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 .
Benefit of Earlier Filing Date
The instant application, filed 01 May 2024, is a national stage application of PCT/US2022/048717, filed 02 November 2022, which claims the benefit of an earlier filing date to U.S. Provisional Patent Application Serial No. 63/274,656, filed 02 November 2021. Acknowledgment is made of Applicant’s claim.
Status of the Claims
The listing of claims filed 18 December 2024 has been examined.
Claims 1-4, 6-8, 14, 16, 20, 22, 29, 32-33, 36, 44, 73-75, and 77 are pending.
Claims 1, 6, 8, 14, 16, 20, 22, 29, 32-33, 44, 73, and 75 are amended.
Claims 5, 9-13, 15, 17-19, 21, 23-28, 30-31, 34-35, 37-43, 45-72, and 76 are cancelled.
Information Disclosure Statement
The Information Disclosure Statements (IDSs) filed on 02 August 2024 and 07 January 2026 are acknowledged and have been considered. Any lined-through references have not been considered and must be submitted or resubmitted in proper format for consideration. Specifically, a copy of an NPL document titled “PCT/US2022/048717, International Search Report and Written Opinion, February 28, 2023, 15 pages.” is missing.
Specification
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because it uses a phrase which can be implied, specifically the phrase, “The disclosure describes…” A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Objections
Claim 1 is objected to because of the following informalities:
Claim 1 recites, “…wherein one or more of the components have been subjected to extended autoclaving.” [Emphasis added.] The “components” are interpreted as being a DNA polymerase, an intercalating agent having the formula X-Ar-R1, and/or an inhibitor tolerance agent. For clarity, Examiner recommends amending to, “…one or more of the composition components have been subjected to extended autoclaving.” [Emphasis added.]
Appropriate correction is requested.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 14 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 14, which depends on claim 1, recites, “The composition of claim 1, wherein X is NH3 or comprises a secondary or tertiary amine by which the intercalating agent is covalently bound to another molecule.” The only exemplary intercalating agents provided in the instant Specification include propidium monoazide (PMA), ethidium monoazide (EMA), and 6-azido-1-(3- (trimethylammonio)propyl)quinolin-1-ium (p. 10-11, ¶ [0040]-[0042]). None of the aforementioned compounds contain an X which is NH3 or comprises a secondary or tertiary amine. Thus, an example to support the claim language in claim 14 is lacking and a person having ordinary skill in the art (PHOSITA) would conclude that Applicant is not in possession of the claim, as currently recited. The instant Specification states, “…the azide can be converted to a charged N, an amino group, or an amine bonded (secondary or tertiary) DNA molecule.” (p. 11, ¶ [0043]). Accordingly, Examiner suggests amending claim 14 to reflect this language in the Specification or amending claim 14 to recite only the intercalating agents supported by the disclosure. Note claim 14 recites, “...by which the intercalating agent is covalently bound to another molecule,” which is interpreted as an intended use.
When discussing intercalating agents used in PCR reactions, the prior art largely suggests including ethidium monoazide (EMA) and/or propidium monoazide (PMA) in said reactions. For example, in a document discussing various means by which DNA contamination may be reduced in PCR reactions, Thermo Fisher (Kauppinen et al., “Cleaning up PCR Samples: An Evaluation of the Pros and Cons of Using Reagents Commonly Applied in the Research Scenario For Food Testing Applications,” Thermo Fisher Scientific, October 2007) suggests using intercalating dyes, specifically EMA or PMA (p. 2, Col. 2, Use of photoreactive intercalating dyes for prevention of dead cell DNA amplification and detection by PCR). Furthermore, Thermo Fisher reviews some advantages and disadvantages of using EMA versus PMA, stating, “EMA has been reported to have the ability to intercalate into the DNA of live cells resulting in false signal suppression from target organisms; PMA has very low affinity for live cells but some affinity for minimally injured cells, meaning that while it does not suppress detection of live cells it can be active against cells that have their membrane compromised but are otherwise viable, and in some cases lead to them not being detected.” (p. 3, Col. 1, Choice of dye). As discussed above, neither EMA nor PMA, shown below, contain an X which is NH3 or comprises a secondary or tertiary amine.
[AltContent: textbox (PMA)][AltContent: textbox (EMA)]
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Thus, the prior art teaches EMA and PMA are useful intercalating agents. Since Thermo Fisher only discloses EMA and PMA and makes no mention of any other intercalating agents, Thermo Fisher’s teachings fail to suggest or draw a clear line as to whether any other groups besides NH2 or an azide can correspond to X. Accordingly, a PHOSITA is not in possession of the knowledge of which structures wherein X is NH3 or comprises a secondary or tertiary amine would or would not be useful as intercalating agents.
Claim Rejections - 35 USC § 112(b)
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 44 and 75 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 44 depends on a cancelled claim, claim 26. Accordingly, claim 44 lacks proper antecedent basis and is rejected as incomplete. See MPEP 608.01(n)(V). Examiner recommends amending claim 44 to recite, “The method of claim 36, further comprising…” [Emphasis added.] For examination purposes, Examiner interprets claim 44 as depending on claim 36.
Claim 75, which depends on claim 73, recites the limitation "the PCR". There is insufficient antecedent basis for this limitation in the claim. Examiner recommends Applicant amend claim 75 to depend on claim 74 instead of claim 73.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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 nonobviousness.
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.
Claim 36 is rejected under 35 U.S.C. 103 as being unpatentable over LaBaer (US 2019/0127778 A1; IDS dated 02 August 2024, Cite No. 001) in view of Shi (CN 110218778 A).
Regarding claim 36, LaBaer teaches a quantitative real-time PCR (qPCR) method, which uses a DNA intercalating dye like propidium monoazide (PMA) or ethidium monoazide (EMA) (p. 1, Col. 2, ¶ [0003]). PMA, shown below, is an intercalating agent having the formula X-Ar-R1, wherein X is an NH2, Ar is a 6-phenylphenanthridine derivative having a charged N, and R1 is a
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attached to the charged N of the Ar by a C3 alkyl:
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LaBaer states PMA covalently modifies DNA upon its exposure to bright light (p. 2, Col. 1, ¶ [0007]). In LaBaer’s method, a DNA-containing sample and an intercalating agent, such as PMA or EMA, are co-incubated (p. 8, Claims 1-2). Then, the intercalating agent-containing sample is exposed to light and, subsequently, the extracted genomic DNA is pre-amplified prior to performing qPCR (p. 8, Claim 1)
LaBaer does not explicitly teach an inhibitor tolerance agent.
Shi teaches PCR methods, “…that alleviates the problem in the prior art of lacking a suitable PCR reaction system for effectively amplifying samples that have not undergone nucleic acid extraction and purification.” (p. 7-8, ¶ [0010]). Shi indicates crude samples may contain substances which may inhibit PCR, like hemoglobin, anticoagulants, immunoglobins, humic acid, and bile sulfonic acid, and inhibitors can be included in PCR reactions to help minimize the inhibitory effect of such substances on PCR reactions (p, 48-49, ¶ [0087]). Shi states, “The anti-inhibitor is preferably a protein-based substance with anti-PCR inhibitory effects, including… BSA (bovine serum albumin)… and gelatin.” (p. 49, ¶ [0087]).
Shi does not explicitly teach an intercalating agent.
Prior to the filing of the instant application, a person having ordinary skill in the art (PHOSITA) following the teachings of LaBaer would have found it prima facie obvious to prepare a mixture comprising an inhibitor tolerance agent and an intercalating agent having the formula X-Ar-R1 and expose said mixture to light based on the teachings of Shi because LaBaer discloses a PCR method which involves exposing a composition comprising a DNA sample and an intercalating agent to light and Shi discloses a PCR method which can include inhibitor tolerance agents. As discussed above, PMA and EMA are intercalating agents having the formula X-Ar-R1. A skilled artisan would have been motivated to amplify nucleic acids by combining an intercalating agent as disclosed by LaBaer and an inhibitor tolerance agent as disclosed by Shi since LaBaer indicates such intercalating agents selectively permeate dead cells, thereby rendering their DNA unusable for PCR amplification (p. 2, ¶ [0017]), and Shi suggests inhibitor tolerance agents alleviate the PCR-inhibition effect of substances like hemoglobin and anticoagulants in the sample (p. 49, ¶ [0087]). Furthermore, the instant Specification indicates inhibitor tolerance agents may include BSA and gelatin (p. 7-8, ¶ [0030]), which are both disclosed by Shi. Thus, a PHOSITA would have had a reasonable expectation of success in combining the aforementioned elements in a single mixture as both elements had been known to improve PCR amplification efficiency (MPEP 2143(I)(A)).
Claims 1-4, 6-8, 16, 20, 22, 29, 33, 44, 73-75, and 77 are rejected under 35 U.S.C. 103 as being unpatentable over LaBaer (US 2019/0127778 A1; IDS dated 02 August 2024, Cite No. 001) in view of Shi (CN 110218778 A) and Gefrides (Gefrides et al., “UV irradiation and autoclave treatment for elimination of contaminating DNA from laboratory consumables”, Forensic Science International: Genetics 4 (2010) 89-94).
Regarding claims 1-4, 6-8, 16, 20, 22, 29, 33, 73-75, and 77, LaBaer in view of Shi teaches all of the claimed elements as stated above. Furthermore, LaBaer describes using TaqMan® probe qPCR, which involves PCR primers, a thermostable polymerase, and dNTPs, to quantify a DNA sequence’s presence in a sample (p. 3, Col. 1, ¶ [0019]). A skilled artisan would recognize the TaqMan® probe relies on Taq polymerase, which is a thermostable DNA polymerase. Additionally, Shi discloses numerous DNA polymerases which can be used, including Taq, Tth, Tfl, TLI, Tne, Tma, Phusion™ Pfu, and KOD (p. 46, ¶ [0083]). Shi indicates the PCR reaction system may include dNTPs (p. 48, ¶ [0086]) and primers (p. 57-58, ¶ [0098]). Furthermore, Shi states, “…when the PCR reaction system is only used for reverse transcription using RNA in the crude sample as a template, the PCR reaction system may contain only reverse transcriptase; when the PCR reaction system uses both DNA and RNA as templates… it is usually necessary to first reverse transcribe the mRNA in the sample into cDNA, and then perform PCR amplification using the cDNA as a template. In this case, the PCR reaction system contains both DNA polymerase and reverse transcriptase.” (p. 45, ¶ [0082]).
With respect to claims 1-4, 6-8, 16, 20, 22, 29, 33, 73-75, and 77, the combination of LaBaer and Shi fails to explicitly teach extended autoclaving of one or more reaction components.
Gefrides teaches methods by which DNA contamination may be removed laboratory consumables (p. 89, Abstract). Gefrides concludes, “... 2 h of autoclave treatment will eliminate nanogram quantities of DNA from laboratory consumables… Autoclaving was more effective than UV irradiation at eliminating small fragments of contaminating DNA (<200 bp) and should be selected over UV irradiation when possible.” (p. 93, Conclusions).
Gefrides does not explicitly teach an inhibitor tolerance agent or an intercalating agent.
Prior to the filing of the instant application, a person having ordinary skill in the art (PHOSITA) following the teachings of LaBaer would have found it prima facie obvious to amplify DNA using a composition comprising a DNA polymerase, an intercalating agent, and an inhibitor tolerance agent wherein at least one component in the composition has been autoclaved based on the teachings of Shi and Gefrides because LaBaer and Shi disclose intercalating agents and inhibitor tolerance agents, respectively, and Gefrides discloses autoclaving as an effective method by which contaminant DNA may be eliminated. Furthermore, LaBaer and Shi each disclose using dNTPs, primers, and/or a thermostable DNA polymerase. Additionally, Shi suggests a reverse transcription reaction can be performed prior to amplification of the target nucleic acid sequence via PCR (p. 45, ¶ [0082]). Since LaBaer discloses using PMA to render DNA from dead cells unusable for PCR and Shi discloses alleviating PCR inhibition by substances like hemoglobin by using BSA, a PHOSITA would have been motivated to further improve reaction efficiency by eliminating additional contaminants. Thus, since Gefrides discloses autoclaving eliminates contaminant DNA, it would have been prima facie obvious to apply Gefrides’ teachings and autoclave certain autoclavable PCR reaction components (i.e., gelatin and/or dH2O) to obtain a purer sample.
Regarding claims 44, LaBaer in view of Shi teaches all of the claimed elements as stated above.
Prior to the filing of the instant application, a person having ordinary skill in the art (PHOSITA) following the teachings of LaBaer would have found it prima facie obvious to autoclave a second mixture comprising one or more nucleic acid amplification components for at least 30 minutes and then combining said second mixture with the first mixture containing at least an inhibitor tolerance agent and an intercalating agent based on the teachings of Shi and Gefrides. Because Gefrides discloses autoclaving laboratory consumables helps remove any contaminating DNA from said consumables, a skilled artisan would have been motivated to apply Gefrides teachings to those of LaBaer and Shi in order to remove non-target DNA from the sample prior to PCR amplification. However, a PHOSITA would also recognize some components in a PCR reaction should not be autoclaved. For example, autoclaving proteins like BSA and DNA polymerase would result in denaturation and autoclaving toxic compounds like PMA would pose a health hazard. Thus, any reaction components which can be autoclaved would necessarily need to be autoclaved separately from any components which would be destroyed or become a health hazard if autoclaved. Thus, a PHOSITA would have found it prima facie obvious to prepare a second mixture containing any components which can be safely autoclaved and combine the second mixture with the first mixture afterwards, once the second mixture has cooled.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over LaBaer (US 2019/0127778 A1; IDS dated 02 August 2024, Cite No. 001) in view of Shi (CN 110218778 A) and Gefrides (Gefrides et al., “UV irradiation and autoclave treatment for elimination of contaminating DNA from laboratory consumables”, Forensic Science International: Genetics 4 (2010) 89-94) and further in view of Josephson (WO 2010/141833 A2).
Regarding claim 14, LaBaer in view of Shi and Gefrides teaches all of the claimed elements as stated above.
With respect to claim 14, the combination of LaBaer, Shi, and Gefrides fails to explicitly teach an intercalating agent having the formula X-Ar-R1 wherein X in NH3 or comprises a secondary or tertiary amine by which the intercalating agent is covalently bound to another molecule. In PMA and EMA, which are disclosed by LaBaer, X is NH2.
Josephson discloses the compound TO-PRO 1, shown below (p. 11, Table 1):
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This compound is a nucleic acid dye containing, “…rings which intercalate between the bases of double-stranded DNA.” (p. 10, Bottom Paragraph). Relative to the instantly claimed formula X-Ar-R1, X comprises a tertiary amine (i.e., 3-methyl-benzothiazoline), Ar is a heterocyclic aromatic group containing one charged N, and R1 is
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.
Josephson does not explicitly teach a DNA polymerase, an inhibitor tolerance agent, or extended autoclaving of one or more reaction components.
Prior to the filing of the instant application, a person having ordinary skill in the art (PHOSITA) following the teachings of LaBaer, Shi, and Gefrides would have found it prima facie obvious to prepare an intercalating agent having the formula X-Ar-R1 wherein X is a tertiary amine based on the teachings of Josephson since Josephson discloses TO-PRO 1, an intercalating agent which comprises a tertiary amine. Since PMA and EMA, which are disclosed by LaBaer, had been known to function as intercalating agents, a PHOSITA would have been motivated to try substituting PMA and/or EMA with other known intercalating agents, such as TO-PRO 1.
Claim 32 is rejected under 35 U.S.C. 103 as being unpatentable over LaBaer (US 2019/0127778 A1; IDS dated 02 August 2024, Cite No. 001) in view of Shi (CN 110218778 A) and Gefrides (Gefrides et al., “UV irradiation and autoclave treatment for elimination of contaminating DNA from laboratory consumables”, Forensic Science International: Genetics 4 (2010) 89-94) and further in view of Clontech (Clontech Laboratories, Inc., “TaqStart™ Antibody User Manual”, Published 2 March 2005).
Regarding claim 32, LaBaer in view of Shi and Gefrides teaches all of the claimed elements as stated above.
Furthermore, Shi states, “In some preferred embodiments, the DNA polymerase includes a hot-start polymerase modified by at least one of antibody, chemical, and ligand methods. The hot-start polymerase is modified to block the enzyme’s active site and exposes the enzyme’s active site at a preset high temperature, which can avoid mismatches caused by poor enzyme activity at low temperatures.” (p. 46-47, ¶ [0084]).
With respect to claim 32, the combination of LaBaer, Shi, and Gefrides fails to explicitly teach a specific polymerase antibody.
Clontech teaches the TaqStart™ Antibody, which inhibits Taq DNA polymerase at ambient temperatures to block polymerase activity while the PCR reaction is being setup, but the inhibition is reversed when the temperature is raised above 70°C (p. 3, ¶ 2). Clontech indicates using the TaqStart Antibody can be advantageous as it helps prevent the generation of nonspecific amplification products and primer-dimer artifacts, particularly in PCR reactions which involve complex genomic DNA or cDNA templates or very low-copy-number targets (p. 3, ¶ 3).
Clontech does not explicitly teach an intercalating agent, an inhibitor tolerance agent, or extended autoclaving of one or more reaction components.
Prior to the filing of the instant application, a person having ordinary skill in the art (PHOSITA) following the teachings of LaBaer, Shi, and Gefrides would have found it prima facie obvious to include a polymerase antibody in a PCR reaction based on the teachings of Clontech because Clontech teaches polymerase antibodies can improve the results of PCR amplifications by preventing the formation/production of undesirable reaction products. Thus, a PHOSITA would have been motivated to improve the PCR reaction’s efficiency by including a polymerase antibody in the reaction, such as the TaqStart™ Antibody when Taq DNA polymerase is being used.
Non-Statutory 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 1-4, 6-8, 14, 16, 20, 22, 29, 33, 44, 73-75, and 77 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4 and 13-16 of copending Application No. 18/689,573 in view of over LaBaer (US 2019/0127778 A1; IDS dated 02 August 2024, Cite No. 001), Shi (CN 110218778 A), and Gefrides (Gefrides et al., “UV irradiation and autoclave treatment for elimination of contaminating DNA from laboratory consumables”, Forensic Science International: Genetics 4 (2010) 89-94).
Application ‘534 claims a composition comprising a DNA polymerase, a crowding agent, and 0.05% (w/v) surfactant (Claim 1). Said crowding agent can be BSA (Claim 4) and the composition may further comprise Taq DNA polymerase (Claim 15) and dNTPs (Claim 16). Additionally, the composition can be used in digital PCR (dPCR), reverse transcription PCR (RT-PCR), or quantitative/real-time PCR (qPCR) (Claim 13).
Application ‘534 does not claim an intercalating agent having the formula X-Ar-R1 or extended autoclaving of one or more reaction components.
Regarding claim 36, LaBaer teaches a quantitative real-time PCR (qPCR) method, which uses a DNA intercalating dye like propidium monoazide (PMA) or ethidium monoazide (EMA) (p. 1, Col. 2, ¶ [0003]). PMA, shown below, is an intercalating agent having the formula X-Ar-R1, wherein X is an NH2, Ar is a 6-phenylphenanthridine derivative having a charged N, and R1 is a
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attached to the charged N of the Ar by a C3 alkyl:
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LaBaer states PMA covalently modifies DNA upon its exposure to bright light (p. 2, Col. 1, ¶ [0007]). In LaBaer’s method, a DNA-containing sample and an intercalating agent, such as PMA or EMA, are co-incubated (p. 8, Claims 1-2). Then, the intercalating agent-containing sample is exposed to light and, subsequently, the extracted genomic DNA is pre-amplified prior to performing qPCR (p. 8, Claim 1)
LaBaer does not explicitly teach an inhibitor tolerance agent.
Shi teaches PCR methods, “…that alleviates the problem in the prior art of lacking a suitable PCR reaction system for effectively amplifying samples that have not undergone nucleic acid extraction and purification.” (p. 7-8, ¶ [0010]). Shi indicates crude samples may contain substances which may inhibit PCR, like hemoglobin, anticoagulants, immunoglobins, humic acid, and bile sulfonic acid, and inhibitors can be included in PCR reactions to help minimize the inhibitory effect of such substances on PCR reactions (p, 48-49, ¶ [0087]). Shi states, “The anti-inhibitor is preferably a protein-based substance with anti-PCR inhibitory effects, including… BSA (bovine serum albumin)… and gelatin.” (p. 49, ¶ [0087]). Additionally, Shi discloses including 0.001% w/v-1.0% w/v of a surfactant in the PCR reaction (p. 35, ¶ [0069]).
Shi does not explicitly teach an intercalating agent.
Gefrides teaches methods by which DNA contamination may be removed laboratory consumables (p. 89, Abstract). Gefrides concludes, “... 2 h of autoclave treatment will eliminate nanogram quantities of DNA from laboratory consumables… Autoclaving was more effective than UV irradiation at eliminating small fragments of contaminating DNA (<200 bp) and should be selected over UV irradiation when possible.” (p. 93, Conclusions).
Gefrides does not explicitly teach an inhibitor tolerance agent or an intercalating agent.
Prior to the filing of the instant application, a person having ordinary skill in the art (PHOSITA) following the teachings of LaBaer would have found it prima facie obvious to amplify DNA using a composition comprising a DNA polymerase, an intercalating agent, and an inhibitor tolerance agent wherein at least one component in the composition has been autoclaved based on the teachings of Shi and Gefrides because LaBaer and Shi disclose intercalating agents and inhibitor tolerance agents, respectively, and Shi discloses autoclaving as an effective method by which contaminant DNA may be eliminated. Furthermore, LaBaer and Shi each disclose using dNTPs, primers, and/or a thermostable DNA polymerase. Additionally, Shi suggests a reverse transcription reaction can be performed prior to amplification of the target nucleic acid sequence via PCR (p. 45, ¶ [0082]). Since LaBaer discloses using PMA to render DNA from dead cells unusable for PCR and Shi discloses alleviating PCR inhibition by substances like hemoglobin by using BSA, a PHOSITA would have been motivated to further improve reaction efficiency by eliminating additional contaminants. Thus, since Gefrides discloses autoclaving eliminates contaminant DNA, it would have been prima facie obvious to apply Gefrides’ teachings and autoclave certain autoclavable PCR reaction components (i.e., gelatin and/or dH2O) to obtain a purer sample.
Because 1-4, 6-8, 14, 16, 20, 22, 29, 33, 44, 73-75, and 77 in the instant application would have been obvious over claims 1-4 and 13-16 of Application No. 2024/0376534 A1 in view of LaBaer, Shi, and Gefrides, 1-4, 6-8, 14, 16, 20, 22, 29, 33, 44, 73-75, and 77 in the instant application are not patentably distinct from claims 1-4 and 13-16of Application No. 2024/0376534 A1.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIANNA L BAUER whose telephone number is (571)272-5752. The examiner can normally be reached 8am-5pm.
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, ADAM C MILLIGAN can be reached at (571)270-7674. 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.
/B.L.B./Examiner, Art Unit 1623
/CLINTON A BROOKS/Supervisory Patent Examiner, Art Unit 1621
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