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 .
Election/Restrictions
Applicant’s election without traverse of Group I (claims 1-19) and withdrawal of claims 20, 21, and 26 (drawn to unelected invention(s)) in the reply filed on March 17, 2026 is acknowledged.
Claims 1-19 are currently pending.
Priority
Applicant’s claim to the benefit of provisional US application 63/411,949 is acknowledged, and the effective filing date of the instant application is considered to be 9/30/22.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 9 and 12 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 9 is rejected over the recitation of “the first inorganic polyphosphate,” as lacking antecedent basis in the claims on which it depends (claims 1 and 8). If the applicant intended that “the first inorganic polyphosphate” be the “first inorganic polyphosphate” of claim 7, which is less than 50 phosphate residues, the claims must be amended to reflect that relationship.
Claim 12 is rejected over the recitation of “PPK3 family,” because there is no one art-specific definition. In some publications, PPK3 is a homolog of PPK2, and a member of class III of family PPK2 (not its own class). Recently, a family of enzymes was discovered in archaea which has been dubbed the PPK3 family (Hofmann et al. J Biol Chem. 2026 Feb 12;302(4):111283. doi: 10.1016/j.jbc.2026.111283), but this discovery was published well after the filing date of the instant application. The specification does not provide a definition of PPK3. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-19 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims have been evaluated using the 2019 Revised Patent Subject Matter Eligibility Guidance (see Federal Register Vol. 84, No. 4, Monday, January 7, 2019).
Step 1: The claims are directed to the statutory category of a composition.
Step 2A, prong one: Evaluate Whether the Claim Recites a Judicial Exception
Claim 1 and those claims that depend from claim 1 are drawn to a composition comprising inorganic polyphosphate and polyphosphate kinase. Claim 13 restricts the polyphosphate kinase to one having an amino acid sequence as defined in SEQ ID NO: 1 to 3, or a functional variant or fragment thereof. The markedly different characteristics analysis has been used to determine if the nature-based products – the polyphosphate(s) and polyphosphate kinase – are an exception. The nature-based products have been compared to their natural counterparts.
The claims broadly encompass naturally occurring polyphosphate and polyphosphate kinases, and there is no indication that the polyphosphate(s) and polyphosphate kinase of the instant claims have any characteristics that are different from the naturally occurring polyphosphates and polyphosphate kinases. SEQ ID NO: 1 represents a sequence which is structurally identical to a naturally occurring polypeptide from Thermus thermophilus, as evidenced by UniProt Database entry: Q72JY1_THET2 (from Henne et al. The genome sequence of the extreme thermophile Thermus thermophilus. Nat. Biotechnol. 22:547-553(2004)). SEQ ID NO: 2 represents a sequence which is structurally identical to a naturally occurring polypeptide from Meiothermus ruber, as evidenced by UniProt Database entry: PK23_MEIRD (from Chin et al. A new subfamily of polyphosphate kinase 2 (class III PPK2) catalyzes both nucleoside monophosphate phosphorylation and nucleoside diphosphate phosphorylation. Appl. Environ. Microbiol. 80:2602-2608(2014)). SEQ ID NO: 3 represents a sequence which is structurally identical to a naturally occurring polypeptide from Escherichia coli, as evidenced by UniProt Database entry A0A0E0XW60_ECO1C (from Ahmed et al. Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including Shiga toxin encoding phage stx2. PLoS ONE 7:E48228-E48228(2012)). There is no difference in function, structure, or other properties from the recited polyphosphate and polyphosphate kinase and those found in nature.
It is noted that the polyphosphate and polyphosphate kinase are recited as being in a “composition.” There is no indication that being present in the composition changes the function, structure, or other properties of the natural products. Claims 18 and 19 are directed toward the composition in the form of a “kit.” The polyphosphate and polyphosphate kinase do not interact with other elements of the composition in the “kit.” There is no indication that the polyphosphate kinase and polyphosphate being present in a “kit” changes the structure, function, or other properties of the natural products. Because the claimed polyphosphate kinase and polyphosphate do not have markedly different characteristics, they are a product of nature exception.
Claims 2-4 and 19 are drawn to the polyphosphate and polyphosphate kinase and additional elements which are themselves judicial exceptions: a recombinase, a single-stranded binding protein, a polymerase, NTPs, and/or magnesium ions. The markedly different characteristics analysis has been used to determine if these nature-based products are an exception. The nature-based products have been compared to their natural counterparts. There is no indication that the enzyme(s), NTPs, or magnesium ions have any characteristics that are different from the naturally occurring enzymes, NTPs, or magnesium ions. There is no difference in function, structure, or other properties. It is noted that the enzymes and NTPs are recited as being in an “amplification composition.” There is no indication that the enzymes and NTPs being present in the composition changes the function, structure, or other properties of the enzymes, NTPs, and magnesium. It is noted that the magnesium ions are present in a “kit.” There is no indication that the magnesium ions being present in the kit changes the function, structure, or other properties of the enzymes and NTPs. Because the claimed enzymes and NTPs do not have markedly different characteristics, they are a product of nature exception.
Step 2A, prong two: Evaluate Whether the Judicial Exception Is Integrated Into a Practical Application
Claims 1-14 do not recite any elements in addition to the natural products and therefore do not integrate the judicial exceptions into a practical application. Claims 15-16 recite the additional element of a buffer. Because some form of reagent is always present in a buffer, this element does not practically integrate the judicial exceptions and is the equivalent of adding the words “apply it” to the judicial exception. Claims 18 and 19 recite the additional element of a “kit.” A “kit” broadly encompasses a collection of reagents. It fails to meaningfully limit the claims and is the equivalent of adding the words “apply it” to the judicial exception.
Step 2B: Evaluate Whether the Claim Provides and Inventive Concept
Claims 1-14 do not recite any elements in addition to the natural products and therefore do not provide an inventive step. Claims 15-16 recite the additional element of a buffer. At the time the invention was made, buffering enzymes (with NTPs and magnesium) was well-known, routine, and conventional in the art. Claims 18-19 recite the additional element of a “kit.” At the time the invention was made, kits were well-established, routine, and conventional. Thus, the claims as whole do not amount to significantly more than each “product of nature” by itself, and the claims do not qualify as eligible subject matter.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of pre-AIA 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) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
Claims 1, 5, 7, 10, 12, 17, 18 and 19 are rejected under 35 U.S.C. 102(a)(1) as anticipated by Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580).
As noted in MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Accordingly, the claim language of “the amplification composition” merely sets forth the intended use of the claimed composition, but does not limit the scope of the claims.
Regarding claim 1, Tavanti teaches compositions comprising inorganic polyphosphate and a polyphosphate kinase (Introduction).
Regarding claim 5, Tavanti teaches concentrations of inorganic phosphate of 200 and 500 mM (pg. 3576, col. 1, 2nd full par.). The values of 200 mM and 500 mM fall within the range about 0.01 mM to about 1000 mM and therefore the limitation is considered to be met.
Regarding claim 7, Tavanti teaches an inorganic polyphosphate with less than 50 phosphate residues (pg. 3568, col. 1). In addition, pyrophosphate is an inorganic polyphosphate that would be present in the amplification composition as a byproduct of amplification (pyrophosphate has two phosphate groups).
Regarding claims 10 and 12, Tavanti teaches the use of thermophilic polyphosphate kinases and polyphosphate kinases (pg. 3570, col. 2: “ATP Regeneration…”) and polyphosphate kinases from the PPK1 and PPK2 families (pg. 3566, col. 2).
Regarding claim 17, Tavanti teaches the composition of claim 1. Although Tavanti does not explicitly teach that the composition is a clustering or sequencing-by-synthesis or resynthesis composition, those limitations are intended uses of the composition. As compositions are analyzed with respect to their structure, these intended uses do not limit the scope of the claims. Therefore, the claim is considered to have been anticipated.
Regarding claims 18 and 19, Tavanti teaches metal cofactor compositions which comprise magnesium ions (pg. 3568, col. 1, last par.). As the term “kit” broadly encompasses a collection of reagents, the limitation of “kit” is considered to have been met.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 2-4, 15, and 16 are rejected under 35 U.S.C. 103 as unpatentable over Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580), as applied to claim 1 above, and in view of Piepenburg et al. (published July 2006; Piepenburg et al. PLoS Biol. 2006 Jul;4(7):e204).
Tavanti teaches the limitations of claim 1, as discussed above.
Regarding claims 2-4, Tavanti does not teach an amplification composition which comprises a recombinase, a single-stranded binding protein, a polymerase, and/or dNTPs. Regarding claims 15 and 16, Tavanti does not teach any particular buffer or pH.
Regarding claims 2-4, Piepenburg teaches an amplification composition which comprises a recombinase, a single-stranded binding protein, a polymerase, and dNTPs (pg. 1118 – “RPA conditions”).
Regarding claims 15 and 16, Piepenburg teaches a buffer (pg. 1118 – “RPA conditions”), which buffers the composition at a pH of 7.9. A pH of 7.9 is within the range required by claim 16 (“buffered to a pH of about 6.0 to about 9.0”), and therefore Piepenburg’s composition is considered to meet the limitation of the claim.
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Piepenburg and Tavanti. One would have been motivated to do so in order to utilize a less expensive and unstable system of ATP-regeneration (Tavanti: pg. 3566, col. 1, par. 1) in a portable and widely accessible nucleic acid-based testing method (Piepenburg: Introduction, par. 1).
Claim 14 is rejected under 35 U.S.C. 103 as unpatentable over Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580), as applied to claim 1 above, and in view of Ge et al. (published Dec 8, 2011; Ge et al. PLoS One. 2011;6(12):e28707).
Tavanti teaches the limitations of claim 1, as discussed above.
Regarding claim 14, Tavanti does not teach that the composition does not comprise PEG.
Ge teaches that for the purposes of macromolecular crowding of enzymatic reactions, PEG is an equivalent of polymers such as Ficoll and dextran (pg. 2, col. 1, par. 1).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to substitute PEG for a different macromolecular crowding agent such as Ficoll or dextran. One would have been motivated to do so because PEG, Ficoll, and dextran were known in the art as macromolecular crowding agents. Furthermore, one may have been motivated to substitute PEG with another crowding agent because it is known to have strong inhibitory effects on processes involving enzymes like polymerases, perhaps due to its ability to cause precipitation (pg. 7, col. 1, 1st par.)
Claims 8 and 9 are rejected under 35 U.S.C. 103 as unpatentable over the combination of Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580), as applied to claim 1 above, and further in view of Zhang et al. (published December 16, 2002; Zhang et al. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16678-83).
Tavanti teaches the limitations of claim 1, as discussed above.
Regarding claims 8 and 9, Tavanti does not explicitly teach that a second inorganic polyphosphate has more than 100 residues, nor any a specific ratio of a first inorganic polyphosphate to a second inorganic phosphate. However, although Tavanti does not explicitly teach that a ratio of the first and second inorganic polyphosphates is about 90:10 to 10:90, Tavanti does teach that the relative concentration of substrate inorganic polyphosphate to product can be altered in the course of routine experimentation to achieve results such as a higher final ATP concentration (pg. 3576, col 1). Absent evidence that the ratio of first and second inorganic polyphosphates is critical, it would be obvious to try optimizing the ratio by altering the concentration of the substrate inorganic polyphosphate. One would be motivated to do so, given that the relative concentration is a known results effective variable.
Regarding claim 8, Zhang teaches a polyphosphate kinase (PPK2) which can use inorganic polyphosphate with between 15 and 700 phosphate residues (pg. 16681, col. 1).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Tavanti with the teachings of Zhang. One would have been motivated to do so in order to use a polyphosphate kinase which has a relatively wide substrate specificity (Tavanti, referring to Zhang’s enzyme: pg. 3567, col 1, 1st par.)
Claims 6, 11, and 13 are rejected under 35 U.S.C. 103 as unpatentable over Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580), as applied to claim 1 above, and further in view of Kuroda et al (published Feb 4, 2013; JP 2013021967A), as evidenced by Motomura et al. (published Apr. 2014; Motomura et al. Appl Environ Microbiol. 2014 Apr;80(8):2602-8).
The limitations of claim 1 are taught by Tavanti, as discussed above.
Regarding claim 6, 11, and 13, Tavanti does not teach any explicit concentration or optimum working temperature of polyphosphate kinase, nor explicitly that polyphosphate kinase comprises an amino acid sequence as defined in SEQ ID NO: 1 to 3 (or a functional variant or functional fragment thereof).
Kuroda teaches multiple polyphosphate kinases, including one from Meiothermus ruber which corresponds to SEQ ID NO: 2 (par. 83). Note that the sequence in Kuroda is also termed “SEQ ID NO: 2”. Kuroda teaches that the optimum working temperature for this enzyme is 70ºC (par. 91-95; Table 1 on page 83) and using the enzyme at a concentration of 8 ug/mL. Given an approximate molecular mass of 31.6 kDa (Motomura, pg. 2603: “Cloning and purification of class III PPK2”), the enzyme is at a concentration of 0.25 µM in the reaction. Kuroda also teaches a preference of 1 – 500 µg/ml (par. 41; for M. ruber, this would be around 0.03 – 16 µM). Therefore, the limitation that concentration be between 0.01µM – 1000µM is considered to be met.
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Tavanti with the teachings of Kuroda. One would have been motivated to do so because a thermophilic PPK2, such as the one from M. ruber, is heat-resistant and can more stably produce ATP from AMP (par. 16).
Claims 1-5, 7, 10, 12, and 15-19 are rejected under 35 U.S.C. 103 as unpatentable over the combination of Piepenburg et al. (published July 2006; Piepenburg et al. PLoS Biol. 2006 Jul;4(7):e204) and Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580).
Regarding claims 1-4 and 17, Piepenburg teaches an amplification composition which comprises a recombinase, a single-stranded binding protein, a polymerase, and dNTPs (pg. 1118 – “RPA conditions”). While Piepenburg does not explicitly teach that the amplification composition is a clustering composition or a sequencing-by-synthesis amplification composition or a resynthesis composition, these limitations are intended uses of the composition which do not limit the scope of the claims.
Regarding claims 15 and 16, Piepenburg teaches a buffer (pg. 1118 – “RPA conditions”), which buffers the composition at a pH of 7.9. A pH of 7.9 is within the range required by claim 16 (“buffered to a pH of about 6.0 to about 9.0”), and therefore Piepenburg’s composition is considered to meet the limitation of the claim.
Regarding claims 18 and 19, the combination of Piepenburg teaches a metal cofactor composition comprising magnesium ions (pg. 1118 – “RPA conditions”). A “kit” broadly encompasses a collection of reagents; therefore, the limitation of “kit” is considered to have been met.
Regarding claim 1 and the claims which depend on it, Piepenburg does not teach inorganic polyphosphate and polyphosphate kinase. Regarding claims 5 and 7, Piepenburg does not teach any concentration of inorganic polyphosphate or any number of phosphate residues. Regarding claims 10 and 12, Piepenburg does not teach polyphosphate kinases which are thermophilic or from any specific family.
Regarding claim 1 and the claims which depend on it, Tavanti teaches inorganic polyphosphate and polyphosphate kinase (pg. 3566, col 2, par 1).
Regarding claims 5 and 7, Tavanti teaches concentrations of inorganic polyphosphate of 200 mM and 500 mM (pg. 3576, col. 1, 2nd full par.). Here, the concentration of inorganic phosphate was varied during routine experimentation, in order to alter the yield of ATP. The values of 200 mM and 500 mM fall within the range about 0.01 mM to about 1000 mM and therefore the limitation is considered to be met. Tavanti teaches an inorganic polyphosphate with less than 50 phosphate residues (pg. 3568, col. 1).
Regarding claims 10 and 12, Tavanti teaches the use of thermophilic polyphosphate kinases and polyphosphate kinases (pg. 3570, col. 2: “ATP Regeneration…”) and polyphosphate kinases from the PPK1 and PPK2 families (pg. 3566, col. 2).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Piepenburg and Tavanti. One would have been motivated to do so in order to utilize an equivalent but alternative ATP-regeneration system which is less expensive and unstable than creatine kinase + creatine phosphate (Tavanti: pg. 3566, col 1).
Claims 8 and 9 are rejected under 35 U.S.C. 103 as unpatentable over the combination of Piepenburg et al. (published July 2006; Piepenburg et al. PLoS Biol. 2006 Jul;4(7):e204) and Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580), as applied to claim 1 above, and further in view of Zhang et al. (published December 16, 2002; Zhang et al. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16678-83).
Piepenburg and Tavanti teach the limitations of claim 1, as discussed above.
Regarding claims 8 and 9, neither Piepenburg nor Tavanti teach that a second inorganic polyphosphate has more than 100 residues, nor any a specific ratio of the first inorganic polyphosphate to the second inorganic phosphate. However, Tavanti teaches that the relative concentration of substrate inorganic polyphosphate to product can be altered in the course of routine experimentation to achieve results such as a higher final ATP concentration (pg. 3576, col 1). Absent evidence that the ratio of first and second inorganic polyphosphates is critical, it would be obvious to try optimizing the ratio by altering the concentration of the substrate inorganic polyphosphate. One would be motivated to do so, given that the relative concentration is a known results effective variable.
Regarding claim 8, Zhang teaches a polyphosphate kinase (PPK2) which can use inorganic polyphosphate with between 15 and 700 phosphate residues (pg. 16681, col. 1).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Piepenburg and Tavanti with the teachings of Zhang. One would have been motivated to do so in order to use a polyphosphate kinase which has a relatively wide substrate specificity (Tavanti, referring to Zhang’s enzyme: pg. 3567, col 1, 1st par.)
Claims 6, 11, and 13 are rejected under 35 U.S.C. 103 as unpatentable over the combination of Piepenburg et al. (published July 2006; Piepenburg et al. PLoS Biol. 2006 Jul;4(7):e204) and Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580), as applied to claim 1 above, and further in view of Kuroda et al (published Feb 4, 2013; JP 2013021967A) and as evidenced by Motomura et al. (published Apr. 2014; Motomura et al. Appl Environ Microbiol. 2014 Apr;80(8):2602-8).
The limitations of claim 1 are taught by Piepenburg and Tavanti, as discussed above.
Regarding claim 6, 11, and 13, neither Piepenburg nor Tavanti teach any explicit concentration or optimum working temperature of the polyphosphate kinase, nor explicitly that the polyphosphate kinase comprises an amino acid sequence as defined in SEQ ID NO: 1 to 3 (or a functional variant or functional fragment thereof).
Kuroda teaches multiple polyphosphate kinases, including one from Meiothermus ruber which corresponds to SEQ ID NO: 2 (par. 83). Note that the sequence in Kuroda is also termed “SEQ ID NO: 2”. Kuroda teaches that the optimum working temperature for this enzyme is 70ºC (par. 91-95; Table 1 on page 83) and using the enzyme at a concentration of 8 ug/mL. Given an approximate molecular mass of 31.6 kDa (Motomura, pg. 2603: “Cloning and purification of class III PPK2”), the enzyme is at a concentration of 0.25 µM in the reaction. Kuroda also teaches a preference of 1 – 500 µg/ml (par. 41; for M. ruber, this would be around 0.03 – 16 µM). Therefore, the limitation that concentration be between 0.01µM – 1000µM is considered to be met.
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Piepenburg and Tavanti with the teachings of Kuroda. One would have been motivated to do so because a thermophilic PPK2, such as the one from M. ruber, is heat-resistant and can more stably produce ATP from AMP (par. 16).
Claims 14 is rejected under 35 U.S.C. 103 as unpatentable over the combination of Piepenburg et al. (published July 2006; Piepenburg et al. PLoS Biol. 2006 Jul;4(7):e204) and Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580), as applied to claim 1 above, and further in view of Ge et al. (published Dec 8, 2011; Ge et al. PLoS One. 2011;6(12):e28707).
Piepenburg and Tavanti teach the limitations of claim 1, as discussed above.
Regarding claim 14, neither Piepenburg nor Tavanti teach that the composition does not comprise PEG.
Ge teaches that for the purposes of macromolecular crowding of enzymatic reactions, PEG is an equivalent of polymers such as Ficoll and dextran (pg. 2, col. 1, par. 1).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to substitute PEG for a different macromolecular crowding agent such as Ficoll or dextran. One would have been motivated to do so because PEG, Ficoll, and dextran were known in the art as macromolecular crowding agents. Furthermore, one may have been motivated to substitute PEG with another crowding agent because it is known to have strong inhibitory effects on processes involving enzymes like polymerases, perhaps due to its ability to cause precipitation (pg. 7, col. 1, 1st par.)
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the 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 1-19 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5-18, and 20-23 of co-pending Application No. 18/476,052, in view of Tavanti et al. (published June 29, 2021; Tavanti et al. ChemCatChem. 2021, 13, 3565-3580).
Although the claims at issue are not identical, they are not patentably distinct from one another. Both sets of claims are drawn to compositions (ref claim 1-3, 5-13). Both sets of claims require:
Amplification compositions (claim 14)
ATP-generating substrate and ATP-generating enzyme (claim 3)
Recombinase, single-stranded binding protein, polymerase, and NTPs (claim 3)
The absence of PEG (claim 6)
Resynthesis or clustering compositions (claim 1, 8)
Although the reference patent does not explicitly require inorganic polyphosphate and a polyphosphate kinase, it would be obvious to one with ordinary skill in the art that inorganic polyphosphate and polyphosphate kinase systems are among the known systems of ATP-generating substrates and enzymes (Tavanti: Introduction). This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Christine M Jones whose telephone number is (571)272-2585. The examiner can normally be reached Monday - Friday, 8AM - 4PM.
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/C.M.J./Examiner, Art Unit 1682
/AMANDA HANEY/Primary Examiner, Art Unit 1682
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