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 1-9 in the reply filed on 3/2/2026 is acknowledged.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
See Table 1, p. 23
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.
Claim1-9 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.
The preamble of claim 1 recites an “isothermal” amplification method, but the body of the claim does not make any requirement that the reaction be isothermal. Therefore it is unclear if the method must be isothermal.
Regarding claims 1-9, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d). See claim 1, preamble line 2, part (a), part (b), part (d) and claims 2, 5, 6, and 8. Any claim not enumerated is indefinite by virtue of dependency on claim 1.
Claim 1 part (a) fails to set forth any required method step. It recites “one single stranded binding protein” and “one…target specific sequence primer(s)” and “one DNA polymerase” but it does not recite any verb in association with these elements, and so it is not clear how they are incorporated into the claimed method. The claim has been interpreted as if the step recites “providing” the protein and primer, similar to part (b) of the claim.
In claim 1(e) the phrase “the at least one amplified target” lacks proper antecedent basis because the claim neither previously recites nor requires an amplified target.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1, 3, 5, 6, 7, 8 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kunze et al. (Anal. Chem. 2016, 88, 898−905).
All elements in the claims that are modified by “preferably” or “optionally” are interpreted as elements that are not required and therefore these elements are not addressed in this rejection.
The reference teaches a method comprising providing a single stranded binding protein (SSBP), two target sequence specific primers, and at least one DNA polymerase (p. 900, the TwistAMP basic kit inherently includes a polymerase and SSBP; See also Figure 2).
The reference teaches providing a biological sample to be analyzed for the presence of the at least one target sequences (p. 903, amplification of waterborne pathogens).
The reference teaches initiating the amplification reaction by adding at least one starting reagent (p. 901, first column).
The reference teaches obtaining at least one amplified target (Figure 5, for example).
The reference teaches providing bacterial target sequence which is a double stranded DNA nucleic acid sequence (p. 903, amplification of waterborne pathogens).
The reference teaches the method is conducted at 39 C. See Figure 5.
The reference teaches forward and reverse primers that are target specific and are provided in different concentrations. See Table 1 and p. 901 first column.
The reference teaches biotin labeled primers, see Figure 2. Biotin is an indirectly detectable moiety.
The reference teaches using an SSBP that is a functional analogue of RB69 insofar as the protein used in the reference, like RB69 has SSBP activity.
Therefore, the claims are anticipated.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 2 and 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kunze et al. in view of Dobnik et al. (J. Agric. Food Chem. 2014, 62, 2989−2996).
The teachings of Kunze et al. as they apply to claims 1 and 3 from which these claims depend are given previously in this Office action and are fully incorporated here.
Kunze et al. does not teach providing at least one reverse transcriptase, or providing DNA and RNA as target sequences.
Dobnick also teaches isothermal amplification. Dobnik teaches that the genome of pathogens is made of DNA or RNA and therefore tools that identify both types of targets are ideal (Abstract). The reference teaches a sequence-based amplification wherein both types of targets (DNA and RNA) are provided along with a reverse transcriptase to prepare targets for subsequent amplification (p. 2990).
It would have been obvious to have modified the method taught by Kunze et al. so as to have provided samples with DNA and RNA templates, and a reverse transcriptase, as taught by Dobnik et al. One would have been motivated to do so because Dobnic teaches that the ideal nucleic acid test would be configured to detect both types of targets since pathogens have DNA or RNA.
Claim(s) 9 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kunze et al. in view of WO 2005/118853 (Pipenburg).
The teachings of Kunze et al. as they apply to claims 1 from which this claim depends are given previously in this Office action and are fully incorporated here.
Kunze et al. does not teach wherein any of the proteins or enzymes used comprise at least one tag and/or label.
Pipenburg teaches SSBP for RPA reactions that have His peptide tags at the N or C termini (p. 64). The reference teaches that the gp32(N) functions at lest as well as the E. coli SSBP (p. 65). The reference teaches differently tagged gp32 molecules have differences in quantity of product, namely that gp2(N) and gp32(C)R4T produce more product than “more cooperative” gp32 variants.
It would have been obvious to have used the tagged SSBP taught by Pipenburg in an effort to increase quantity of product in the RPA reaction taught by Kunze.
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 1-9 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of copending Application No. 18248903 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the reference claims anticipate the instant claims.
All elements in the claims that are modified by “preferably” or “optionally” are interpreted as elements that are not required and therefore these elements are not addressed in this rejection.
The reference claims teach a method comprising providing a single stranded binding protein (SSBP), two target sequence specific primers, and at least one DNA polymerase (See at least reference claim 1).
The reference claims teach providing a biological sample to be analyzed for the presence of the at least one target sequences (See at least reference claim 1).
The reference claims teach initiating the amplification reaction by adding at least one starting reagent (See at least reference claim 1).
The reference claims teach obtaining at least one amplified target (See at least reference claim 1).
The reference claims teach providing a reverse transcriptase (see claim 1).
The reference teaches target sequence which is a double stranded DNA nucleic acid sequence, and the reference claims teach providing DNA and RNA nucleic acid sequence target (reference claim 9).
The reference claims teach the method is conducted at 40-55 C. See reference claim 10.
The reference claims teach forward and reverse primers that are target specific and provided at different amounts or concentrations. See claim 6.
The reference claims teach labeled primers, claim 7.
The reference claims teach using an SSBP that is a functional analogue of RB69 insofar as the protein used in the reference, like RB69 has SSBP activity (claim 1 and claim 8).
Therefore, the claims are anticipated by the reference claims.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Juliet Switzer whose telephone number is (571)272-0753. The examiner can normally be reached Monday to Thursday, 8:00 AM-3:30 PM.
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, Winston 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.
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Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/Primary Examiner, Art Unit 1682
Prosecution Insights