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 .
Status of the Application
The Amendment and Response and the Request for Continued Examination, each filed July 25, 2025, are acknowledged. The Amendment and Response filed July 25, 2025 is also acknowledged.
Claims 1, 3-6, 8-9, 11-12, 14-15, 17-19, 22-23, 25-28, 30-31, 33, 35, 37-38, 40-46 and 48 were pending. Claims 1, 3-6, 8-9, 11-12, 14-15, 17-19, 22-23, 25-28, 30-31, 33, 35, 37-38 and 40-45 are being examined on the merits. Claims 46 and 48 are rejoined, and are also being examined on the merits.
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 final rejection. 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on July 25, 2025 has been entered.
Election/Restrictions
The Examiner has re-considered the Requirement for Unity of Invention mailed April 4, 2024 in view of the claim amendments and is withdrawing the Requirement. Thus, claims 46 and 48 are hereby rejoined and fully examined for patentability under 37 CFR 1.104.
Because all claims previously withdrawn from consideration under 37 CFR 1.142 have been rejoined, the restriction requirement as set forth in the Office action mailed on April 4, 2024 is hereby withdrawn. In view of the withdrawal of the restriction requirement as to the rejoined inventions, applicant(s) are advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application. Once the restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Response to Arguments
Applicant’s arguments filed July 25, 2025 have been fully considered.
The following objections are WITHDRAWN in view of Applicant’s arguments and amendments to the claims:
Objection to claim 15
The following rejection are MODIFIED in view of Applicant’s arguments and claim amendments:
Rejection of all pending claims under 35 USC § 112(a), lack of enablement
Response to arguments regarding lack of enablement rejections
The Examiner acknowledges Applicant’s arguments, and agrees that the instant claim amendments address the lack of enablement rejections in the Final Office Action mailed March 26, 2025. However, the instant claim amendments raise new lack of enablement issues. The rejections below are modified in view of the instant claim amendments.
Claim Interpretation
Independent claim 1 comprises, in part, the following:
Step (a)(i): a first CRISPR/Cas complex, comprising a first Cas-based nickase and a first guide molecule that guides the first CRISPR/Cas complex to bind to a first strand of a double-stranded target nucleic acid at a first location and nick the first strand at a first cutting site; and a corresponding second CRISPR/Cas complex with a corresponding second Cas-based nickase and second guide molecule that bind to a second location on the second strand and nick a second cutting site.
Step (a)(iii): a primer pair, where the first primer comprises a nucleotide sequence that is complementary to a region downstream of the first cutting site on the first target nucleic acid and a nucleotide sequence that enables regeneration of the first guide molecule binding site upon extension, and a corresponding second primer with a complementary region and nucleotide sequence that correspond to the second target nucleic acid and the second guide molecule binding site.
Step (b) (i): nicking a first strand of a double-stranded nucleic acid at the first target nucleic acid location with a first CRISPR/Cas complex and nicking a second strand of a double-stranded nucleic acid at the second target nucleic acid location with a second CRISPR/Cas complex. The resulting structure is shown in instant Fig. 1, second pane:
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Step (b) (ii): extending the nicked strands from the 3’ ends of each of the first and second strand cutting sites with a strand-displacing polymerase, as shown in Fig. 1, third pane:
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… thereby displacing the downstream strand and generating single-stranded DNA, as follows (for simplicity, only the top/first displaced strand is labeled):
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Step (b) (iii): annealing the first primer (P1) to the single-stranded DNA displaced from the first strand downstream of the first cutting site, … and extending the primer[] across the region between the first and second cutting sites to generate a double-stranded amplified product comprising the target nucleic acid sequence between the first and second guide molecule binding sites (for simplicity, only the top/first displaced strand is labeled):
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Claim Rejections - 35 USC § 112
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.
Claims 1, 3-6, 8-9, 11-12, 14-15, 17-19, 22-23, 25-28, 30-31, 33, 35, 37-38, 40-46 and 48 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
In considering whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is “undue,” the factors set forth in In re Wands (858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)) should be considered. These factors are:
The breadth of the claims,
The nature of the invention,
The state of the prior art,
The level of one of ordinary skill in the art,
The level of predictability in the art,
The amount of direction provided by the inventor,
The existence of working examples; and
The quantity of experimentation needed to make or use the invention based on the content of the disclosure.
Each of these will be discussed in turn below.
Nature of the Invention and the Breadth of the Claims
The invention of independent claim 1 is directed to a method of amplifying and detecting a target double-stranded nucleic acid comprising, in part, combining the target nucleic acid with first and second CRISPR/Cas complexes having first and second Cas-based nickases, respectively, and a strand-displacing polymerase. In subsequent steps, the Cas-based nickases nick the target nucleic acid thus creating sub-strands of the target nucleic acid, while the polymerase extends each sub-strand that is located 5’ of a nick and simultaneously displaces each sub-strand that is 3’ of a nick. Claim 1 also recites an additional amplification step where a primer is annealed to each displaced sub-strand and is extended toward the nick site. Finally, claim 1 additionally recites that each of the first and second primer comprises a nucleotide sequence that enables regeneration of the first and second, respectively, guide molecule binding site upon extension. However, since the first and second primers are complementary to and thus anneal to the first and second strand of the target nucleic acid, respectively, and the first and second primers additionally anneal downstream of their corresponding cutting sites, then each primer will anneal to the corresponding displaced sub-strand of the original molecule. Since each displaced sub-strand is no longer attached to the portion of the original molecule which comprises the corresponding guide molecule binding site, it is not possible for the primers to enable regeneration of the site upon extension, as required by claim 1. This is shown above in the claim interpretation step (f). That is, the primer will extend until it reaches the cut site, as the guide molecule binding site is no longer attached to the displaced sub-strand.
The dependent claims further define the first and second target locations (claim 3), amplification conditions (claims 4, 17-19), characteristics of the Cas-based nickases (claims 5-6, 8-9, 11-12, 14-15), characteristics of the target nucleic acid sequence and the sample (claims 22-23, 28, 30-31, 33, 35, 37-38, 40), characteristics of the primers (claim 25), and downstream processing steps (26-27).
In addition, independent claim 41 is directed to a system for amplifying and/or detecting a target double-stranded nucleic acid, where the limitations correspond closely to the method steps in claim 1. Dependent claims 42-45 are directed to aspects of the system that correspond to some of the aspects of the dependent method claims, and dependent claims 46 and 48 are kits directed to the claim 41 system components.
In view of the disclosure in the specification, the claims are not overly broad.
The State of the Prior Art
Claims 1 and 41 are directed to a method and system, respectively, that essentially use a nicking and extension amplification reaction (NEAR) system, but where the nicking is performed by CRISPR/Cas complexes and Cas-based nickases. Mandell1 (WO 2016/077350) teaches using CRISPR/Cas complexes for amplifying target nucleic acids (e.g., Figs. 1A-1C; paras. 14-15, 28, 60-61, 66-68, 87, 90), while Maples2 (US Patent App. Pub. No. 2009/0017453) teaches NEAR (e.g., Figs. 1A-1C). However, the prior art does not teach sets of primers that have the structures recited in claims 1 and 41, and that function to amplify the target nucleic acid in the manner stated in the claims.
Level of One of Ordinary Skill in the Art
One of ordinary skill in the art would have the knowledge equivalent to a graduate-level degree in molecular biology.
Level of Predictability and Amount of Direction Provided by Inventor
While the level of predictability in the art of assays involving nucleic acid amplification is generally high, the specification does not provide any teaching relating to an assay wherein the sets of primers that have the structures recited in claims 1 and 41 function to amplify the target nucleic acid in the manner stated in the claims.
Existence of Working Examples
The specification provides one working example (paras. 240-246) directed to the using the combined CRISPR and NEAR methods to amplify a target nucleic acid, as well as the use of SHERLOCK detection to detect the amplification products. However, the specification does not provide the sequence or structure of the target nucleic acid, the various CRISPR components (e.g., the guide molecule) or the primers.
Quantity of Experimentation Needed to Make or Use the Invention Based on the Content of the Disclosure
Considering the disclosures in the specification as a whole, to make and use the invention of instant claims 1 and 41, one of ordinary skill in the art would have to determine how to perform a method or generate a system, respectively, directed to a nicking and extension amplification reaction (NEAR) method which is modified so that the nicking is performed by CRISPR/Cas complexes and Cas-based nickases, and further, to do so with the primer and guide molecule structures described in the claims 1 and 41. As noted above, these primers do not have the capability to function in the method in such a way as to participate in amplification in the described manner, or to interact with the guide molecule binding site limitations, as described. Therefore, the ordinary artisan would have to experiment in order to identify additional steps or structures that would function to allow, e.g., the first primer to anneal to the displaced first strand, which does not comprise the first guide molecule binding site, and somehow still regenerate the first guide molecule binding site during primer extension. Neither the specification, nor the art teaches the ordinary artisan how to do that. If the teachings in the specification provide no more than a “plan” for those of skill in the art to experiment using the technology, the entire breadth of the claims are not enabled. MPEP 2164.06(b).
Claims 3-6, 8-9, 11-12, 14-15, 17-19, 22-23, 25-28, 30-31, 33, 35, 37-38 and 40 depend directly or indirectly from claim 1, and consequently incorporate the lack of enablement issues of claim 1.
Claims 42-46 and 48 depend directly or indirectly from claim 41, and consequently incorporate the lack of enablement issues of claim 41.
For the above reasons, one of ordinary skill in the art would not be able to make and use the claimed invention without undue experimentation.
Appropriate correction is required.
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 17, 26-28 and 43 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.
Claims 26 and 27 each contain the trademark/trade name “SHERLOCK”, while claims 17 and 43 each contain the trademark/tradename “WarmStart”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name “SHELROCK” is used to identify/describe the source of a nucleic acid assay while trademark/trade name “WarmStart” is used to identify/describe the source of an enzyme and, accordingly, the identifications/descriptions are indefinite.
Claim 28 depends from claims 26 and 27 and consequently incorporate the indefiniteness issues of these claims.
Conclusion
Claims 1, 3-6, 8-9, 11-12, 14-15, 17-19, 22-23, 25-28, 30-31, 33, 35, 37-38, 40-46 and 48 are being examined, and are rejected. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached on 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CAROLYN L GREENE/Examiner, Art Unit 1681
1 Mandell was cited in the PTO-892 Notice of References Cited mailed August 27, 2024.
2 Maples was cited in the Information Disclosure Statement submitted November 9, 2023.