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 .
DETAILED ACTION
Pursuant to a preliminary amendment filed February 2, 2026, claims 1, 2, 7, 9, 10, 12, 13, 22, 23, 30, 38, 50, 53-57 and 60 are currently pending in the instant application.
Response to Election/Restriction
Applicant's election without traverse of Group I, claims 1, 2, 7, 9, 10, 12, 13, 53-57 and 60, directed to a complex; and the election of Species as follows:
Species (A): wherein the first protein binding moiety is a first aptamer, antibody, antigen-binding antibody fragment or receptor; and the second protein binding moiety is a second is an aptamer, antibody, antigen-binding antibody fragment or receptor (claim 2);
Species (B): wherein the substrate polynucleotide barcode and the protein polynucleotide barcode are different and comprise substantially non-complementary sequences (claim 60);
Species (C): wherein the analyte is a protein or a protein fragment (claim 55); and
Species (D): further comprising crosslinking the first protein-binding moiety with the second protein binding moiety (claim 50), in the reply filed February 2, 2026 is acknowledged.
Claims 22, 23, 30, 38 and 50 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim.
Claims 7, 10, 12, 53, 54, 56, and 57 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim.
Therefore, claims 1, 2, 9, 13, 55 and 60 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed October 5, 2022 is a DIV of US Patent Application 17/169352 (now abandoned), filed February 5, 2021, which is a CON of PCT/US2020/14449, filed January 21, 2020, which claims the benefit of US Provisional Patent Application 62795474, filed January 22, 2019.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on December 20, 2022; April 7, 2023; June 7, 2023; and February 2, 2026 have been considered. Initialed copies of the IDSs accompany this Office Action.
Claim Objections/Rejections
Specification Objection
The disclosure is objected to because of the following informalities: the as-filed Specification, filed October 5, 2022, does not include the current status of US Patent Application No. 17169352 (now abandoned).
Appropriate correction is required.
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 1, 2, 9, 13, 55 and 60 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 1 is indefinite for the recitation of the term “are both bound to an analyte” such as recited in claim 1, lines 7-8 because the specific structure of the complex is unclear. For example, it is unclear whether the first protein-binding moiety (pbm1) and the second protein-binding moiety (pbm2) are bound to one another, to the same analyte, to different analytes, etc. such as, for example:
substrate---pbm1---analyte---pbm2;
substrate---pbm1—analyte and pbm2—analyte (or substrate---pbm2—analyte);
analyte—pbm2---substrate---pbm1—analyte, etc.; whether each component is directly bound or attached to a substrate, protein-binding moiety, analyte, barcode, etc. and/or whether the complex comprises other components such as spacers, linkers, UMI, tags, etc. and, thus, the metes and bounds of the claim cannot be determined.
Claim 13 is indefinite for the recitation of the term “comprises a polymerase comprising a labeled nucleotide at a 3’-end of said oligonucleotide” such as recited in claim 13, lines 2-3 because the specific structure of the complex comprising a polymerase is unclear. It is unclear how the oligonucleotide hybridized to the protein polynucleotide barcode comprises a polymerase enzyme comprising a labeled nucleotide at the 3’-end of said oligonucleotide and, thus, the metes and bounds of the claim cannot be determined.
Claim 60 is indefinite for the recitation of the term “are different comprise substantially non-complementary sequences” such as recited in claim 60, lines 2-3 because the claim appears to be missing words that might clarify the meaning of the claim language, such that the meaning of the claim is unclear and, thus, the metes and bounds of the claim cannot be determined.
Claims 2, 9 and 55 are indefinite insofar as they ultimately depend from instant claim 1.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 2, 9, 13, 55 and 60 are rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Mirkin et. al. (hereinafter “Mirkin”) (US Patent Application Publication 20100081134, published April 1, 2010).
Regarding claims 1 and 9, Mirkin teaches screening methods, compositions, and kits for detecting for the presence or absence of one or more target analytes, e.g. biomolecules, in a sample including methods that utilize reporter oligonucleotides as biochemical barcodes for detecting multiple protein structures or other target analytes in a solution (Abstract). Mirkin teaches providing a substrate; providing one or more types of particle probes, each type of probe comprising a particle having one or more specific binding complements to a specific target analyte and one or more DNA barcodes bound thereto, wherein the specific binding complement of each type of particle probe is specific for a particular target analyte, and the DNA barcode for each type of particle probe serves as a marker for the particular target analyte (first and second protein binding moieties attached to a substrate; barcodes; oligonucleotides comprising labels, claims 1 and 9) (paragraph [0009]). Mirkin teaches in Figure 1A, a DNA/Au nanoparticle-based protein detection scheme, wherein (A) shows the preparation of hapten-modified nanoparticle probes; and (B) shows protein detection using protein binding probes (paragraph [0099]; Figure 1A and 1B), Figures 1A and 1B are shown below:
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Mirkin teaches that an antibody such as immunoglobulin E (IgE) or immunoglobulin G1 (IgG 1) shown in the Examples below can be detected with oligonucleotide-modified probes prehybridized with oligonucleotide strands modified with the appropriate hapten (biotin in the case of lgG and dinitrophenyl (DNP) in the case of IgE as shown in Figure 1A) (interpreting beads as a substrate; hapten, biotin, and DNP as detectable labels bound to the 3’-end of an oligonucleotide and hybridized to the barcodes to form a protein-binding moieties bound to barcodes; and modified probes as first and second protein-binding moieties, claims 1, 2 and 9) (paragraph [0266]; and Figure 1A).
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Figure 1B
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Regarding claims 2 and 55, Mirkin teaches that the specific binding complement and the target analyte are members of a specific binding pair which comprise nucleic acid, oligonucleotide, peptide nucleic acid, polypeptide, antibody, antigen, carbohydrate, protein, peptide, amino acid, hormone, steroid, vitamin, drug, virus, polysaccharides, lipids, etc. (interpreting the protein binding moieties, and analytes are proteins, antibodies, receptors, etc., claims 2 and 55) (paragraph [0254], lines 1-6).
Regarding claim 13, Mirkin teaches oligonucleotide-nanoparticle conjugates prepared using linkers comprising a steroid residue attached to a cyclic disulfide have unexpectedly been found to be remarkably stable to thiols (e.g., dithiothreitol used in polymerase chain reaction (PCR) solutions) as compared to conjugates prepared using alkanethiols or acyclic disulfides as the linker (interpreted as comprising a polymerase, claim 13) (paragraph [0148], lines 5-10). Mirkin teaches polymerase chain reaction (PCR) for barcode DNA amplification (Step 4, Figure 6B), wherein isolated barcode DNA is added to the PCR reaction mixture (interpreted as comprising a polymerase, claim 13) (paragraph [0361], lines 1-2). Mirkin teaches the use of Taq DNA polymerase for a final extension (paragraph [0362]).
Regarding claim 60, Mirkin teaches that the DNA barcode in each type of particle complex probe has a sequence that is different and that serves as an identifier for a particular target analyte (interpreted as the protein polynucleotide barcode and the substrate polynucleotide barcode are different, claim 60) (paragraph [0060]).
Mirkin meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Claims 1, 2, 9, 13, 55 and 60 are rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Chee et. al. (hereinafter “Chee”) (US Patent Application Publication 20190145982, published May 16, 2019; also published as WO2017/192633, filed May 2, 2017).
Regarding claims 1, 2, 9, 13 and 55, Chee teaches in Figure 2A, and the following steps, Step 1: immobilize protein with associated recording tag; Step 2: bind antibody-coding tag; and Step 3: transfer information from coding tag to recording tag (interpreted as a solid support comprising a first protein-binding moiety comprising a barcode; a second protein-binding moiety comprising a barcode, claim 1) (Figure 2A). Figure 2A is shown below:
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Chee teaches in Figure 2C, the immobilization of a protein by capture agent on a solid support (interpreted as a solid support comprising a first protein-binding moiety comprising a barcode; a second protein-binding moiety are antibodies comprising a barcode; and the analyte is a protein, claims 1, 2 and 55) (Figure 2C). Figure 2C (in part) is shown below:
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Chee teaches method using multiple cycles of binding agents such as antibodies, anticalins, N-recognins proteins, aptamers, etc. (and variants/homologues thereof) comprising coding tags interacting with an immobilized protein that is co-localized or co-labeled with a single or multiple recording tags, wherein a recording tag is comprised of a universal priming site, a barcode (e.g., partition barcode, compartment barcode, fraction barcode), an optional unique molecular identifier (UMI) sequence, and a spacer sequence (Sp) used in information transfer of the coding tag, such that the spacer sequence (Sp) can be constant across all binding cycles, be binding agent specific, or be binding cycle number specific; and the coding tag is comprised of an encoder sequence providing identifying information for the binding agent, an optional UMI, and a spacer sequence that hybridizes to the complementary spacer sequence on the recording tag, facilitating transfer of coding tag information to the recording tag (e.g., primer extension, also referred to herein as polymerase extension) (interpreted as a solid support comprising a first protein-binding moiety comprising a barcode; a second protein-binding moiety comprising a barcode; and a polymerase, claim 1) (paragraph [0257]). Chee teaches that the substrate can comprise barcoded beads, where Figure 13B illustrates specific amino acid residues on the peptides are chemically labeled with DNA coding tags that are conjugated to site-specific labeling moieties, such that the DNA coding tags comprise amino acid barcode information and optionally an amino acid UMI (interpreted as a substrate barcode; comprising labels; and beads, claims 1 and 9) (paragraph [0268]; and Figures 13A-E). Chee teaches in Figures 17A-B show: (A) a plurality of extended recording tags representing a plurality of peptides; and (B) an exemplary method of target peptide enrichment via standard hybrid capture techniques, wherein hybrid capture enrichment can use one or more biotinylated "bait" oligonucleotides that hybridize to extended recording tags representing one or more peptides of interest ("target peptides") from a library of extended recording tags representing a library of peptides (interpreting biotin bait tags as labeled oligonucleotides that hybridize to a barcode sequence; and at the 3’-end of the oligonucleotide, claim 1) (paragraph [0272], lines 1-9; and Figures 17A-B).
Regarding claim 60, Chee teaches that the plurality of compartment tags are the same within an individual compartment and are different from the compartment tags of other compartments (interpreted as barcodes having different sequences, claim 60) (paragraph [0117]). Chee teaches that Figure 20(B) shows that the universal DNA tagged-polypeptides are hybridized to nucleic acid molecules bound to bead, wherein the nucleic acid molecules bound to an individual bead comprise a unique population of compartment tags (barcode sequences) (interpreted as barcodes having different sequences, claim 60) (paragraph [0275], lines 12-17; and Figure 20B). Chee teaches that coding tags A and B, and coding tags C and D are different in sequence, and are also of different length (interpreted as barcodes having different sequences, claim 60) (paragraph [0279]).
Chee meets all the limitations of the claims and, therefore, anticipates the claimed invention.
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, 2, 9, 13, 55 and 60 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over: Claims 22-28 of copending US Patent Application 18/365476, which teaches a solid support, comprising: a first biomolecule-specific binding agent attached to the solid support; a second biomolecule-specific binding agent attached to the solid support via a cleavable linker, wherein the cleavable linker is a divalent linker comprising one or more cleavable sites, wherein the second biomolecule-specific binding agent comprises a detectable moiety (claim 22); and further comprising oligonucleotides (claim 24).
Although the claims at issue are not identical, they are not patentably distinct from each other because the copending claims of US Application 18/365476 encompass a first protein binding moiety attached to a substrate; a second polynucleotide barcode attached to the substrate or the first protein binding moiety; a second protein binding moiety comprising a protein polynucleotide barcode; both binding moieties are bound to an analyte; and a labeled oligonucleotide hybridized to the protein polynucleotide barcode.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Claims 1, 2, 9, 13, 55 and 60 are rejected.
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/AMY M BUNKER/Primary Examiner, Art Unit 1684