DETAILED ACTION
Response to Amendment
Applicant’s response to the office action filed on January 30, 2026 has been entered. The claims pending in this application are claims 21-42 and 44 wherein claims 24-38 have been withdrawn due to the restriction requirements mailed on September 13, 2024. The objection and rejections not reiterated from the previous office action are hereby withdrawn in view of applicant’s amendment filed on January 30, 2026. Claims 21-23, 39-42, and 44 will be examined.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 23 is rejected under 35 U.S.C. 102(a)(2) as being anticipated by Doudna et al., (US 2016/0289659 A1, priority date: December 12, 2013).
The rejection is different from the rejection under 35 U.S.C. 102(a)(2) mailed on November 5, 2025 because different parts of above priority art are used in this rejection.
Regrading claim 23, Doudna et al., teach a reaction mixture for selective depletion of a target nucleic acid from a sample, the reaction mixture comprising: (a) a sample comprising a target nucleic acid, wherein the target nucleic acid is a DNA sequence that can be transcribed into an RNA such as a rRNA; (b) at least one nuclease component (ie., Cas9 polypeptide), and (c) at least one guide RNA that has the capacity to complex with and guide the nuclease component to the target nucleic acid, wherein the nuclease component, the guide RNA, and the target nucleic acid have the capacity to form a complex where the guide RNA specifically hybridizes with the target nucleic acid (see paragraphs [0012], [0019], [0056], and [0068]). Although Doudna et al., do not disclose that the target nucleic acid is a reverse transcription product made by a ribosomal RNA (rRNA), the DNA sequence that can be transcribed into a rRNA taught by Doudna et al., and the reverse transcription product made by a rRNA recited in claim 23 can be an identical product and claim 23 can be read as a product-by process claim. It is well established that even though product-by process claims are limited by and defined by the process, the determination of the patentability of the product is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process. In re Thorpe, 227 USPQ 964, 966 (Fed. Cir. 1985).
Therefore, Doudna et al., teach all limitations recited in claim 23.
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.
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 21, 22, 39-41, and 44 are rejected under 35 U.S.C. 103 as being unpatentable over Carstens (US 2015/0211058 A1, filed on January 29, 2014) in view of Doudna et al., and 1988 Stratagene catalog (page 39).
Regarding claims 21, 22, 39, and 40, Carstens teaches a kit for selectively depleting at least one target nucleic acid from a sample, the kit comprising: (a) at least one RNA-guided nuclease component (eg., Cas 9 mutants); (b) at least one guide RNA that has the capacity to guide the RNA-guided nuclease component to the target nucleic acid, wherein the RNA-guided nuclease component, the guide RNA, and the target nucleic acid have the capacity to form a complex where the guide RNA specifically hybridizes with the target nucleic acid, wherein said guide RNA comprises nucleotide sequence capable of hybridizing to said target nucleic acid, said target nucleic acid selected from: a ribosomal RNA (rRNA) or reverse transcription product thereof, a mitochondrial RNA (mtRNA) or reverse transcription product thereof, a transfer RNA (tRNA) or reverse transcription product thereof, a highly expressed clinically irrelevant mRNA or transcription reverse product thereof, a globulin mRNA or a transcription reverse product thereof, an actin mRNA or a reverse transcription product thereof, and a globin mRNA or a reverse transcription product thereof; and (c) a polymerase as recited in claims 21 wherein the at least one guide RNA is 2 or more than 2 guide RNAs as recited in claim 22, the 2 or more than 2 guide RNAs are 2 or more than 2 different guide RNAs as recited in claim 39, and the polymerase is a DNA polymerase (ie., Bst DNA polymerase) as recited in claim 40 (see paragraphs [0011], [0012], [0041] to [0044], [0050]), [0061], [0085], and [0094], and claim 20).
Regarding claim 41, since Bst 2.0® has significantly higher reverse transcriptase activity (see “Does Bst DNA polymerase have reverse transcriptase activity?” from New England Biolabs), Carstens teaches that the DNA polymerase (ie., Bst DNA polymerase, see paragraph [0061]) is a reverse transcriptase as recited in clam 41.
Carstens does not disclose that kit comprising a primer wherein the RNA-guided nuclease
component cleaves the target nucleic acid by generating double-stranded breaks as recited in claim 21 wherein the primer is a reverse primer as recited in claim 44. However, Carstens teaches that the kits of the invention comprise at least one RNA-guided nuclease component (eg., Cas 9 mutants), and any number of additional reagents or substances that are useful for practicing a method of the invention such as amplification reaction reagents (including buffers), and teaches that a double-stranded nucleic acid template containing a target of interest can be obtained as a product of the RT reaction from the ssRNA template for subsequent analysis by the isothermal amplification which can be done by Loop-mediated isothermal amplification (LAMP) (see claim 1 and paragraphs [0026], [0050], and [0097]) wherein LAMP requires at least one reverse primer (see page 3 of “Isothermal amplification” from New England Biolabs).
Doudna et al., teach a kit comprising a wild type Cas9 polypeptide, a variant Cas9 polypeptide that exhibits reduced nuclease activity relative to wild-type Cas9, and one or more additional reagents, where such additional reagents can be selected from: a buffer; a wash buffer; a control reagent; a control expression vector or RNA polynucleotide; a reagent for in vitro production of a Cas9 polypeptide from DNA; and the like (see paragraphs [0493] to [0495]).
1988 Stratagene catalog teaches a motivation to combine reagents into kit format (page 39).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have made the kits recited in claims 21 and 44 by adding a reverse primer and a wild type Cas9 polypeptide that cleaves a target nucleic acid such as a DNA by generating double-stranded breaks to the kit taught by Carstens in view of the prior arts of Carstens, Doudna et al., and 1988 Stratagene catalog. One having ordinary skill in the art would have been motivated to do so because Carstens teaches that the kits of the invention can comprise any number of additional reagents or substances that are useful for practicing a method of the invention such as amplification reaction reagents (including buffers) and teaches that nucleic a double-stranded acid template containing a target of interest can be obtained as a product of the RT reaction from the ssRNA template for subsequent analysis by the isothermal amplification which can be done by Loop-mediated isothermal amplification (LAMP) (see paragraphs [0026], [0050], and [0097]) wherein LAMP requires at least one reverse primer (see page 3 of “Isothermal amplification” from New England Biolabs) and the amplification reaction reagents taught by Carstens must include a reverse primer, Doudna et al., teach a kit comprising a wild type Cas9 polypeptide, a variant Cas9 polypeptide that exhibits reduced nuclease activity relative to wild-type Cas9, and one or more additional reagents, where such additional reagents can be selected from: a buffer; a wash buffer; a control reagent; a control expression vector or RNA polynucleotide; a reagent for in vitro production of a Cas9 polypeptide from DNA; and the like (see paragraphs [0493] to [0495]), and the Stratagene catalog teaches a motivation for combining reagents of use in an assay into a kit, “[E]ach kit provides two services: 1) a variety of different reagents have been assembled and pre-mixed specifically for a defined set of experiments. 2) The other service provided in a kit is quality control” (page 39, column 1). One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to make the kits recited in claims 21 and 44 by adding a reverse primer and a wild type Cas9 polypeptide that cleaves a target nucleic acid such as a DNA by generating double-stranded breaks to the kit taught by Carstens in view of the prior art of Carstens, Doudna et al., and 1988 Stratagene catalog in order to provide a positive control (ie., a wild type Cas9 polypeptide) for the at least one RNA-guided nuclease component (eg., Cas 9 mutants) in the kit taught by Carstens and subsequent analyze a product of the RT reaction from the ssRNA template by the isothermal amplification.
Claim 42 is rejected under 35 U.S.C. 103 as being unpatentable over Carstens in view of Doudna et al., and 1988 Stratagene as applied to claims 21, 22, 39-41, and 44 above, and further in view of Aviel-Ronen et al., (BMC Genomics, 7, 312, 2006).
The teachings of Carstens, Doudna et al., and 1988 Stratagene have been summarized previously, supra.
Carstens, Doudna et al., and 1988 Stratagene do not disclose that the reverse transcriptase (ie., Bst DNA polymerase) is capable of template switching as recited in claim 42.
Since Aviel-Ronen et al., teach that Bst DNA polymerase can switch templates (see page 7, left column, second paragraph), Aviel-Ronen et al., disclose that the reverse transcriptase (ie., Bst DNA polymerase) is capable of template switching as recited in clam 42.
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have made the kit recited in claim 42 using a reverse transcriptase (ie., Bst DNA polymerase) which is capable of template switching in view of the prior arts of Carstens, Doudna et al., 1988 Stratagene catalog, and Aviel-Ronen et al.. One having ordinary skill in the art would have been motivated to do so because Aviel-Ronen et al., have successfully shown that Bst DNA polymerase can switch templates (see page 7, left column, second paragraph). One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to make the kit recited in claims 42 using the reverse transcriptase (ie., Bst DNA polymerase) recited in claim 41 in view of the prior arts of Carstens, Doudna et al., 1988 Stratagene catalog, and Aviel-Ronen et al..
Claims 21, 22, 39-42, and 44 are rejected under 35 U.S.C. 103 as being unpatentable over Jakimo et al., (US 2014/0349,400 A1, priority date: March 15, 2013) in view of 1988 Stratagene catalog (page 39).
Regarding claims 21, 22, 39-42, and 44, since Jakimo et al., teach that a method for programmable self-modification of a cellular genome, the method comprising the steps of: for a self-reconfiguring cassette, the cassette comprising operons or DNA sequences that code for a guide RNA, a reverse transcriptase, donor RNA, and a cleavage enzyme from the CRISPR system; introducing the cassette to a biological cell; transcribing the guide RNA from the cassette; associating the transcribed guide RNA with the CRISPR enzyme; intercalating a region of complimentary sequence within an integration site of the cellular genome; cutting, using the CRISPR enzyme, upstream of a PAM site located within the integration site; transcribing the donor RNA from the cassette; translating the donor RNA to double-stranded DNA using the reverse transcriptase; and recombining the double-stranded DNA via homologous recombination at the cut site of the integration site, thereby producing a genomic modification within the integration site of the cellular genome and guide RNAs in Figure 6 can be either SEQ ID No: 4 or 5 (see paragraphs [0004], [0012], [0015], and [0037] to [0041], claim 11, and Figures 6 and 8) and teach that DNA cassette 1010 comprising an RNA polymerase promoter 1020, a first oligonucleotide sequence 1030, a terminator/reverse primer 1040, and then a second oligonucleotide sequence is incorporated into a cell and inside the cell, polymerase transcribes 1150 single stranded copies 1165 of the template, producing ssDNA 1165 by rolling circle (strand displacing) amplification (see paragraphs [0045] and [0046], and Figure 10), Jakimo et al., teach a biological cell comprising (a) at least one RNA-guided nuclease component (eg., Cas 9), wherein the RNA-guided nuclease component cleaves the target nucleic acid by generating double-stranded breaks; (b) at least one guide RNA (ie., SEQ ID Nos: 4 and 5) that has the capacity to guide the RNA-guided nuclease component to the target nucleic acid, wherein the RNA-guided nuclease component, the guide RNA, and the target nucleic acid have the capacity to form a complex where the guide RNA specifically hybridizes with the target nucleic acid, wherein said guide RNA comprises nucleotide sequence capable of hybridizing to said target nucleic acid, said target nucleic acid selected from: a ribosomal RNA (rRNA) or reverse transcription product thereof, a mitochondrial RNA (mtRNA) or reverse transcription product thereof, a transfer RNA (tRNA) or reverse transcription product thereof, a highly expressed clinically irrelevant mRNA or reverse transcription product thereof, a globulin mRNA or a reverse transcription product thereof, an actin mRNA or a reverse transcription product thereof, and a globin mRNA or a reverse transcription product thereof, and (c) a polymerase (ie., a reverse transcriptase); and a cell comprising (d) a primer as recited in claims 21 wherein the at least one guide RNA is 2 or more than 2 guide RNAs (ie., SEQ ID Nos: 4 and 5) as recited in claim 22, the 2 or more than 2 guide RNAs are 2 or more than 2 different guide RNAs as recited in claim 39, the polymerase is a DNA polymerase (ie., a reverse transcriptase) as recited in claim 40, the DNA polymerase is a reverse transcriptase as recited in claim 41, the reverse transcriptase is capable of template switching as recited in claim 42, and the primer is a reverse primer as recited in claim 44.
Jakimo et al., do not disclose a kit as recited in claims 21, 22, 39-42, and 44.
1988 Stratagene catalog teaches a motivation to combine reagents into kit format (page 39).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have made the kits recited in claims 21, 22, 39-42, and 44 by putting a biological cell comprising the at least one nuclease component (eg., Cas 9), the two different guide RNAs (ie., (ie., SEQ ID Nos: 4 and 5), and the reverse transcriptase, and a cell comprising the reverse primer taught by Jakimo et al., into a kit format in view of the prior arts of Jakimo et al., and 1988 Stratagene. One having ordinary skill in the art would have been motivated to do so because the Stratagene catalog teaches a motivation for combining reagents of use in an assay into a kit, “[E]ach kit provides two services: 1) a variety of different reagents have been assembled and pre-mixed specifically for a defined set of experiments. 2) The other service provided in a kit is quality control” (page 39, column 1).
Response to Arguments
In page 13, sixth paragraph bridging to page 15, last paragraph of applicant’s remarks, applicant argues that “[T]urning now to Jakimo, as acknowledged by the Office, Jakimo is directed to a cassette comprising ‘operons or DNA sequences which code for i) a guide RNA to recognize and cleave at an integration site, ii) the CRISPR protein Cas9, iii) reverse transcriptase, and iv) Donor RNA, which is reverse transcribed into double stranded donor DNA’ (Jakimo, paragraph [0033]). As such, Jakimo utilizes a DNA cassette comprising DNA sequences which code for various elements. As such, Jakimo fails to teach a kit comprising (a) at least one nuclease component, (b) at least one guide RNA, (c) a polymerase and (d) a primer.
Further, contrary to the Office's assertion that Jakimo's method for programmable self-modification of a cellular genome describes the components of the instantly claimed kit, a method of transcribing RNA and translating proteins in a cell is not the equivalent of a kit comprising (a) at least one RNA-guided nuclease component, (b) at least one guide RNA, (c) a polymerase and (d) a primer. Even further, based on the teachings of Jakimo, there would be no motivation to make a kit of proteins and RNA since the purpose of Jakimo is to use a DNA cassette to directly produce oligonucleotides in the cell. See, e.g., paragraph [0044] of Jakimo” and “[A]ccordingly, as highlighted above, Jakimo underscores the need for using a DNA cassette to directly produce oligonucleotides in a cell to self-reconfigure the genome of the cell, rather than introducing components to a cell separately (e.g., as exogenous nucleic acids). Therefore, Jakimo fails to teach or suggest a kit comprising (a) at least one RNA-guided nuclease component, (b) at least one guide RNA, (c) a polymerase and (d) a primer. As Stratagene is merely cited for the element of a kit, Stratagene fails to make up for the deficiencies in Jakimo. As such, Claim 21 and all claims that depend therefrom are not obvious over Jakimo in view of Stratagene”.
The above arguments have been fully considered but they are not persuasive toward the withdrawal of the rejection. Since Jakimo et al., teach that a method for programmable self-modification of a cellular genome, the method comprising the steps of: for a self-reconfiguring cassette, the cassette comprising operons or DNA sequences that code for a guide RNA, a reverse transcriptase, donor RNA, and a cleavage enzyme from the CRISPR system; introducing the cassette to a biological cell; transcribing the guide RNA from the cassette; associating the transcribed guide RNA with the CRISPR enzyme; intercalating a region of complimentary sequence within an integration site of the cellular genome; cutting, using the CRISPR enzyme, upstream of a PAM site located within the integration site; transcribing the donor RNA from the cassette; translating the donor RNA to double-stranded DNA using the reverse transcriptase; and recombining the double-stranded DNA via homologous recombination at the cut site of the integration site, thereby producing a genomic modification within the integration site of the cellular genome and guide RNAs in Figure 6 can be either SEQ ID No: 4 or 5 (see paragraphs [0004], [0012], [0015], and [0037] to [0041], claim 11, and Figures 6 and 8) and teach that DNA cassette 1010 comprising an RNA polymerase promoter 1020, a first oligonucleotide sequence 1030, a terminator/reverse primer 1040, and then a second oligonucleotide sequence is incorporated into a cell and inside the cell, polymerase transcribes 1150 single stranded copies 1165 of the template, producing ssDNA 1165 by rolling circle (strand displacing) amplification (see paragraphs [0045] and [0046], and Figure 10), Jakimo et al., teach a biological cell comprising (a) at least one RNA-guided nuclease component (eg., Cas 9), wherein the RNA-guided nuclease component cleaves the target nucleic acid by generating double-stranded breaks; (b) at least one guide RNA (ie., SEQ ID Nos: 4 and 5) that has the capacity to guide the RNA-guided nuclease component to the target nucleic acid, wherein the RNA-guided nuclease component, the guide RNA, and the target nucleic acid have the capacity to form a complex where the guide RNA specifically hybridizes with the target nucleic acid, wherein said guide RNA comprises nucleotide sequence capable of hybridizing to said target nucleic acid, said target nucleic acid selected from: a ribosomal RNA (rRNA) or reverse transcription product thereof, a mitochondrial RNA (mtRNA) or reverse transcription product thereof, a transfer RNA (tRNA) or reverse transcription product thereof, a highly expressed clinically irrelevant mRNA or reverse transcription product thereof, a globulin mRNA or a reverse transcription product thereof, an actin mRNA or a reverse transcription product thereof, and a globin mRNA or a reverse transcription product thereof, and (c) a polymerase (ie., a reverse transcriptase); and a cell comprising (d) a primer as recited in claims 21 and 1988 Stratagene is used for provide a motivation for combining the reagents taught by Jakimo et al., into a kit because “[E]ach kit provides two services: 1) a variety of different reagents have been assembled and pre-mixed specifically for a defined set of experiments. 2) The other service provided in a kit is quality control” (page 39, column 1).
Conclusion
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 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.
No claim is allowed.
Papers related to this application may be submitted to Group 1600 by facsimile transmission. Papers should be faxed to Group 1600 via the PTO Fax Center. The faxing of such papers must conform with the notices published in the Official Gazette, 1096 OG 30 (November 15, 1988), 1156 OG 61 (November 16, 1993), and 1157 OG 94 (December 28, 1993)(See 37 CAR § 1.6(d)). The CM Fax Center number is (571)273-8300.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Frank Lu, Ph.D., whose telephone number is (571)272-0746. The examiner can normally be reached on Monday-Friday from 9 A.M. to 5 P.M.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Dr. Anne Gussow, Ph.D., can be reached on (571)272-6047.
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/FRANK W LU/Primary Examiner, Art Unit 1683
March 12, 2026