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 Claims
Claims 1, 2, 7, 9, 10, 12, 13, 53-57 and 61-66 are currently pending. Claims 1 and 13 have been amended by Applicants’ amendment filed 05-21-2026. Claims 22, 23, 30, 38, 50 and 58-60 have been canceled by Applicants’ amendment filed 05-21-2026. Claims 61-66 have been added by Applicants’ amendment filed 05-21-2026.
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 was previously acknowledged.
Regarding newly submitted claim 66, the claim is directed to an invention that is independent or distinct from the invention originally claimed for the following reasons: Newly submitted claim 66 is directed to a composition comprising the complex of claim1 and a second complex on the same substrate, wherein the second complex comprises a third protein-binding moiety; a fourth protein-binding moiety; and an oligonucleotide hybridized to the second protein polynucleotide comprising a fluorescent label (claim 66). Claim 1 of the claims filed 02-24-2023 was directed to a complex comprising a substrate, a first protein-binding moiety, a substrate polynucleotide barcode, a second protein-binding moiety comprising a protein polynucleotide barcode, and an oligonucleotide comprising a label (clam 1). Claim 22 of the claims filed 02-24-2023 was directed to a method, comprising: applying different electrical fields to each detection device; and identifying cells that pass through the fluidic channel (claim 9). Claim 58 of the claims filed 02-24-2023 was directed to a complex comprising: a substrate; a first protein-binding moiety; a first oligonucleotide attached to the substrate; a second protein-binding moiety comprising a second oligonucleotide, wherein said first oligonucleotide and said second oligonucleotide are different; an analyte; wherein the first protein binding moiety and the second protein-binding moiety are both bound to an analyte (claim 58). Claim 59 of the claims filed 02-24-2023 complex comprising: a substrate; a first protein-binding moiety attached to the substrate; a first oligonucleotide attached to the first protein-binding moiety a second protein-binding moiety comprising a second oligonucleotide, wherein said first oligonucleotide and said second oligonucleotide are different; an analyte; wherein the first protein-binding moiety and the second protein-binding moiety are both bound to an analyte (claim 59). Thus, newly submitted claim 66 requires a search and examination beyond the claims as originally presented, and constructively elected. The different species of methods and/or compositions would require a different field of search; the prior art applicable to one species would not likely be applicable to another species; and/or the species are likely to raise different non-prior art issues under 35 U.S.C. 101 and/or 35 U.S.C. 112(a). For example, the limitations of newly submitted claim 16 recites an independent and distinct cell preparation system comprising different system components as compared to the elected invention of instant claim 1 of the claims filed June 6, 2022.
As noted in MPEP 818.02(a), wherein subsequently presented claims to an invention other than that acted upon should be treated as provided in MPEP § 821.03. As recited in MPEP 821.04 (¶ 8.04), since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits.
Accordingly, newly submitted claim 66 is withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
Claims 22, 23, 30, 38 and 50 were previously withdrawn, and claim 66 is newly 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. Applicant timely traversed the restriction (election) requirement in the reply filed on September 23, 2019.
Claims 7, 10, 12, 53, 54, 56, and 57 were previously withdrawn, and claims 62, 63 and 65 are newly 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.
Please Note: in the reply filed February 2, 2026, Applicant elected for Species (A), wherein the first protein binding moiety is a first aptamer, antibody… or receptor (claim 2). Thus, claim 63 is withdrawn as being directed to a non-elected species. Applicant elected for Species (B), wherein the substrate polynucleotide barcode and the protein polynucleotide barcode are different and comprise substantially non-complementary sequences (claim 60). Thus, claims 64 and 65 are withdrawn as being directed to a non-elected species. Applicant elected for Species (D), the method of claim 1, further comprising crosslinking the first protein-binding moiety with the second protein binding moiety (claim 50). Thus, claims 13 and 62 are withdrawn as being directed to a non-elected species.
The restriction requirement was deemed proper and was made FINAL.
The restriction requirement was deemed proper and was made FINAL.
A complete reply to the final rejection must include cancellation of nonelected claims or other appropriate action (37 CFR 1.144) See MPEP § 821.01.
Therefore, claims 1, 2, 9, 55 and 61 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.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed May 21, 2026 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection not specifically addressed below are herein withdrawn.
Claim Rejections - 35 USC § 102
The rejection of claims 1, 2, 9 and 55 is withdrawn 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).
Mirkin does not specifically exemplify the barcodes as recited in claim 1.
In view of the withdrawn rejection, Applicant’s arguments are rendered moot.
The rejection of claims 1, 2, 9 and 55 is withdrawn 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).
Chee does not specifically exemplify the complex as recited in claim 1.
In view of the withdrawn rejection, Applicant’s arguments are rendered moot.
Maintained Objections/Rejections
Claim Interpretation: the components of the complex as recited in claim 1 are interpreted to be attached/bound to the substrate and/or attached/bound one to another either directly or indirectly, except as clearly recited in claim 1.
The term “bound to the same analyte” as recited in claim 1 is interpreted to refer to: (i) a first protein-binding moiety and a second protein-binding moiety being bound to the same analyte molecule (e.g., both bound to a single protein) and/or (ii) to refer to a first protein-binding moiety and a second protein-binding moiety being bound to the same type of analyte (e.g., both are bound to antibodies).
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1, 2, 9 and 55 is maintained, and claim 61 is newly 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 “the oligonucleotide” such as recited in claim 1, line 9. There is insufficient antecedent basis for the term “the oligonucleotide” in the claim.
Claim 1 is indefinite for the recitation of the term “the protein polynucleotide barcodes” such as recited in claim 1, line 9. There is insufficient antecedent basis for the term “the protein polynucleotide barcodes” in the claim because claim 1, lines 6-7 recites the term “a protein polynucleotide barcode”. The Examiner suggests that Applicant amend the claim to recite, for example, “to the protein polynucleotide barcode.”
Claim 1 is indefinite for the recitation of the term “the same analyte” such as recited in claim 1, line 11. There is insufficient antecedent basis for the term “the same analyte” in the claim.
Claim 1 is indefinite for the recitation of the term “an oligonucleotide hybridized to the protein polynucleotide barcode” such as recited in claim 1, line 12 because it is unclear whether an oligonucleotide is hybridized to the polynucleotide barcodes of both the first protein-binding moiety and the second protein-binding moiety; or whether an oligonucleotide is hybridized to only one polynucleotide barcode of either the first protein-binding moiety or the second protein-binding moiety and, thus, the metes and bounds of the claim cannot be determined.
Claims 2, 9, 55 and 61 are indefinite insofar as they ultimately depend from instant claim 1.
Double Patenting
The provisional rejection of claims 1, 2, 9 and 55 is maintained, and claim 61 is newly provisionally rejected, on the ground of nonstatutory double patenting as being unpatentable over claims 22-28 of copending US Patent Application 18/365476 for the reasons of record.
Response to Arguments
Applicant’s arguments filed May 21, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) Applicant requests the Examiner to hold the rejections in abeyance until the copending application issues, if ever (Applicant Remarks, pg. 6, Double Patenting).
Regrading (a), Applicant did not specifically indicate how the claims of the copending applications recited supra are patentably distinct from the instant claims as required by 37 CFR 1.111(b). Thus, the claims remain rejected for the reasons already of record.
New Objections/Rejections
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, 55 and 61 are rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Gaublomme et. al. (hereinafter “Gaublomme”) (US Patent Application Publication 20180320224, published November 8, 2018) as evidenced by Hermanson et al. (hereinafter “Hermanson”) (Bioconjugate Technique, 2nd Edition, Chapter 9, 2008, 396-497; 10.1016/B978-0-12-370501-3.X0001-X). This is a new rejection necessitated by amendment of the claims in the response filed 05-21-2026.
Regarding claims 1 and 2, Gaublomme teaches high throughput methods of detecting proteins in single cells using barcoding, aptamers and single cell sequencing, wherein solid supports used in recording the cell-of-origin of target proteins and target proteins expressed in the cell-of-origin are disclosed (interpreting the solid support as a substrate, claim 1) (Abstract, lines 2-6). Gaublomme teaches an oligonucleotide-adorned solid support for the identification of proteins expressed in single cells, wherein the solid support comprises a plurality oligonucleotides, wherein each oligonucleotide comprising: a linker directly attached to the solid support; an identical sequence for use as a sequencing priming site; a uniform or near-uniform cell barcode sequence, which is the same across all oligonucleotides on said solid support (interpreted as a substrate barcode), but varies among the oligonucleotides on any other individual solid support; a uniform or near-uniform target barcode sequence, wherein the uniform or near-uniform target barcode sequence is specific to an individual aptamer (interpreted as protein polynucleotide barcode); and an aptamer specific to the target barcode sequence configured for binding to a target protein (interpreted as first and second protein-binding moieties), wherein the solid support binds to a plurality of target proteins (interpreting aptamers as protein-binding moieties; and interpreting target proteins as the analyte, claims 1 and 2) (paragraph [0007], lines 1-16). Gaublomme teaches that the oligonucleotides can be attached to a solid support, such as a binding surface (e.g., the surface of a microwell or of a microbead) via a linkage, which can comprise any moiety, functionalization, or modification of the binding surface and/or oligonucleotide that facilitates the attachment of the oligonucleotide to the surface (interpreted as an oligonucleotide comprising a linker to the support) (paragraph [0007], lines 19-25). Gaublomme teaches that each oligonucleotide can further comprise a Unique Molecular Identifier (UMI) which differs for each oligonucleotide, wherein the oligonucleotide-adorned solid support can further comprise a spacer between the aptamer and the oligonucleotide strand conjugated to said aptamer (interpreting the UMI as protein polynucleotide barcodes, claim 1) (paragraph [0007], lines 30-35). Gaublomme teaches that the oligonucleotide-adorned solid support comprises oligonucleotides further comprising a 6 to 12 nucleotide universal hybridization sequence on the opposite DNA strand as the aptamer, which is complementary to a hybridization sequence linked a set of second oligonucleotide linked affinity reagents, wherein the affinity reagents can comprise an aptamer, antibody or antibody fragment (interpreted as first and second protein binding moieties including aptamers, antibody, antibody fragments, claims 1 and 2) (paragraph [0009]). Gaublomme teaches a method of identifying proteins expressed in single cells comprising: segregating single cells with a solid support as described herein by a method comprising merging one uniquely barcoded bead with a single-cell in an emulsion droplet, microfluidic drop, or microwell, or a method comprising adding a single cell to a microwell comprising a barcoded surface, wherein the cells are lysed in a buffer that preserves highly specific aptamer-target recognition; incubating the lysed cells with the beads or surfaces thereby capturing expressed aptamer target proteins on each bead or surface; wherein beads are used, breaking droplets or isolating beads from microwells and pooling the beads in solution; washing the beads or surfaces, wherein unbound proteins are removed; cleaving the linkers; isolating oligo-aptamer protein complexes from oligo-aptamer molecules; and preparing and sequencing a single composite sequencing library, whereby the cell barcodes record the cell-of-origin of each oligonucleotide sequence and target barcodes record expressed proteins from the same cell (paragraph [0013]). Gaublomme teaches in Figure 2I, an illustration of an oligonucleotide for detecting protein interactions including showing that a target protein binds to aptamer 1; the oligonucleotide aptamer complexes are then incubated with second aptamer oligonucleotides comprising a complementary hybridization 3 sequence, protein 2 barcode, sequencing primer NXT3, spacer and aptamer 2, such that upon binding of the second aptamer oligonucleotide to a protein-protein complex, the hybridization 3 sequences can hybridize; wherein extension using the hybridization 3 sequence as a primer results in a sequence including the three barcodes and sequencing primer sites (interpreted as the complex of claim 1 comprising a substrate; aptamer 1 and aptamer 2 as a first and second protein-binding moieties comprising protein polynucleotide barcodes, a substrate polynucleotide barcode attached to the substrate, aptamer 1 and aptamer 2 bound to the same analyte; and an oligonucleotide hybridized to the protein polynucleotide barcode, claim 1) (paragraph [0039]; and Figure 2I]). Figure 2I is shown below:
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Gaublomme teaches that one or more nucleic acid identifiers such as a nucleic acid barcode can be attached or “tagged” to a target molecule (paragraph [0067], lines 1-3). Gaublomme teaches that highly conserved sequences present a technical limitation on some sequencing platforms that utilize fluorescent detection (i.e., Illumina). Gaublomme teaches other means for labeling, capturing, and detecting an origin-specific barcode include: incorporation of aminoallyl-labeled nucleotides, the incorporation of sulfhydryl-labeled nucleotide, the incorporation of allyl- or azide-containing nucleotides; as well as, many other methods described in Bioconjugate Techniques (2nd Ed), Greg T. Hermanson, Elsevier (2008), which is specifically incorporated herein by reference (interpreting sulfhydryl-labeled nucleotides to be fluorescently labeled, claim 1) (paragraph [0078], lines 11-15), where it is known fluorescent probes, labels, and dyes for labeling biomolecules including proteins are known in the art, wherein dyes and processes include fluorescently tagging biomolecules with fluoresceine, Dylight 488, Alexa 488, RPE-Texas Red, RPE-Alexa 750, and labeling sulfhydryl-containing oligonucleotide residues for antibody labeling as evidenced by Hermanson (pg. 396, last partial paragraph; pg. 434, second full paragraph; pg. 436, first and second full paragraphs; and pg. 463, Table 9.3).
Regarding claim 9, Gaublomme teaches that the solid support can be a bead (interpreting the substrate as a bead, claim 9) (paragraph [0008], line 1).
Regarding claim 55, Gaublomme teaches an aptamer specific to the target barcode sequence configured for binding to a target protein (interpreted as first and second protein-binding moieties), wherein the solid support binds to a plurality of target proteins (interpreting aptamers as protein-binding moieties; and interpreting target proteins as the analyte, claims 1 and 55) (paragraph [0007], lines 1-16). Gaublomme teaches covalently linking the aptamers to captured proteins after washing the beads or surfaces (interpreting proteins as analytes, claim 55) (paragraph [0014], lines 1-3). Gaublomme teaches incubating the captured oligo-aptamer protein complexes with a set of second oligonucleotide linked affinity reagents comprising: (i) an aptamer, antibody or antibody fragment, (ii) a sequencing primer sequence, (iii) a target barcode and (iv) a 6 to 12 nucleotide hybridization sequence, wherein when a second affinity reagent binds to an interacting protein the hybridization sequence binds to the universal hybridization sequence (interpreting proteins as analytes, claim 55) (paragraph [0023], lines 15-23).
Regarding claim 61, Gaublomme teaches that Figure 2A shows a common DNA primer comprising a photo-cleavable spacer and sequence primer NXT1 (interpreted as a cleavable linker, claim 61) (paragraph [0039], lines 1-4; Figure 2A). Gaublomme teaches that the oligonucleotides can also contain one or more cleavable spacers, e.g., photocleavable linker, wherein the oligonucleotide can be attached to a particle chemically (e.g., via a linker) or physically (e.g., without necessarily requiring a linker), e.g., such that the oligonucleotides can be removed from the particle via cleavage (interpreted as a cleavable linker, claim 61) (paragraph [0085], lines 7-14). Gaublomme teaches that a nucleic acid barcode can be cleavable from a specific binding agent, for example, after the specific binding agent has bound to a target molecule, wherein the origin-specific barcode further comprises one or more cleavage sites (interpreted as a cleavable linker, claim 61) (paragraph [0076], lines 1-5).
Gaublomme meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Claim Rejections - 35 USC § 103
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 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.
Claims 1, 2, 9, 55 and 61 are rejected under 35 U.S.C. 103 as being unpatentable over Gaublomme et. al. (hereinafter “Gaublomme”) (US Patent Application Publication 20180320224, published November 8, 2018) in view of Strauss et. al. (hereinafter “Strauss”) (US Patent Application Publication 20180253528, published September 6, 2018) as evidenced by Hermanson et al. (hereinafter “Hermanson”) (Bioconjugate Technique, 2nd Edition, Chapter 9, 2008, 396-497; 10.1016/B978-0-12-370501-3.X0001-X). This is a new rejection necessitated by amendment of the claims in the response filed 05-21-2026.
The teachings of Gaublomme as applied to claims 1, 2, 9, 55 and 61 are described supra.
Gaublomme does not specifically exemplify a fluorescently labeled nucleotide comprising cleavable linker (instant claim 61, in part).
Regarding claim 61 (in part), Strauss teaches that fluorescently labeled nucleotides can be added using a sequencing primer that has been added to a complementary region of each polynucleotide to be sequenced, wherein each type of nucleotide found in DNA, or RNA in some situations, can be coupled to a different fluorophore using a cleavable bond, such that for example each type of nucleotide, G, C, A, T, or U in the case of RNA, can be associated with a respective fluorophore, wherein the different fluorophores coupled to the nucleotides can emit electromagnetic radiation at different wavelength distributions; and that the first set of wavelengths can be different from a second set of wavelengths (interpreted as a fluorescently labeled nucleotide comprising cleavable linker, claim 61) (paragraph [0048]).
It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of fluorescently labeling polynucleotides as exemplified by Strauss, it would have been prima facie obvious for one of ordinary skill in the art at the time the invention was made to modify the method of detecting proteins in single cells using barcoded, tagged and/or labeled oligonucleotides attached to uniquely barcoded solid supports as disclosed by Gaublomme to include one or more different fluorophores coupled to an oligonucleotide through cleavable linkers as taught by Strauss with a reasonable expectation of success in producing fluorescently labeled polynucleotides; in selectively removing one or more fluorescent labels including from polynucleotide barcodes under different conditions such as the application of different wavelengths of light; and/or for the selective cleavage, amplification, and/or sequencing of oligonucleotide barcodes to determine the cell-of-origin for a particular protein.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly
rejected under 35 USC §103(a) as obvious over the art.
Conclusion
Claims 1, 2, 9, 55 and 61 are rejected.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMY M BUNKER whose telephone number is (313) 446-4833. The examiner can normally be reached on Monday-Friday (6am-2:30pm).
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/AMY M BUNKER/Primary Examiner, Art Unit 1684
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