Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after allowance or after an Office action under Ex Parte Quayle, 25 USPQ 74, 453 O.G. 213 (Comm'r Pat. 1935). Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, prosecution in this application has been reopened pursuant to 37 CFR 1.114. Applicant's submission filed on 1/20/26 has been entered.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 63/115291, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application.
The instant claims are sufficiently broad so as to be practiced without a reverse transcription step, where no warm-start isothermal amplification plus CRISPR 12a detection in a digital format is disclosed in the provisional as being carried out without an RT step.
Further, the instant claims are sufficiently broad so as to be practiced with any possible DNA polymerase based isothermal amplification, whereas only Bst is taught in combination with pyrophosphatase and phosphorothioated inner primers.
The provisional teaches “it is an advantageous feature of the disclosed method to use pyrophosphatase and phosphorothioated primers, thereby successfully enabling one-pot, one-step isothermal CRISPR reaction with Bst DNA polymerase-based reverse transcription isothermal amplifications” (Specification, p. 2).
The provisional provides no written description of a method that is not “reverse transcription isothermal amplification” in combination with the other claimed elements, nor does the provisional application provide basis for the other claimed elements (ppase and phosphorothioated primers) in an assay in combination with an isothermal method that does not employ Bst DNA polymerase or LAMP.
The provisional teaches that the pyrophosphatase and phosphorothioated inner primers are necessary to mediate efficient reverse transcription isothermal amplification at unfavorable temperature such as 52 degrees (21 page Appendix, p. 15).
There is no written description in the provisional application to support the breadth of the claimed assay which does not require Bst polymerase or reverse transcription isothermal amplification.
Therefore, the effective filing date of the instant assay/method claims is 11/17/2021.
With regard to the kit claims, the provisional application does not provide written description for oligonucleotides that have less than 100% identity to the recited SEQ ID NO.
Therefore, the effective filing date of the instant claims is 11/17/2021.
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, 4, 8, 9, 14, 16, 17, 18, 19, 20, 21, 22, 23, 25, and 30-36 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ding et al. (Biosensors and Bioelectronics 184 (2021) 113218., including supplemental data; 27 pages; Available online 17 April 2021).
The reference teaches a method which includes the steps recited in claim 1, see Supplementary Information, section 2.3, table S1, section 2.4.
With regard to claims 30-34, Table S1 teaches the claimed oligonucleotides, and the reference teaches these combined pyrophosphatase, see section 2.3. The specification does not provide a limiting definition of a kit, and so the set of reagents taught by the reference is considered to be a “kit.”
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) 1, 8, 14, 16, 25, 35, and 36 is/are rejected under 35 U.S.C. 103 as being unpatentable over Tan et al. (WO 2021/262099) in view of Rolando et al. (Analytical Chemistry 2019 91 (1), 1034-1042) and Cai et al. (Analytical Chemistry 2018 90 (14), 8290-8294).
Tan teaches a method that includes contacting a sample with a warm-start CRISPR reaction mixture comprising a Cas12a endonuclease, a target specific crRNA, outer primers for amplification of the target, inner primers for amplification of the target and pyrophosphatase.
In particular, the reference teaches a method in which RT-LAMP is performed to reverse transcribe and amplify viral RNA to generate double stranded substrates for Cas12 enzymes, for example Cas12a. The Cas12 proteins are assembled with target specific crRNA (referred to also as guide RNA. The reaction is carried out within the presence of a single stranded reporter molecule and the reporter is cleaved upon Cas12a binding and cleavage results in the generation of a fluorescent signal. The reference teaches amplifying the target, if present in the sample by DNA polymerase-based isothermal amplification, and detecting the presence or absence of a fluorescent signal. The reference teaches that including pyrophosphatase in the reaction enhances the kinetics of the Cas detection reaction. See p. 3, discussion of VaNGuard test; p. 6, 3rd paragraph; 65, section 7 discussing WarmStart LAMP which is a polymerase based isothermal amplification; p. 57, second and third paragraphs; p. 65, section 8; Figure 1; p. 21 figure 63 description and p. 22 figure 66 description describing a reaction where the CRISPR reagents are added into a tube with LAMP reagents; p. 54 reaction completed at 60C).
With regard to claim 8, the references LAMP amplification at 60C which is “about” 55C, for at up to 60 minutes; p. 39, 4th full paragraph.
With regard to claims 14 and 16, Tan teaches detecting viral SARS-CoV2-2, particularly a target within the nucleoprotein gene; p. 35 and Example 1.
With regard to claim 25, Tan teaches testing nasal swabs, which are clinical samples; p. 57, 3rd paragraph.
With regard to claim 35, Tan teaches using Bst2.0; p. 47, lines 2-3.
With regard to claim 36, the LAMP is reverse transcription LAMP; p. 65, section 7.
Tan does not teach a method wherein the inner primers are phosphorotioated inner primers, nor does the reference teach partitioning the reaction mixture into a plurality of microwells wherein each microwell comprises a portion of the sample.
Rolando teaches digital LAMP, a method wherein a reaction mixture is formed and then loaded by pipetting the sample mixture onto a chip with a plurality of microwells (p. 1036, 2nd column). As the reaction proceeds a fluorescent signal is generated and the detection of the signal in a given microwell indicates the presence of the target in a microwell. Rolando teaches that a digital approach allows determination of the efficiency of an amplification reaction and provides absolute quantification with high resolution (p. 1035, 1st column). Furthermore, Rolando teaches that the assay can be performed completely with commercially available and open-source components (p. 1035, 1st column).
Cai et al. teaches that LAMP is an extremely power tool for the detection of nucleic acid, and that the use of phosphorotioated primers enables more efficient hairpin formation and extension at the termini of growing concatemers, enabling the assay to work at much lower temperatures (abstract and throughout).
It would have been obvious before the effective filing date to have modified the method taught by Tan et al. so as to have employed a digital system as taught by Rolando. One would have been motivated to do so in order to provide a technique could be used to determine efficiency of an amplification reaction and also to provide absolute quantification of a target. Furthermore, since the method taught by Tan is a LAMP based method, it would have been obvious to have modified the method as taught by Cai et al. by using phosphorotioated primers. One would have been motivated to make this modification because Cai teaches that phosphorotioated primers enable more efficient hairpin formation and extension at the termini of growing concatemers, enabling the assay to work at much lower temperatures, which is a benefit for point-of-diagnostics (p. 8290, 2nd column).
Claim(s) 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Tan in view of Rolando and Cai as applied to claims 1, 8, 14, 16, 25, 35, and 36 above, and further in view of Ding et al. (Analytical Chemistry 2019 91 (20), 12852-12858).
The teachings of Tan in view of Rolando and Cai are presented previously in this Office action and are fully incorporated here. Tan, Rolando and Cai do not teach a method wherein the isothermal amplification mixture further includes a competition primer and a reverse competition primer.
Ding teaches an improvement to LAMP wherein two competition primers are added to a reaction mixture and results in a dual-priming isothermal amplification (DAMP) for rapid nucleic acid detection with ultra-low non-specific signals (Abstract, Figure 1).
It would have been obvious before the effective filing date to have modified the method taught by Tan so as to have used a DAMP assay, including the two competition primers instead of a LAMP assay since Ding et al. teaches DAMP offers ultra-low non-specific amplification signals. One would have been motivated to do so because Cai reports that DAMP had equal or better sensitivity with faster amplification speed compared to conventional LAMP and PCR assays, and that it has ultralow nonspecific background, even after a 2-hour incubation (p. 12853, Col. 1).
Claim(s) 1, 8, 9, 14, 16, 23, 25, 35, and 36 is/are rejected under 35 U.S.C. 103 as being unpatentable over Tan in view of Rolando and Cai as applied to claims 1, 8, 14, 16, 25, 35, and 36 above, and further in view of Mahfouz et al. (WO 2021/240443).
The teachings of Tan in view of Rolando and Cai are presented previously in this Office action and are fully incorporated here. Tan, Rolando and Cai do not teach a method wherein the reaction is incubated for at least about 90 minutes, or wherein the pyrophosphatase is present at between 0.2 and 0.4U/ul.
Mahfouz teaches a similar RT-LAMP coupled CRISPR-Cas12 module for the rapid sensitive detection of SARS-COV-2 (title, abstract and throughout). The reference teaches an embodiment that is a one-pot detection reaction wherein pyrophosphatase is present in the reaction mixture at 0.4U/uL, and the reaction mixture is incubated in a 96-well plate at 56C for 1-2 hours; p 76, lines 14 and following.
It would have been prima facie obvious to have modified the method taught by Tan in view of Rolando and Cai by employing the reaction conditions taught by Mahfouz in order to provide a true “one-pot” detection system for the detection of target virus. One would have been motivated to do so because a one-pot system has fewer opportunities for contamination and is simpler to implement.
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Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/Primary Examiner, Art Unit 1682