DNA editing agent is applied to the cell as DNA, RNA or RNP.
37. (Previously Presented) The method of claim 1, wherein said plant cell is a protoplast.
38. (Previously Presented) The method of claim 1, wherein:(i) said dsRNA molecule is processable by cellular RNAi processing machinery; and/or (ii) said dsRNA molecule is processed into secondary small RNAs; and/or (iii) said dsRNA and/or said secondary small RNAs comprise a silencing specificity towards a pest gene.
41. (Previously Presented) A method of generating a pest tolerant or resistant plant, the method comprising producing a long dsRNA molecule in a plant cell capable of silencing a pest gene according to claim 1, optionally wherein said pest is an invertebrate, and/or wherein said pest is selected from the group consisting of a virus, an ant, a termite, a bee, a wasp, a caterpillar, a cricket, a locust, a beetle, a snail, a slug, a nematode, a bug, a fly, a fruit fly, a whitefly, a mosquito, a grasshopper, a planthopper, an earwig, an aphid, a scale, a thrip, a spider, a mite, a psyllid, a tick, a moth, a worm, a scorpion, and a fungus.
49. (Previously Presented) A method of producing a pest tolerant or resistant plant, the method comprising:(a) breeding the plant generated in claim 41; and(b) selecting for progeny plants that express the long dsRNA molecule capable of suppressing the pest gene, and which do not comprise said DNA editing agent, thereby producing said pest tolerant or resistant plant.
This is a provisional rejection because the copending claims have not yet been patented.
Response to Arguments
Applicant acknowledges the terminal disclaimer filed 8/18/25.
Regarding the 112b rejection of claim 4, Applicants argue (Remarks pg 9) that one of skill in the art would understand the term "distinct" in view of the normal meaning of "distinct" being "non-identical", i.e. the target RNA and the second target RNA are not the same. Applicant’s arguments have been thoroughly reviewed and found unpersuasive. Examiner maintains it is unclear what is meant by distinct and how the required distinctness may be determined. Given the broad language of claim 4, there is no specificity in what this second RNA should be or how it is “distinct” from the first target RNA.
Regarding the 35 USC §103 rejection of claim 4, Applicants argue (Remarks pg 10) that the Examiner has not provided sufficient reasoning as to why one of skill in the art would have arrived at any of the pending claims with a reasonable expectation of success based on the disclosure of Zhou in view of Kawahara, and Bhattacharya and that the Examiner has not established a prima facie case of obviousness. Applicants argue (Remarks pg 10) that the present invention utilizes DNA editing agents to redirect endogenous RNA silencing molecules to silence a new target RNA of interest and that this platform is highly flexible and effective and achieves targeted silencing with minimal genetic changes in such a way that is fundamentally different from the methods disclosed in Zhou. Applicants argue that “Zhou is focused on knocking out miRNAs and does not even attempt to silence a new target RNA. Therefore, Zhou would not have led the skilled person to develop the claimed method.” Applicant’s arguments have been thoroughly reviewed and found unpersuasive for the following reasons:
Applicants arguments are related to the individual teachings of each reference. 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). The 35 USC §103 rejection of record utilizes the combination of teachings of Zhou in view of Kawahara, and Bhattacharya. The deficiencies of Zhou are cured by the supporting references thoroughly described in the 35 USC §103 rejection detailed above.
Kawahara teaches that the editing of miRNA molecules from an A to I changes the target selection of miRNAs, therefore redirecting the miRNA to a second target (see throughout and figures), thus establishing that it was known as of 2007 that editing miRNAs in specific positions with specific bases would change the target site for the miRNA (pg 1139 col 3 para 1). Kawahara teaches the edited miR-376 RNA silences specifically a different set of genes (Fig. 3).
Bhattacharya teaches the systematic prediction of the impacts of mutations in miRNA sequences including changed target sites (pg 1 para 3 and Fig. 4). It would have been predictable that specific mutations could redirect targeting to anticipated alternative sites because Bhattacharya teaches the systematic prediction of the impacts of mutations in miRNA sequences including changed target sites. Thus, the skilled artisan would be motivated to employ the controlled redirection of anticipated new targets by known base editing techniques as an improved means of genetic control. Examiner maintains the combination of reference teachings read on the instant invention given the broad claim language of claim 4. Given the applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (for example, that the present invention uses precise edits to redirect miRNA specificity at the nucleic acid level) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Conclusion
No claims are allowable.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 extension fee 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 date of this final action.
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/JOHN CHARLES MCKILLOP/Examiner, Art Unit 1637
/EKATERINA POLIAKOVA-GEORGANTAS/Primary Examiner, Art Unit 1637