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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 07/07/2025 has been entered.
Application Status
Amendments received 07/07/2025 are hereby acknowledged. Claims 1-35, 43, and 49 are cancelled. Claim 36is currently amended. Claims 55 and 56 are newly added. Claims 36-42, 44-48 and 50-56 are currently pending and under examination in this office action.
Any objection or rejection not reiterated herein has been overcome by Applicant’s amendments and is therefore withdrawn.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 07/07/2025 was filed after the mailing date of the office action on 02/04/2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
The following new rejections under 35 U.S.C. § 103 are necessitated by Applicant’s amendments filed 07/07/2025.
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 non-obviousness.
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 36-41, 46-48 and 51 are rejected under 35 U.S.C. §103 as being unpatentable over Haynie (Haynie, S.L. et al. Applied Biochemistry and Biotechnology, Vol. 23 (1990), pp: 205-220; previously cited), Guo-Qing (Guo-Qing, Y. et al. Process Biochemistry, Vol. 41 (2006), pp: 1276-1281; previously cited) and Motomura (Motomura, K. et al. Applied and Environmental Microbiology, Vol. 80, No. 8 (2014), pp: 2602-2608).
Regarding claim 36, Haynie teaches a Method for producing nucleoside triphosphates (NTPs) comprising:
Incubating (i) cellular RNA (in the form of yeast extract RNA) and (ii) a ribonuclease (RNAse P1) to produce a mixture comprising 5’ nucleoside monophosphates (NMPs) (see page 214 “[P]reparation of AMP, GMP, CMP, and UMP from Ribonucleic Acid” section) (claim 36 step (a));
Incubating the 5’ NMPs with at least one kinase (i.e. pyruvate kinase or acetate kinase ; enzymes from yeast) and a phosphate compound in the form of phospho-enol pyruvate or diammonium acetyl phosphate, to produce NTPs (see pages 209, 211 and 218 ) (claim 36, step (c )).
Regarding (b) Heating the mixture produced in (a) to eliminate the ribonuclease,
Haynie teaches that nuclease P1 is naturally deactivated by a first order process at pH 5.6 and 65 ⁰C and loses its thermal stability at 65 ⁰C, dictating the use of large quantities of the enzyme ( see page 206 and 207). Haynie teaches that the deactivation is thermal and accelerated with the use of thiol reducing agents and EDTA (see page 207, line 2).
Regarding claim 37, Haynie teaches a method with a step incubating the NMPs with at least one NMP kinase (guanylate kinase and adenylate kinase, see Table 2, page 214, “[P]reparation of AMP, GMP, CMP, and UMP from Ribonucleic Acid” section).
Regarding claim 38, Haynie teaches cellular RNA from yeast. The “yeast RNA” is understood to be total RNA, which includes ribosomal, messenger and transfer RNA (see page 206, “[I]ntroduction” section, line 7, and page 213, “[A]ssay of Nuclease P1” section) , lines 1 and 7).
Regarding claim 39, Haynie teaches a ribonuclease that is Nuclease P1 (see page 213, “[A]ssay of Nuclease P1” section).
Regarding claim 40, Haynie teaches spontaneously occurring deactivation of Nuclease P1 using temperature, at pH 5.6 and 65⁰ C (see page 207, lines 1-3), but not as a method step. Haynie also teaches that under pH from 6 to 9, the pure enzyme can be deactivated completely (see Figure 3).
Regarding claims 41 and 51, Haynie teaches an AMP kinase (adenylate kinase) and a GMP kinase (Guanylate kinase (guanylate kinase and adenylate kinase, see Table 2, page 214). Haynie also teaches a NDP kinase (acetate kinase ; see figure 1, page 207 and Table 1, page 209).
Regarding claim 46, Haynie teaches the use of enzyme preparation from cells (yeast) that produce NMP and NDP kinase (see page 206, “[I]ntroduction” section, line 28).
Regarding claim 47, Haynie teaches the use of multiple methods to eliminate the activity of one or more native enzymes from the cell (yeast), i.e., autolysis, addition of DTT and gel chromatography (see page 207, ‘[P]urification of Nucleoside Monophosphokinases from Brewer’s yeast” section, and Table 2), ethanol fractionation (see page 206, “[E]thanol Fractionation” section) and the use of β-Mercaptoethanol during separation with Sephadex beads ( see page 216, line 4).
Regarding claim 48, Haynie teaches that the brewer’s yeast contains one or more oxidoreductases and oxidase (NADH-oxidase activity; see page 215, “[E]thanol Fractionation” section, line 4).
Haynie does not teach the express use of heat to eliminate the ribonuclease on purpose as a method step, but rather Haynie teaches that a combination of heat and reducing agents does this inactivation naturally (claim 36 step (b)). Haynie does not teach the use of a polyphosphate kinase and polyphosphates (claim 36 step (c )). Haynie does not teach a PPK from a PPK1 family enzyme or a PPK2 family enzyme (claim 43). Haynie does not teach the use of an enzyme preparation or cells that produce specifically PPKs (claim 46).
However, regarding claims 36 (b) and 40, Guo-Qing teaches the use of temperature to eliminate contaminants as a method step for producing a purified nuclease P1 enzyme (page 1277, see section 2.5). Guo-Qing also teaches the use of temperature (from 50 to 95 ⁰C) to deactivate nuclease P1 (see page 1278, section 2.13, and figure 4). Guo-Qing teaches deactivation of nuclease P1 expressly as a method step to test thermostability from 50 ⁰C to 95 ⁰C (section 2.13 “Determination of temperature optimum and thermal stability”, and see figure 4).
Regarding claim 36 (c ), Motomura teaches the use of Polyphosphate kinase 2 (PPK2) to synthesize ATP from AMP (see abstract). Motomura teaches that a single enzyme from Class III PPK2 can catalyze both nucleoside monophosphate phosphorylation and nucleoside diphosphate phosphorylation and make ATP (see title and abstract).
Motomura specifically teaches a new subfamily of PPK2, i.e. class III PPK2 enzymes with one domain PPK2 catalyzing both nucleoside monophosphate and nucleoside diphosphate phosphorylation (see Introduction section, page 2602, right column).
Motomura also teaches the use of a polyphosphate (poly(P)) in the form of polyP65 or polyP700 as phospho-donors (see page 2603, left column, “Enzyme assay” paragraph ).
Motomura specifically teaches enzymes cloned from Deinococcus geothermalis ( see page 2603, left column, “Comparison of polyP-driven ATP production between class I, II, and III PPK2s” section; and see Figure 1).
Motomura also teaches that the class III PPK2 enzyme from Deinococcus geothermalis is active to synthesize ATP at an optimal temperature of 70⁰C (see Figure 6).
Regarding claim 46, Motomura teaches a preparation comprising the Deinococcus geothermalis PPK2 enzyme isolated from E.coli after recombinant expression ( see page 2603, right column, first paragraph).
It would have been obvious to one with ordinary skills in the art to have modified the method taught by Haynie and introduced a heating step as taught by Guo-Qing to deactivate the ribonuclease in the mixture. Haynie teaches that the enzyme could be deactivated at 65 ⁰C under specific pH conditions. In the event of the nuclease P1 becoming a contaminant to the following reaction steps, Guo_Qing teaches that the nuclease P1 can be deactivated at temperatures ranging from 80 to 95 ⁰C.
Modifying Haynie with the method step based on the teachings of Guo-Qing would be an application of a known technique to a known method and the basic technique of denaturing the nuclease enzyme in a method step would have yielded no more than the predictable outcome which one of ordinary skill would have expected to achieve with this common tool of the trade and was therefore an obvious expedient. The Court in KSR Int'l v. Teleflex lnc. (127 S. Ct. 1727, 1740, 2007) held that "[t]he gap between the prior art and [the claimed subject matter] is simply not so great as to render the system nonobvious to one reasonably skilled in the art."
One with ordinary skills in the art before the effective filing date could have performed this modification and arrived at the claimed invention with a reasonable expectation of success.
It would have been obvious to one with ordinary skills in the art, before the effective filing date to have substituted the pyruvate kinase taught by Haynie, in the method taught by Haynie modified by Guo-Qing, with a polyphosphate kinase and use polyphosphates as phospho-donors as taught by Motomura (see Figure 6). It would have been obvious to use an enzyme preparation containing a class III PPK2 from Deinococcus geothermalis (D. geothermalis) or a cell extract containing the recombinant PPK2 from D. geothermalis to perform this substitution, as taught by Motomura.
Motomura provides motivation for using the PPK2 enzyme from Deinococcus geothermalis, as it is an enzyme from the class III PPK2, with the ability to enable synthesis of ATP from AMP by a single enzyme (see abstract and page 2602, Introduction section, right column), therefore simplifying/reducing the numbers of steps in the method, using a Nuclease P1 denaturation temperature that also is optimum for the thermostable D. Geothermalis enzyme. One with ordinary skills in the art could have performed this substitution with a reasonable expectation of success, and arrived at the claimed invention.
Claims 42 and 50 are rejected under 35 U.S.C. § 103 as being unpatentable over Haynie (Haynie, S.L. et al. Applied Biochemistry and Biotechnology, Vol. 23 (1990), pp: 205-220), Guo-Qing (Guo-Qing, Y. et al. Process Biochemistry, Vol. 41 (2006), pp: 1276-1281) and Motomura ( Motomura, K. et al. Applied and Environmental Microbiology, Vol. 80, No. 8 (2014), pp: 2602-2608), as applied to claims 36 and 37 above, and in further view of Pdf-1 describing Guanylate kinase of Thermotoga maritima sequence in UniProtKB. Accession No. Q9X215 (2001); referred here as Pdf-1 (previously cited).
Regarding claims 42 and 50, the combinations of Haynie, Guo-Qing and Motomura renders claims 36 and 37 obvious, as required. However, the combination does not teach elements of claims 42, i.e. “at least one NMP kinase is AMP kinase from Thermus thermophilus, CMP kinase from Thermus thermophilus, UMP kinase from Pyrococcus furiosus, and/or GMP kinase from Thermotoga maritima”.
It would have been obvious to one with ordinary skills in the art, before the effective filing date, to have modified the method taught by Haynie modified by Guo-Qing and Motomura, and substituted one NMP kinase with a thermostable GMP kinase from Thermotoga maritima as taught by seq-pdf-1.
Modifying Haynie/Guo-Qing and Motomura with a thermostable GMP kinase would be an application of a known tool to a known method and the basic technique of applying heat for denaturing the nuclease enzyme in a method step, while sparing other enzymes, i.e. GMP kinase, that are thermostable, would have yielded no more than the predictable outcome which one of ordinary skill would have expected to achieve with this common tool of the art and was therefore an obvious expedient. The Court in KSR Int'l v. Teleflex lnc. (127 S. Ct. 1727, 1740, 2007) held that "[t]he gap between the prior art and [the claimed subject matter] is simply not so great as to render the system nonobvious to one reasonably skilled in the art."
One with ordinary skills in the art before the effective filing date could have performed this modification and arrived at the claimed invention with a reasonable expectation of success.
.
Claims 52 and 53 are rejected under 35 U.S.C. § 103 as being unpatentable over Haynie (Haynie, S.L. et al. Applied Biochemistry and Biotechnology, Vol. 23 (1990), pp: 205-220), Guo-Qing (Guo-Qing, Y. et al. Process Biochemistry, Vol. 41 (2006), pp: 1276-1281) and Motomura ( Motomura, K. et al. Applied and Environmental Microbiology, Vol. 80, No. 8 (2014), pp: 2602-2608), as applied to claims 36, 37 and 51 above, and in further view of Pdf-2 describing a Nucleoside diphosphate kinase from Aquifex aeolicus, (UniprotKB/Swiss-Prot Accession No. O67528.1 (2006); referred here as Pdf-2; previously cited).
Regarding claims 52 and 53, the combination of Haynie, Guo-Qing and Motomura renders the elements of claims 36, 37 and 51 obvious as required. However, the combination does not teach elements of claims 52 and 53, i.e. a NDP kinase from Aquifex aeolicus and having an amino acid sequence set forth in SEQ ID NO: 16.
Pdf-2 teaches further teaches a NDP kinase that is an ADP kinase from Aquifex aoelicus with an Uniprot Accession No. O67528, that is 100% identical to instant application SEQ ID NO: 16.
It would have been obvious to one with ordinary skills in the art, before the effective filing date, to have modified the method taught by Haynie modified by Guo-Qing and Motomura, and substituted one NDP kinase with a thermostable NDP kinase from Aquifex aeolicus as taught by pdf-2.
Modifying Haynie/Guo-Qing and Motomura with a thermostable NDP kinase would be an application of a known tool to a known method and the basic technique of applying heat for denaturing the nuclease enzyme in a method step, while sparing other enzymes, i.e. NDP kinase, that are thermostable, would have yielded no more than the predictable outcome which one of ordinary skill would have expected to achieve with this common tool of the art and was therefore an obvious expedient. The Court in KSR Int'l v. Teleflex lnc. (127 S. Ct. 1727, 1740, 2007) held that "[t]he gap between the prior art and [the claimed subject matter] is simply not so great as to render the system nonobvious to one reasonably skilled in the art."
One with ordinary skills in the art before the effective filing date could have performed this modification and arrived at the claimed invention with a reasonable expectation of success.
Claims 44 and 54 are rejected under 35 U.S.C. § 103 as being unpatentable over Haynie (Haynie, S.L. et al. Applied Biochemistry and Biotechnology, Vol. 23 (1990), pp: 205-220), Guo-Qing (Guo-Qing, Y. et al. Process Biochemistry, Vol. 41 (2006), pp: 1276-1281) and Motomura ( Motomura, K. et al. Applied and Environmental Microbiology, Vol. 80, No. 8 (2014), pp: 2602-2608), as applied to claims 36 above, and in further view of pdf-3 describing a Polyphosphate kinase 2 family protein from Deinococcus geothermalis (NCBI reference sequence: WP_011531362.1 (2008)), referred to as pdf-3 (previously cited).
Regarding claims 44 and 54, the combination of Haynie, Guo-Qing and Motomura does render obvious elements of claim 36 as required. However, the combination does not teach a PPK2 family enzyme from Deinococcus geothermalis, having an amino acid sequence as set forth in SEQ ID NO: 1.
Pdf-3 teaches a PPK2 family enzyme with an amino acid sequence that is 100% identical to SEQ ID NO:1 in instant application.
It would have been obvious to one with ordinary skills in the art, before the effective filing date, to have modified the method taught by Haynie modified by Guo-Qing and Motomura, and used the equivalent polyphosphate kinase from D. geothermalis with a thermostable polyphosphate kinase 2 family protein with an amino acid sequence as set forth in SEQ ID NO: 1 as taught by Pdf-3.
Modifying Haynie/Guo-Qing and Motomura with a thermostable PPK2 would be an application of a known tool to a known method and the basic technique of applying heat for denaturing the nuclease enzyme in a method step, while sparing other enzymes, i.e. PPK2, that are thermostable, would have yielded no more than the predictable outcome which one of ordinary skill would have expected to achieve with this common tool of the art and was therefore an obvious expedient. The Court in KSR Int'l v. Teleflex lnc. (127 S. Ct. 1727, 1740, 2007) held that "[t]he gap between the prior art and [the claimed subject matter] is simply not so great as to render the system nonobvious to one reasonably skilled in the art."
One with ordinary skills in the art before the effective filing date could have performed this modification and arrived at the claimed invention with a reasonable expectation of success.
Claim 45 is rejected under 35 U.S.C. § 103 as being unpatentable over Haynie (Haynie, S.L. et al. Applied Biochemistry and Biotechnology, Vol. 23 (1990), pp: 205-220), Guo-Qing (Guo-Qing, Y. et al. Process Biochemistry, Vol. 41 (2006), pp: 1276-1281) and Motomura ( Motomura, K. et al. Applied and Environmental Microbiology, Vol. 80, No. 8 (2014), pp: 2602-2608), as applied to claims 36 above, and in further view of Sato (Sato, M. et al. Journal of Bioscience and Bioengineering, Vol. 103 (2007), pp: 179-184; previously cited).
Regarding claim 45, the combination of Haynie, Guo-Qing and Motomura renders the elements of claim 36 obvious. However, the combination does not teach polyphosphates that are specifically tetrapolyphosphates, pentapolyphosphates and hexametaphosphate, as substrate. Motomura teaches polyP65 (a linear chain of about 65 Pi residues; see page 2603, left column, “Enzyme assay” section).
However, Sato teaches hexametaphosphate, tetrapolyphosphate in a method of generating ATPs (see page 180, left column, “[M]aterials and methods” section, first ¶). These polyphosphates are high-energy phosphate donors efficient when fed to reactions with thermostable kinases such as the polyphosphate kinase from Thermosynechococcus elongatus (see title).
It would be obvious to one with ordinary skills, before the effective filing date, to have substituted the polyphosphate taught in Haynie modified by Guo-Qing and Motomura, with a hexametaphosphate or tetrapolyphosphate as substrate as taught by Sato. One with ordinary skills in the art, motivated in optimizing the making of NTPs using high-energy and efficient phosphate donors to enhance efficiency, could have performed this substitution with a reasonable expectation of success, and arrived at the claimed invention.
Claims 55 and 56 are rejected under 35 U.S.C. § 103 as being unpatentable over Haynie (Haynie, S.L. et al. Applied Biochemistry and Biotechnology, Vol. 23 (1990), pp: 205-220), Guo-Qing (Guo-Qing, Y. et al. Process Biochemistry, Vol. 41 (2006), pp: 1276-1281) and Motomura ( Motomura, K. et al. Applied and Environmental Microbiology, Vol. 80, No. 8 (2014), pp: 2602-2608), as applied to claims 36 above, and in further view of Pati (Pati, A. et al. “Complete genome sequence of Oceanithermus profundus type strain (506)”. Standards in Genomic Sciences, Vol. 4 (2011), pp: 210-220) and Lucas (Lucas, S. et al. “Oceanithermus profundus DSM 14977 chromosome, complete genome”. NCBI RefSeq: NC_014761.1. Direct submission Feb, 04, 2011) .
The rejection of claim 36 is described above. The combination of Haynie, Guo-Qing and Motomura renders obvious elements of claim 36. However, the elements of dependent claims 55 and 56 are not rendered obvious by the combination of references.
Regarding claims 55 and 56, Motomura teaches in Figure 1 multiple branches of the phylogenetic tree describing Class III PPK2 enzymes family in which Deinococcus species’ PPK2 enzymes belong. Motomura teaches that there are 39 1-domain PPK2 enzymes without naming the microorganisms they belong to.
However, Pati teaches that Oceanithermus profundus belongs to the family Thermaceae (see page 210, “Introduction” section, left column). Deinococcus also belong to the same family, according to Pati (see Figure 1 and Table 1).
Pati teaches the complete genome sequence of Oceanithermus profundus. And Lucas submitted the sequences directly into NCBI database under accession number NC_014761. Among the genes identified by Lucas and Pati, a sequence corresponding to a PPK2 gene is identified and presents with 100% sequence similarity to instant application’s SEQ ID NO: 8. See alignment below:
EMBL; CP002361; ADR37448.1; -; Genomic_DNA.
DR RefSeq; WP_013458618.1; NC_014761.1.
DR AlphaFoldDB; E4U536; -.
DR STRING; 670487.Ocepr_1997; -.
DR KEGG; opr:Ocepr_1997; -.
DR eggNOG; COG2326; Bacteria.
DR HOGENOM; CLU_048699_1_0_0; -.
DR OrthoDB; 9775224at2; -.
DR Proteomes; UP000008722; Chromosome.
DR GO; GO:0008976; F:polyphosphate kinase activity; IEA:InterPro.
DR GO; GO:0006797; P:polyphosphate metabolic process; IEA:InterPro.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR016898; Polyphosphate_phosphotransfera.
DR InterPro; IPR022300; PPK2-rel_1.
DR InterPro; IPR022488; PPK2-related.
DR NCBIfam; TIGR03709; PPK2_rel_1; 1.
DR PANTHER; PTHR34383:SF3; POLYPHOSPHATE:AMP PHOSPHOTRANSFERASE; 1.
DR PANTHER; PTHR34383; POLYPHOSPHATE:AMP PHOSPHOTRANSFERASE-RELATED; 1.
DR Pfam; PF03976; PPK2; 1.
DR PIRSF; PIRSF028756; PPK2_prd; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
PE 4: Predicted;
KW Kinase {ECO:0000256|ARBA:ARBA00022777};
KW Reference proteome {ECO:0000313|Proteomes:UP000008722};
KW Transferase {ECO:0000313|EMBL:ADR37448.1}.
FT DOMAIN 31..255
FT /note="Polyphosphate kinase-2-related"
FT /evidence="ECO:0000259|Pfam:PF03976"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 269 AA; 31026 MW; E547BB7F5DA1EB10 CRC64;
Query Match 100.0%; Score 1420; Length 269;
Best Local Similarity 100.0%;
Matches 269; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MDVSRYRVPPGSGFDPEAWPTREDDDFAGGKKEAKKELARLAVRLGELQARLYAEGRQAL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MDVSRYRVPPGSGFDPEAWPTREDDDFAGGKKEAKKELARLAVRLGELQARLYAEGRQAL 60
Qy 61 LIVLQGMDTAGKDGTIRHVFRAVNPQGVRVTSFKKPTALELAHDYLWRVHRHAPARGEIG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 LIVLQGMDTAGKDGTIRHVFRAVNPQGVRVTSFKKPTALELAHDYLWRVHRHAPARGEIG 120
Qy 121 IFNRSHYEDVLVVRVHELVPPEVWGRRYDHINAFERLLADEGTRIVKFFLHISKDEQKRR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 IFNRSHYEDVLVVRVHELVPPEVWGRRYDHINAFERLLADEGTRIVKFFLHISKDEQKRR 180
Qy 181 LEARLENPRKHWKFNPADLSERARWGDYAAAYAEALSRTSSDRAPWYAVPADRKWQRNRI 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LEARLENPRKHWKFNPADLSERARWGDYAAAYAEALSRTSSDRAPWYAVPADRKWQRNRI 240
Qy 241 VAQVLVDALEAMDPRFPRVDFDPASVRVE 269
|||||||||||||||||||||||||||||
Db 241 VAQVLVDALEAMDPRFPRVDFDPASVRVE 269
Pati also teaches that Oceanithermus profundus (O. profundus) was isolated from a deep-sea hot vent (see Table 1) and can be cultivated at temperature ranging from 40 ⁰C to 68 ⁰C (see page 211, right column, lines 7-19). Therefore, one can deduct that O. profundus’s PPK2 enzyme is thermostable, as the PPK2 enzyme from D. geothermalis.
It would have been obvious to one with ordinary skills in the art, before the effective filing date, to have substituted the PPK2 enzyme from Deinococcus geothermalis taught by Motomura, to a PPK2 enzyme from Oceanithermus profundus taught by Lucas and Pati, since both enzymes are expressed by phylogenetically closely related organisms in the Thermaceae family. Both enzymes present the same advantage of being a 1-domain PPK2 that are functional at high temperatures. One motivated in using an equivalent thermostable PPK2 enzyme at high temperature in an ATP forming reaction, would performed this modification with a reasonable expectation of success and arrived at the claimed invention.
Response to Arguments
Applicant's arguments filed 07/07/2025 have been fully considered but they are not persuasive.
On pages 6 and 7 of “Remarks” filed 07/07/2025, regarding the Claims rejection
under 35 U.S.C. § 103, Applicant states “Applicant reiterates that explanation and the arguments why Haynie does not render the pending claim obvious in view of either Guo-Qing or Shiba, either separately or together”. Applicant is referring to a response to the Final Action dated 02/04/2025, in page 5 of Remarks filed 06/04/2025.
In response, Examiner would like to refer to the response to arguments within the Advisory Action dated 06/20/2025, regarding the combination of Haynie and Guo-Qing. Examiner would like to remind that the current rejection includes Motomura instead of Shiba. Motomura provides motivation for a convenient “combined one-pot reaction” since one can use a single enzyme to phosphorylate nucleoside monophosphate and nucleoside diphosphate and synthesize ATP using a class III PPK2.
In summary, reiterating the response to arguments in the Advisory action: Haynie acknowledges the effect of temperature on the nuclease P1 (see pages 206 and 207, line 2). Guo-Qing teaches a method step of heating the nuclease for denaturation studies on page 1278, in section 2.13 “Determination of temperature optimum and thermal stability”. Guo-Qing’s teachings complements Haynie’s, rendering a heating step for denaturing/inactivating nuclease P1 in a method of making ATP obvious and necessary. Claim 36 as amended, including PPK2 from D. geothermalis or O. profundus that are thermostable but with optimum temperature around 60 to 70 ⁰C for catalytic activity, it becomes necessary to deactivate an enzyme that is still active at 70 to 75 ⁰C, as taught by Guo-Qing in Figure 4.
Applicant argues on page 8 of Remarks, that “Nevertheless, the Examiner did not provide an explanation as to why a person skilled in the art would have combined the PPK as allegedly disclosed in Shiba and Pdf-3 with any method as disclosed in Haynie. Instead, the Examiner pointed to the present application as disclosing that polyphosphate kinase such as PPK1 and PPK2 would function in the claimed method. However, pointing to the present application as motivation for the combination of references is impermissible hindsight.”
In response to applicant's arguments, Examiner would like to point out that the current rejection does not include Shiba. The current rejection is relying upon Motomura who is providing motivation for the use of PPK2 from a class III enzymes family. One with ordinary skills in the art would have been motivated in simplifying the method by using in the reaction an enzyme capable of catalyzing both nucleoside monophosphate and nucleoside diphosphate phosphorylation and synthesizing ATP in one step.
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
Double Patenting
The non-statutory double patenting rejections from office action filed previously on 02/04/2025 are maintained and modified to address Applicant’s current amendments.
The non-statutory 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 non-statutory 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 non-statutory 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 non-statutory 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 36-42, 44-48 and 50-54 are rejected on the ground of non-statutory double patenting as being unpatentable over claims 1-28, of U.S. Patent No. 10,858,385_B2.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding claim 36, claim 1 of Patent ‘385 recites “ (a) incubating cellular RNA”, “(b) eliminating the ribonuclease” and “(c) incubating the 5’NMPs with polyphosphate kinase, polyphosphate”. Claim 3 of Patent’ 385 recites 5’NMPs include 5’AMP, 5’GMP, 5’ CMP, and/or 5’UMP”. Claims 4 and 15 of Patent’ 385 recite “the ribonuclease is eliminated via temperature”. Claim 20 of Patent’ 385 recites a Class III PPK2 enzyme from Deinococcus geothermalis.
Regarding claim 37, claim 11(c) of Patent ‘385 recites “ at least one NMP kinase, at least one NDP kinase (…)”.
Regarding claim 38, claim 1 of Patent ‘385 recites “a ribosomal RNA, messenger RNA, and/or transfer RNA”.
Regarding claim 39, claims 2, 13 and 29 of Patent ‘385 recite “ the ribonuclease is Nuclease P1 or RNase R”.
Regarding claim 40, claim 15 of Patent ‘385 recites “the ribonuclease is eliminated via temperature, pH, salt, detergent, alcohol, chemical inhibitors, separation, precipitation, filtration, capture, and/or chromatography”.
Regarding claims 41 and 50, claim 16 of Patent ‘385 recites “ at least one NMP kinase is an AMP Kinase, a CMP kinase, a UMP kinase, or a GMP kinase”.
Regarding claim 42 and 50, claims 17 and 26 of Patent ‘385 also teach an AMP Kinase from Thermus thermophilus (SEQ ID NO: 12), a CMP kinase from Thermus thermophilus (SEQ ID NO: 13), an UMP kinase from Pyrococcus furiosus (SEQ ID NO: 14) and a GMP kinase from Thermotoga maritima (SEQ ID NO: 15).
Regarding claims 51-53, claims 18 and 27 of Patent ‘385 recite “at least one NDP kinase is from Aquifex aeolicus (SEQ ID NO: 16)”.
Regarding claim 54, claims 5 and 30 of Patent ‘385 recite “the PPK is a PPK1 family enzyme or a PPK2 family enzyme”.
Regarding claims 44 and 54, claims 6 and 25 of Patent ‘385 recite “ a class III PPK2 enzyme from Deinococcus geothermalis (SEQ ID NO: 1)”.
Regarding claim 45, claim 7 of Patent ‘385 recites “tetrapolyphosphates, pentapolyphosphates, and hexametaphosphates”.
Regarding claim 46, claim 8 of Patent ‘385 recites the use of one or more enzymes from cell lysate, reciting “an enzyme preparation or cell lysate obtained from cell that produce the PPK…and/or the RNA polymerase”
Regarding claim 47, claims 9 and 23 of Patent ‘385 recite the “activity of native enzyme in the cell lysate or enzyme preparation has been eliminated via genetic modification, enzyme secretion from a cell, protease targeting, temperature, pH, salt, detergent, alcohol, chemical inhibitors, separation, precipitation, filtration, capture, and/or chromatography”.
Regarding claims 47 and 48 reciting “one or more native enzymes”, claims 10 and 24 of Patent ‘385 recite “wherein the native enzymes are selected from the group consisting of phosphatases, nucleases, proteases, deaminases, oxidoreductases, and hydrolases”.
Claims 36-42, 44-46, 51, 52 and 54-56 are rejected on the ground of non-statutory double patenting as being unpatentable over claims 1-16, 19, 20, 21, 24, and 29 of U.S. Patent No. 10,954,541_B2. Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding claim 36, claim 1 of Patent ‘541 recites “ (a) incubating a cell lysate mixture that comprises cellular RNA”, “(b) heating the cell lysate mixture… that depolymerize RNA” and “(c) producing nucleoside triphosphates”. Claim 1 also recites producing the NMPs with thermostable kinase”. Claim 2 of Patent’ ‘541 recites “cellular RNA”, “ a ribonuclease, a kinase”. Claim 3 of Patent ‘541 recites that “ the enzyme that depolymerizes RNA is a ribonuclease”. Claim 16 of Patent ‘541 recites “ at least one ribonuclease, at least one thermostable NMP kinase, at least one thermostable NDP kinase, and at least one polyphosphate kinase”. Claim 12 of Patent’ 541 recites “thermostable class III PPK2 enzymes” selected from Deinococcus geothermalis or Oceanithermus profundus among other enzymes.
Regarding claim 37, claim 5 of Patent ‘541 recites “ a group consisting of thermostable NMP kinase, thermostable NDP kinase (…)”.
Regarding claim 38, claim 1 of Patent ‘541 recites “a cellular RNA”.
Regarding claim 39, claim 4 of Patent ‘541 recites “the ribonuclease is selected from the group consisting of Nuclease P1, RNase R, (…)”.
Regarding claim 40, claims 1(b) and 29 of Patent ‘541 recite “heating to inactivate” the ribonuclease via “temperature”.
Regarding claim 41, claim 5 of Patent ‘541 recites “ thermostable NMP kinase selected from the group consisting of thermostable UMP kinases, thermostable CMP kinases, thermostable GMP kinases and thermostable AMP Kinases”.
Regarding claim 42, claim 7 of Patent ‘541 also teaches an AMP Kinase from Thermus thermophilus, a CMP kinase from Thermus thermophilus, a UMP kinase from Pyrococcus furiosus and a GMP kinase from Thermotoga maritima.
Regarding claims 51 and 52, claim 8 of Patent ‘541 teaches a NDP kinase from Aquifex aeolicus.
Regarding claims 44 and 54, claims 12-15 of Patent ‘541 teach a class III PPK2 enzyme from Deinococcus geothermalis (SEQ ID NO: 8-18). SEQ ID NO: 1 of instant application is 100% identical to SEQ ID NO: 10 of Patent ‘541.
Regarding claim 45, claim 21 of Patent ‘541 recites “the polyphosphate is hexametaphosphate”.
Regarding claim 46, claim 16 of Patent ‘541 teaches the use of an enzyme preparation or cell lysate obtained from cell that produce the PPK, the NMP kinase and the NDP kinase.
Regarding claims 55 and 56, claims 12 of Patent’ 541 teaches class III PPK2 enzymes from Deinococcus geothermalis and Oceanithermus profundus. Claim 13 of patent’ 541 teaches SEQ ID NO: 8-18. Patent’ 541 column 21, Table 6 teaches that SEQ ID NO: 15 is a class III PPK2 enzyme from Oceanithermus profundus. Alignment of Patent’ 541 SEQ ID NO: 15 and instant Application SEQ ID NO: 8 is shown below:
RESULT 1
US-15-480-617-15
(NOTE: this sequence has 1 duplicate in the database searched.
See complete list at the end of this report)
Sequence 15, US/15480617
Patent No. 10954541
GENERAL INFORMATION
APPLICANT: GreenLight Biosciences, Inc.
TITLE OF INVENTION: CELL-FREE PRODUCTION OF RIBONUCLEIC ACID
FILE REFERENCE: G0830.70020US02
CURRENT APPLICATION NUMBER: US/15/480,617
CURRENT FILING DATE: 2017-04-06
PRIOR APPLICATION NUMBER: US 62/452,550
PRIOR FILING DATE: 2017-01-31
PRIOR APPLICATION NUMBER: US 62/319,220
PRIOR FILING DATE: 2016-04-06
NUMBER OF SEQ ID NOS: 28
SEQ ID NO 15
LENGTH: 269
TYPE: PRT
ORGANISM: Oceanithermus profundus
Query Match 100.0%; Score 1420; Length 269;
Best Local Similarity 100.0%;
Matches 269; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MDVSRYRVPPGSGFDPEAWPTREDDDFAGGKKEAKKELARLAVRLGELQARLYAEGRQAL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MDVSRYRVPPGSGFDPEAWPTREDDDFAGGKKEAKKELARLAVRLGELQARLYAEGRQAL 60
Qy 61 LIVLQGMDTAGKDGTIRHVFRAVNPQGVRVTSFKKPTALELAHDYLWRVHRHAPARGEIG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 LIVLQGMDTAGKDGTIRHVFRAVNPQGVRVTSFKKPTALELAHDYLWRVHRHAPARGEIG 120
Qy 121 IFNRSHYEDVLVVRVHELVPPEVWGRRYDHINAFERLLADEGTRIVKFFLHISKDEQKRR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 IFNRSHYEDVLVVRVHELVPPEVWGRRYDHINAFERLLADEGTRIVKFFLHISKDEQKRR 180
Qy 181 LEARLENPRKHWKFNPADLSERARWGDYAAAYAEALSRTSSDRAPWYAVPADRKWQRNRI 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LEARLENPRKHWKFNPADLSERARWGDYAAAYAEALSRTSSDRAPWYAVPADRKWQRNRI 240
Qy 241 VAQVLVDALEAMDPRFPRVDFDPASVRVE 269
|||||||||||||||||||||||||||||
Db 241 VAQVLVDALEAMDPRFPRVDFDPASVRVE 269
SEQ ID NO: 15 of Patent’ 541 is a 100% match for SEQ ID NO: 8 of instant Application.
Claims 36-42, 44, 51, 52 and 54-56 provisionally rejected on the ground of non-statutory double patenting as being unpatentable over claims 1, 4, 6, 8, 9, 11,12, 91-94 and 105 of co-pending Application No. 17/202,029.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding claim 36, claims 1 of co-pending application ‘029 recites “ (a) a cellular RNA”, and “a ribonuclease”, “(b) inactivating the ribonuclease” with temperature and mixture comprises “(c) NMPs”. Claim 1 of co-pending app. ‘029 recites “at least one kinase”. Claim 4 of co-pending app. ‘029 teaches that RNA is mRNA, tRNA or rRNA.
Claim 8 of co-pending app. ‘029 also teaches a NMP kinase, a NDP kinase, and polyphosphate kinase.
Claim 105 of co-pending app. ‘029 also teaches “a method comprising: (a) incubating a mixture that comprises RNA, Nuclease P1 to produce a mixture that comprises NMPs; (b) heating the mixture (…) inactivates Nuclease P1; and (c) incubating NMPs from step (b) in the presence of polyphosphate, (….), RNA, (…), CMP kinase, a GMP kinase, a UMP kinase, an NDP kinase and a polyphosphate kinase (…)”.
Claims 92 and 93 of co-pending app.’029 teaches class III PPK2 enzymes that can be from Deinococcus geothermalis or Oceanithermus profundus.
Regarding claim 37, claim 8 of co-pending app. ‘029 teaches “NMP kinase, NDP kinase (…)”.
Regarding claim 38, claim 4 of co-pending app.‘029 recites “a ribosomal RNA, messenger RNA, and/or transfer RNA”.
Regarding claim 39, claim 6 of co-pending app. ‘029 recite “ the ribonuclease is selected from the group consisting of (…), Nuclease P1, (…), RNase R, (…)”.
Regarding claim 40, claim 1 of co-pending app. ‘029 teaches that the ribonuclease is inactivated via temperature.
Regarding claim 41, claim 9 of co-pending app. ‘029 teaches that the NMP kinase is selected from the group consisting of UMP kinase, GMP kinase and AMP kinase”.
Regarding claim 42, claim 91 of co-pending app. ‘029 also teach an AMP Kinase from Thermus thermophilus, a CMP kinase from Thermus thermophilus, a UMP kinase from Pyrococcus furiosus and a GMP kinase from Thermotoga maritima.
Regarding claims 51 and 52, claim 11 of co-pending app. ‘029 recite “NDP kinase is an Aquifex aeolicus nucleoside diphosphate kinase”.
Regarding claims 44 and 54, claims 92-94 of co-pending app. ‘029 recite “ a class III PPK2 enzyme” and claim 93 teaches a class III PPK2 enzyme from Deinococcus geothermalis. Claim 94 teaches SEQ ID NO: 10 that is identical to instant application’s SEQ ID NO: 1.
Regarding claims 55 and 56, claim 94 of co-pending app. ‘029 teaches class III PPK2 enzymes with SEQ ID NO: 8-18. Co-pending app. ‘029 teaches that SEQ ID NO: 15 corresponds to a Class III PPK2 enzyme from Oceanithermus profundus (see page 26, [0089], Table 6). A sequence alignment between SEQ ID NO: 15 and instant apps’ SEQ ID NO: 8 shows 100% similarity. See below:
Title: US-17-094-718-8
Perfect score: 1420
Sequence: 1 MDVSRYRVPPGSGFDPEAWP..........EAMDPRFPRVDFDPASVRVE 269
Scoring table: BLOSUM62
Gapop 10.0 , Gapext 0.5
Searched: 1 seqs, 269 residues
Total number of hits satisfying chosen parameters: 1
Minimum DB seq length: 0
Maximum DB seq length: inf
Post-processing: Minimum Match 0%
Maximum Match 100%
Listing first 1 summaries
Database : US-17-202-029-15.pep:*
SUMMARIES
%
Result Query
No. Score Match Length DB ID Description
----------------------------------------------------------------------------
1 1420 100.0 269 1 US-17-202-029-15 CELL-FREE PRODUCTI
ALIGNMENTS
RESULT 1
US-17-202-029-15
Query Match 100.0%; Score 1420; DB 1; Length 269;
Best Local Similarity 100.0%;
Matches 269; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MDVSRYRVPPGSGFDPEAWPTREDDDFAGGKKEAKKELARLAVRLGELQARLYAEGRQAL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MDVSRYRVPPGSGFDPEAWPTREDDDFAGGKKEAKKELARLAVRLGELQARLYAEGRQAL 60
Qy 61 LIVLQGMDTAGKDGTIRHVFRAVNPQGVRVTSFKKPTALELAHDYLWRVHRHAPARGEIG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 LIVLQGMDTAGKDGTIRHVFRAVNPQGVRVTSFKKPTALELAHDYLWRVHRHAPARGEIG 120
Qy 121 IFNRSHYEDVLVVRVHELVPPEVWGRRYDHINAFERLLADEGTRIVKFFLHISKDEQKRR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 IFNRSHYEDVLVVRVHELVPPEVWGRRYDHINAFERLLADEGTRIVKFFLHISKDEQKRR 180
Qy 181 LEARLENPRKHWKFNPADLSERARWGDYAAAYAEALSRTSSDRAPWYAVPADRKWQRNRI 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LEARLENPRKHWKFNPADLSERARWGDYAAAYAEALSRTSSDRAPWYAVPADRKWQRNRI 240
Qy 241 VAQVLVDALEAMDPRFPRVDFDPASVRVE 269
|||||||||||||||||||||||||||||
Db 241 VAQVLVDALEAMDPRFPRVDFDPASVRVE 269
This is a provisional non-statutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ALEXANDRA G DACE DENITO whose telephone number is (703)756-4752. The examiner can normally be reached Monday-Friday, 8:30-5:00EST.
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/A.D./Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636