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
Claim 14 is drawn to a ‘use of’ the clustering composition of claim 1. After further consideration, because the claim is drawn to a method, claim 14 belongs to Invention II.
Applicant’s election without traverse of Invention I and withdrawal of claims 14, 15, 17-18, and 20-23, drawn to unelected invention II, in the reply filed 1/27/26 is acknowledged.
Claims 1-3, 5-15, 17, 18, and 20-23 are currently pending.
The claims have been examined to the extent that they read on elected Invention I (claims 1-3 and 5-13).
Priority
Applicant’s claim to the benefit of provisional application 63/411,973 is acknowledged, and the effective filing date of the instant application is considered to be 9/30/22.
Claim Objections
Claim 11 is objected to under 37 CFR 1.75 as being a substantial duplicate of claim 1. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
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 5 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 5 is rejected for the recitation because it requires that “the polymerase is DNA Polymerase I and the recombinase is Recombinase A.” This recitation is confusing because the polymerase and recombinase are both optional in claim 3 and are not necessarily comprised in the composition. For example, it is not clear whether the limitation the that polymerase be DNA Polymerase I would apply to a composition which includes the polymerase but not the recombinase. As a result, a person with ordinary skill in the art would not be reasonably apprised of the scope of the invention 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 1-3 and 5-13 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 the enzyme inorganic pyrophosphatase. The markedly different characteristics analysis has been used to determine if the nature-based product is a judicial exception. The nature-based product has been compared to its natural counterparts.
The claims broadly encompass naturally occurring inorganic pyrophosphatase and there is no indication that the inorganic pyrophosphatase of the instant claims has any characteristics that are different from naturally occurring enzymes. There is no difference in function, structure, or other properties.
It is noted that the enzymes are recited as being in a “composition.” There is no indication that the enzyme being present in the composition changes the function, structure, or other properties of the enzyme. Claims 11 and 12 are directed toward the composition in the form of a “kit.” The enzyme does not interact with other elements of the composition in the “kit.” There is no indication that the enzyme being present in a “kit” changes the structure, function, or other properties of the enzyme. Because the claimed natural products do not have markedly different characteristics, they are a product of nature exception.
Claims 3, 5, 12, and 13 are drawn to the inorganic pyrophosphate and additional elements which are themselves judicial exceptions: a recombinase, a single-stranded binding protein, a polymerase, NTPs, and ATP-generating substrate, and ATP-generating enzyme, magnesium ions, and the absence of primers having a length of between 18 to 22 base pairs. 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 natural products have any characteristics that are different from the naturally occurring enzymes, NTPs, ions, and substrates. There is no difference in function, structure, or other properties.
It is noted that in claim 13, the natural products are recited as being absent from primers having a length between 18 to 22 base pairs. There is no indication that the lack of these elements changes the function, structure, or other properties of the natural products. It is noted that the natural products are recited as being in a “composition.” There is no indication that the natural products being present in the composition changes the function, structure, or other properties of the natural products. Because the claimed natural products 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 1-3, 5, 7-10, and 13 do not recite any elements in addition to the natural products and therefore do not integrate the judicial exceptions into a practical application. Claim 6 recites the additional element of a lack of PEG. The absence of a reagent does not provide integration. Claims 11 and 12 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 1-3, 5, 7-10, and 13 do not recite any elements in addition to the natural products and therefore do not provide an inventive step. Claim 6 recites the additional element of a lack of PEG. The absence of a reagent does not provide an inventive concept. Claims 11 and 12 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 a 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 1-3, 6-8, and 10-13 are rejected under 35 U.S.C. 102(a)(1) as anticipated by Tabor et al. (published Jul 28, 2005; Patent Application Publication No. US2005/0164213).
Regarding claims 1 and 8, Tabor teaches compositions comprising an inorganic pyrophosphatase (par. 23, 83). Although the instant claims are directed to a “clustering” composition, 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 “clustering” merely sets forth the intended use of the claimed composition, but does not limit the scope of the claims. Similarly, although Tabor does not explicitly teach that the composition is a ”resynthesis” composition, this limitation is an intended use of the composition. Since compositions are analyzed with respect to their structure, intended uses do not limit the scope of the claims.
Regarding claim 2, Tabor teaches adding 20ng of inorganic pyrophosphatase to a 50µL reaction (par. 83). With a molar mass of approximately 71 kDa for the enzyme in Saccharomyces cerevisiae, the concentration of the inorganic pyrophosphatase is approximately 0.006 µM. Claim 2 broadly encompasses this value, given the recitation of “about.” Therefore, the claim is considered to be anticipated.
Regarding claim 3, Tabor teaches compositions additionally comprising (Examples 1, 2): single-stranded nucleotide binding protein, a polymerase, NTPs (par. 69; 73), and an ATP-generating substrate and enzyme (par. 79).
Regarding claim 6, Tabor teaches a composition which does not comprise PEG (Examples 1, 2). Here, Tabor is silent regarding use of polyethylene glycol in the composition and uses a different macromolecular crowding agent in the form of dextran. Therefore, the limitation is considered to have been met.
Regarding claim 7, Tabor teaches that the composition comprises a buffer, and that the composition is buffered to a pH of 7.5 (par. 69). As pH 7.5 lies within the claimed range of 7.0 to 8.5, the limitation is considered to have been met.
Regarding claim 10, Tabor teaches a composition comprising a mesophilic inorganic pyrophosphatase (par. 83).
Regarding claims 11 and 12, Tabor teaches kits comprising inorganic pyrophosphatase (par. 35). Tabor also teaches inorganic pyrophosphatase compositions comprising a metal cofactor composition, wherein the metal cofactor composition comprises magnesium ions (par. 63). Although Tabor does not explicitly teach that the metal cofactor composition is used with a kit, the term “kit” broadly encompasses a collection of reagents. Therefore, the limitation of “kit” is considered to be anticipated.
Regarding claim 13, Tabor teaches that the composition does not comprise primers having a length between 18 to 22 base pairs (par. 50, Abstract).
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.
Claims 2 and 9 are rejected under 35 U.S.C. 103 as unpatentable over Tabor et al. (published Jul 28, 2005; Patent Application Publication No. US2005/0164213), as applied to claim 1 above, and further in view of Park et al. (published Oct 31, 2009; Park et al. Facilitation of polymerase chain reaction with thermostable inorganic pyrophosphatase from hyperthermophilic archaeon Pyrococcus horikoshii. Appl Microbiol Biotechnol. 2010 Jan;85(3):807-12).
Tabor teaches the limitations of claim 1, as discussed above.
Regarding claim 2, Tabor does not teach a concentration of an inorganic pyrophosphatase which lies precisely between 0.01 µM and 1000 µM. Regarding claim 9, Tabor doesn’t teach a thermophilic inorganic pyrophosphatase.
Regarding claims 2 and 9, Park teaches a thermophilic inorganic pyrophosphatase (pg. 807, col. 2). Park teaches adding the inorganic pyrophosphatase to a composition at a concentration of 0.2 µM (pg. 808, col. 2, par. 2). This concentration lies within the range of 0.01 µM and 1000 µM, and therefore meets the limitation of claim 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 Tabor and Park. One would have been motivated to do, in order to utilize a thermostable enzyme in a biotechnological application (pg. 807, col. 2), such as in produce a higher yield in PCR (pg. 811, col. 2).
Claim 5 is rejected under 35 U.S.C. 103 as unpatentable over Tabor et al. (published Jul 28, 2005; Patent Application Publication No. US2005/0164213), as applied to claims 1 and 3 above, and in view of Piepenburg (published Apr 23, 2013; U.S. Patent No. 8,426,134)
Tabor teaches the limitations of claims 1 and 3, as discussed above.
Regarding claim 5, Tabor does not teach that the polymerase is DNA Polymerase I and the recombinase is Recombinase A. Instead, Tabor teaches DNA polymerases generally with a preferred embodiment of T7 DNA polymerase.
Piepenburg teaches recombinase polymerase amplification compositions comprising DNA Polymerase I (col. 15, ln. 42-49) and Recombinase A (col. 15, ln. 28-29). Regarding the polymerase, 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 the T7 of Tabor’s invention with the DNA Polymerase I of Piepenburg because Piepenburg demonstrates that the two are functional equivalents (col. 15, ln. 42-52).
Regarding the recombinase, 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 Recombinase A of Piepenburg with Tabor’s invention. One would have been motivated to do so to increase the fidelity and sensitivity of nucleic acid amplification via strand displacement (col. 2, ln. 52 – col. 3, ln. 5).
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 1-3 and 5-13 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of co-pending Application No. 18/475,939, in view of Tabor et al. (published Jul 28, 2005; Patent Application Publication No. US2005/0164213).
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 claims 1-17). Both sets of claims require:
Amplification compositions (ref claims 1-17), resynthesis, or clustering compositions (ref claim 17)
ATP-generating substrate and ATP-generating enzyme (ref claims 1-21)
Recombinase, single-stranded binding protein, polymerase, and NTPs (ref claims 2-4)
The absence of PEG (ref claim 14)
The reference application does not explicitly require inorganic pyrophosphatase. However, it would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to add an inorganic pyrophosphatase to the composition in order to reduce inhibition of DNA synthesis due to pyrophosphate accumulation (Tabor: par. 56).
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.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Shen can be reached at (571)272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/C.M.J./Examiner, Art Unit 1682
/AMANDA HANEY/Primary Examiner, Art Unit 1682
Prosecution Insights