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 .
Claims 40-43, 46, 48, 51-52, 54-55, 57-64, 94-96 and 100-102 are pending and are being examined on the merits.
Preliminary Amendment
The Preliminary Amendment filed May 3, 2024 is acknowledged.
Information Disclosure Statement
The Information Disclosure Statement submitted July 30, 2024 has been considered.
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 40-43, 46, 48, 51-52, 54-55, 57-64, 94-96 and 100-102 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 40 recites the limitation “restricting movement of the blocking construct relative
to the SBO construct to inhibit generation of a reverse complement of the barcode construct with the blocking construct”, the meaning of which is unclear. Specifically, it is not clear if “restricting movement” refers to designing the blocking construct so that it hybridizes to the SBO construct in such a way as to prevent extension by a polymerase, or if it is intended to mean perhaps some type covalent bonding or something else. The instant specification describes an embodiment of “restricting movement” at para. 69 where the oligonucleotide comprises one or more LNAs which creates a more rigid structure. However, it is unclear what other structural arrangements are referred to by “restricting movement.” Since the ordinary artisan would not be able to determine the metes and bounds of the claim, it is indefinite.
Claims 41-43, 46, 48, 51-52, 54-55, 57-64 and 101-102 depend directly or indirectly from claim 40 and consequently incorporate the indefiniteness issues of claim 40.
Claim 59 recites the limitation “increasing an affinity between the SBO construct and the blocking construct”, the meaning of which is unclear. Specifically, the affinity is being increased relative to what metric? Since the ordinary artisan would not be able to determine the metes and bounds of the claim, it is indefinite.
Claim 94 recites the limitation “a blocking construct”, the meaning of which is unclear. Specifically, it is not clear what the blocking construct is intended to be capable of blocking, and what structural components correspond to the “blocking” functional limitation. Since the ordinary artisan would not be able to determine the metes and bounds of the claim, it is indefinite.
Claims 95-96 and 100 depend from claim 94, and consequently incorporate the indefiniteness limitations of claim 94.
Prior Art
Independent claims 94 and 40 are free of the art. Claim 94 recites, in part, a kit comprising a cleavable substrate with two portions, a substrate barcoded oligonucleotide comprising a first oligonucleotide which comprises a barcode and which is connected to the first portion of the substrate via a first linker, and a blocking construct comprising a second oligonucleotide which is complementary to at least a portion of the first oligonucleotide and which is connected to the second portion of the substrate via a second linker. Claim 40 recites a method for assessing enzymatic activity using the claim 94 kit components, where an enzyme contacts and cleaves the substrate, thus releasing the blocking construct from the substrate barcoded oligonucleotide. Dependent claims further recite amplifying and detecting the barcode sequence.
The closest prior art is Boutet1 (US Patent App. Pub. No. 2019/0323088 A1). Boutet is
directed to compositions and methods for processing nucleic acids, including the use of sample-specific barcode sequences. Boutet teaches coupling first and second tagged oligonucleotides, where the coupling can comprise hybridization of complementary sequences on the first and second tags, ligation, chemical binding, etc. (para. 228). Boutet also teaches hybridizing an additional oligonucleotide to the barcoded oligonucleotide and extending the additional oligonucleotide with an amplification enzyme (paras. 120-121). Boutet further teaches that the barcoded oligonucleotides can be coupled to various moieties, including peptides, lipophilic or amphiphilic moieties, and small molecules (e.g., paras. 5, 26, 115, 117, 120, 150 and 180), but does not explicitly teach that any of these moieties are enzyme substrates.
Additional relevant art includes Corn (US Patent App. Pub. No. 2006/0211024 A1), Peter (US Patent No. 9834814 B2), Blazej2 (WO 2017/177153 A1) and Dawson (US 2022/0249597 A1).
Each of these references teach one or more of the various components of the instantly recited substrate complex and method, however, none of the references teach all of the components, and there does not appear to be any reason to modify these various references to select the particular combinations of the instant components and method steps to arrive at the claimed invention. Thus, the instant claims are free of the art.
Conclusion
Claims 40-43, 46, 48, 51-52, 54-55, 57-64, 94-96 and 100-102 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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/CAROLYN L GREENE/Primary Examiner, Art Unit 1681
1 Boutet was cited in the Information Disclosure Statement submitted July 30, 2024.
2 Blazej was cited in the Information Disclosure Statement submitted July 30, 2024.
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