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
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Status of Claims
Claims 6-18, 20-32 and 36-40 are currently pending. Claims 6 and 36-39 have been amended by Applicants’ amendment filed 05-19-2026. No claims have been added or canceled by Applicants’ amendment filed 05-19-2026.
Applicant elected Group II, claims 6-33 drawn to a method for preparing a population functionalized solid support; and the election of Species with traverse as follows:
Species (A): Applicant did not elect a species of method of claim 1 further comprising an additional step (claims 2 and 4);
Species (B): wherein reacting comprises reacting the nucleic acid molecule with a dinucleotide or a trinucleotide (claim 7);
Species (C): surface reactive nucleic acid molecules in sequences of a universal sequence, barcode, a UMI and a capture sequence (claim 9);
Species (D): wherein the nucleic acid molecules comprise one or more of oligonucleotides, nucleotides…surface reactive nucleic acid molecules (claim 25);
Species (E): wherein the solid support comprises a spacer, the spacer having a functional group exposed for reaction (claim 19);
Species (F): wherein the solid support comprises a bead that is a silica bead, a hydrogel bead or a magnetic bead (clam 14);
Species (G): wherein the spacer optionally comprises: (i) a polyethylene glycol polymer (PEG) (claim 21);
Species (H): wherein PEG has a molecular weight range of about 2,0000 to 10,000 Daltons (claim 23);
Species (I): wherein the spacer comprises a photolabile linker, a fluoride ion labile linker, or a cleavable linker (claim 26), in the reply filed on May 3, 2023 was previously acknowledged.
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election of invention has been treated as an election without traverse (MPEP
§ 818.03(a)).
Claims 1-5 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim.
Claims 8-18, 20-24 and 26-30 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 01-26-2023.
The restriction requirement was deemed proper and was made FINAL.
The claims will be examined insofar as they read on the elected species.
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 6, 7, 25 and 36-40 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed July 20, 2022 claims the benefit of multiple US Provisional Patent Applications including 62/876,909, filed July 22, 2019.
Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 120 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 the first paragraph of 35 U.S.C. 112. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosures of the prior-filed applications including US Provisional Patent Application 62/876,909, filed July 22, 2019 fails to provide adequate support or enablement in the manner provided by the first paragraph of 35 U.S.C. 112 for one or more claims of this application. The specific method steps recited in independent claim 6 does not have support for: “a second functional group of the heterobifunctional spacer is exposed distally from the activated surface” and “a nucleic acid capture sequence that is exposed distally from the activated surface” in lines 5-6 and 10-11.
Therefore, the priority date for the presently claimed invention is July 22, 2020, the filing date of US16/936,197.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed May 19, 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.
Maintained Objections/Rejections
Claim Interpretation: the term “exposed distally” as recited in claim 6 is interpreted to refer to a second, unprotected, functional group and/or capture sequence that are located at any distance from the activated surface.
The term “further comprises a dinucleotide or a trinucleotide” as recited in claim 7 to refer to a solid support comprising one or more oligonucleotides (individually/separately or in series); to refer to an additional sequence comprising dinucleotides and/or trinucleotides; and/or to refer to a reaction involving dinucleotides or trinucleotides (e.g., dNTPs in PCR, sequencing, etc.).
Double Patenting
The provisional rejection of claims 6, 7, 25 and 36-40 is maintained on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6-10, 12, 14-16, 19-23, 26, 28, 29, 32, 34-37, 39, 41-46, 48, 49, 51-53 and 57-59 of copending US Patent Application No. 16/758,504, for the reasons of record.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant’s arguments filed May 19, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) regarding US16/758,504, Applicant requests that the provisional double patenting rejections be held in abeyance (Applicant Remarks, pg. 8, second and third full paragraphs).
Regarding (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.
Claim Rejections - 35 USC § 112(b)
The rejection of claims 6, 7, 25 and 36-40 is maintained under 35 U.S.C. 112(b) paragraph as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claims 6, 7, 25, 38 and 39 are indefinite for the recitation of the term “the one or more oligonucleotides” such as recited in claim 6, line 10. There is insufficient antecedent basis for the term “the one or more oligonucleotide” in the claim because claim 6, line 8 recites the term “more than one oligonucleotide”. The Examiner suggests that Applicant amend the claim to recite, for example, “wherein each of the more than one oligonucleotides”, or “a plurality of oligonucleotides…wherein each of the plurality of oligonucleotides”.
Claim 6 is indefinite for the recitation of the term “the nucleic acid capture sequence is at an end of each oligonucleotide” such as recited in claim 6, line 13 because location of the capture sequence is completely unclear. The oligonucleotide is recited to comprise in order from the second functional group: a universal sequence, a barcode, a UMI, and the capture sequence, such that it is unclear whether the oligonucleotide comprises a capture sequence at the end of the oligonucleotide farthest from the surface of the solid support, or whether the capture sequence can be located at either end of the oligonucleotide (e.g., 3’, 5’, the end closest to the bead, and/or the end farthest from the bead) and, thus, the metes and bounds of the claim cannot be determined.
Claim 25 is indefinite for the recitation of the term “the capture sequence” such as recited in claim 25, line 5. There is insufficient antecedent basis for the term “the capture sequence” in the claim because claim 6, line 12 recites the term “a nucleic acid capture sequence.”
Claim 36 is indefinite for the recitation of the term “surface hydroxyl groups” such as recited in claim 36, line 2 because claim 36 depends from instant claim 6, wherein claim 6 does not recite that the surface of the solid supports comprise hydroxyl groups and, thus, the metes and bounds of the claim cannot be determined.
Claim 37 is indefinite for the recitation of the term “the solid supports” such as recited in claim 37, line 1. There is insufficient antecedent basis for the term “the solid supports” in the claim because claim 6, lines 8-9 recite that the solid supports comprising a heterobifunctional spacer are “functionalized solid supports.”
Claim 38 is indefinite for the recitation of the terms “via a photolabile linkage” and “to confirm sequence fidelity or yield” such as recited in claim 38, lines 4-5 because claim 38 depends from instant claim 6, wherein claim 6 does not recite that the heterobifunctional spacer comprises a photolabile linkage, and/or a determination of fidelity and/or yield and, thus, the metes and bounds of the claim cannot be determined.
Claim 39 is indefinite for the recitation of the term “the fluorescent probe binding to assess oligonucleotide density and distribution” such as recited in claim 39, lines 3-4 because it is unclear how measuring the binding between a portion of one or more oligonucleotides (e.g., a single oligonucleotide) provides an assessment of oligonucleotide density and distribution and, thus, the metes and bounds of the claim cannot be determined.
Claim 40 is indefinite for the recitation of the term “to select beads” such as recited in claim 40, line 2 because claim 40 depends from amended claims 6 and 38, wherein amended claims 6 and 38 recite the presence of a population of functionalized solid supports, such that the claims do not recite the presence of beads and, thus, the metes and bounds of the claim cannot be determined.
Claim Rejections - 35 USC § 112(d)
The rejection of claims 38 and 40 is maintained, and claims 7, 25, 36 and 39 are newly rejected, under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 7, 25, 38 and 39 recite (in part): “wherein each of the one or more oligonucleotides” in lines 1-2 because claims 7, 25, 38 and 39 depend from instant claim 6, wherein claim 6 recites the synthesis or attachment of more than on oligonucleotide. Thus, claim 7 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 36 recites (in part): “wherein activating the surface of the solid supports comprises activating surface hydroxyl groups” in lines 1-2 because claim 36 depends from instant claim 6, wherein claim 6 does not recite that the surface of the solid supports comprise hydroxyl groups. Thus, claim 36 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 40 recites (in part): “based on size gates to select beads having a uniform density of oligonucleotides” in lines 2-3 because claim 40 depends from amended claims 6 and 38, wherein claims 6 and 38 do not recite the presence beads, but instead recite “attaching more than one oligonucleotide to…to provide a population of functionalized solid supports” (claim 6) and “a population of functionalized solid supports” (claim 38). Thus, claim 40 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 102
The rejection of claims 6, 7, 25 and 37-40 is maintained under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Bent et al. (hereinafter “Bent”) (US Patent No. 10745742, issued August 18, 2020; filed December 21, 2018; effective filing date November 15, 2017; of record).
Regarding claim 6, Bent teaches methods of generating supports (e.g., beads) comprising barcode molecules coupled thereto, wherein the barcode can comprise a barcode sequence and a functional sequence, such that the barcode molecule can be generated using two or more ligation reactions in a combinatorial fashion; as well as, a support comprising two or more different barcode molecules can be useful for analyzing or processing one or more analytes such as nucleic acid molecules, proteins, and/or perturbation agents (interpreted as beads comprising barcodes bound to a bead, claim 6) (Abstract). Bent teaches that in cases where the polymer precursor material comprises a linear polymer material, such as a linear polyacrylamide, PEG, or other linear polymeric material, the activation agent can comprise a cross-linking agent, or a chemical that activates a cross-linking agent within the formed droplets, such that for polymer precursors that comprise polymerizable monomers, the activation agent can comprise a polymerization initiator (interpreted as activating a surface of solid supports with a reactive group; and reacting the surface with a heterobifunctional spacer, where the second functional group is exposed distally from the activated surface, claim 6) (col 49, lines 14-25). Bent teaches that the polymer or gel can include one or more of disulfide cross-linked polyacrylamide, agarose, alginate, polyvinyl alcohol, polyethylene glycol (PEG)-diacrylate, PEG-acrylate, PEG-thiol, PEG-azide, PEG-alkyne, other acrylates, chitosan, hyaluronic acid, collagen, fibrin, gelatin, or elastin, where the polymer or gel can comprise any other polymer or gel (interpreted as activating the surface with reactive groups, and reacting the activated surface with heterobifunctional spacers, claim 6) (col 50, lines 9-16). Bent teaches that the bead can comprise covalent or ionic bonds between polymeric precursors (e.g., monomers, oligomers, linear polymers), nucleic acid molecules (e.g., oligonucleotides), primers, and other entities (interpreted as covalent coupling to reactive groups, claim 6) (col 54, lines 25-29). Bent teaches that acrydite moieties can be modified with thiol groups capable of forming a disulfide bond or can be modified with groups already comprising a disulfide bond, wherein the thiol or disulfide (via disulfide exchange) can be used as an anchor point for a species to be attached, or another part of the acrydite moiety can be used for reversible attachment, such that when the disulfide bond is broken (e.g., in the presence of a reducing agent), and the attached species is released from the bead; and/or an acrydite moiety can comprise a reactive hydroxyl group that can be used for attachment (interpreted as forming reactive groups on an activated surface) (col 55, lines 6-17). Bent teaches that a first molecule (e.g., a first nucleic acid molecule) can be provided that is capable of attaching to a starter sequence attached to a bead, wherein the first molecule can be a nucleic acid molecule and/or can comprise an amino acid, peptide, polyethylene glycol (PEG) moiety, hydrocarbon chain, or another moiety (interpreted as a PEG linker; and comprising amine, hydroxyl, thiol, and methoxy groups, claims 6 and 37) (col 18, lines 15-20). Bent teaches that functionalization of beads for attachment of nucleic acid molecules (e.g., oligonucleotides) can be achieved through a wide range of different approaches, including activation of chemical groups within a polymer, incorporation of active or activatable functional groups in the polymer structure, or attachment at the pre-polymer or monomer stage in bead production (interpreted as activating the surface with reactive groups, and reacting the activated surface with heterobifunctional spacers; and attaching one or more oligonucleotides to a second functional group, claim 6) (col 55, lines 18-24). Bent teaches that precursors (e.g., monomers, cross-linkers) that are polymerized to form a bead can comprise acrydite moieties, such that when a bead is generated, the bead also comprises acrydite moieties, which can be attached to a nucleic acid molecule (e.g., oligonucleotide), which can include a priming sequence (e.g., a primer for amplifying target nucleic acids, random primer, primer sequence for messenger RNA) and/or one or more barcode sequences (interpreting acrydite moieties as a heterobifunctional spacer; interpreting the method as attaching one or more oligonucleotides to a second functional group; interpreted as comprising a barcode and a capture sequence; and exposed distally from the surface, claim 6) (col 55, lines 25-34). Bent teaches that Figure 8 illustrates an example of a barcode carrying bead, where nucleic acid molecule 802, such as an oligonucleotide, can be coupled to a bead 804 by a releasable linkage 806, such as a disulfide linker; and the same bead 804 can be coupled (e.g., via releasable linkage) to one or more other nucleic acid molecules 818, 820, such that the nucleic acid molecule 802 can be or comprise a barcode including a number of sequence elements described herein; as well as, a functional sequence 808, which can be used in subsequent processing (col 55, lines 59-67; and Figure 8). Figure 8 is shown below:
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Figure 8
Bent teaches that nucleic acid molecule 802 can comprise a functional sequence 808 that can be used in subsequent processing, wherein the functional sequence 808 can include one or more of a sequencer-specific flow cell attachment sequence such as a P5 sequence for Illumina sequencing systems (interpreted as a universal sequence) and a sequencing primer sequence (e.g., a R1 primer for Illumina sequencing systems) (interpreted as a universal sequence); and the nucleic acid molecule 802 can comprise a barcode sequence 810 for use in barcoding the sample (interpreted as comprising in order: a universal sequence, an origin-specific barcode, a UMI and a capture sequence, claim 6) (col 55, line 67; and col 56, lines 1-8). Bent teaches that the barcode sequence 810 can be bead-specific such that the barcode sequence 810 is common to all nucleic acid molecules (e.g., including nucleic acid molecule 802) coupled to the same bead 804; and/or alternatively or in addition, the barcode sequence 810 can be partition-specific (interpreted as attaching barcoded nucleic acids to a bead; and comprising well-specific barcodes, claim 6) (col 56, lines 9-14). Bent teaches that nucleic acid molecule 802 can comprise a specific priming sequence 812, such as an mRNA specific priming sequence (e.g., poly-T sequence), a targeted priming sequence, and/or a random priming sequence, wherein the nucleic acid molecule 802 can comprise an anchoring sequence 814 to ensure that the specific priming sequence 812 hybridizes at the sequence end (e.g., of the mRNA), such that the anchoring sequence 814 can include a random short sequence of nucleotides, such as a 1-mer, 2-mer, 3-mer or longer sequence, which can ensure that a poly-T segment is more likely to hybridize at the sequence end of the poly-A tail of the mRNA (interpreting the polyT sequence as a capture sequence; oligonucleotides further comprise dinucleotides or trinucleotides; and including an amplification primer, claims 6, 7 and 25) (col 56, lines 17-28). Bent teaches that the nucleic acid molecule 802 can comprise a unique molecular identifying sequence 816 (UMI), where the UMI can provide a unique identifier of the starting mRNA molecule that was captured in order to allow quantitation of the number of original expressed RNA (interpreted as comprising a UMI; and UMIs as origin-specific barcodes, claim 6) (col 56, lines 29-31 and 41-44). Bent teaches that the number of different UMIs can be indicative of the quantity of mRNA originating from a given partition, and thus from the biological particle (e.g., the cell) (interpreting UMIs as origin-specific barcodes, claim 6) (col 57, lines 9-12). Bent teaches that the addition of moieties to a gel bead after gel bead formation can be advantageous, where the addition of an oligonucleotide (e.g., barcoded oligonucleotide) after gel bead formation can avoid loss of the species during chain transfer termination that can occur during polymerization (col 58, lines 25-30). Bent teaches that a barcode molecule can comprise a functional sequence designed to interact with a particular nucleic acid sequence or type of sequence, for example, the functional sequence is selected from the group including universal primer sequences (interpreting 808 to comprise a universal sequence, claim 6) (col 21, lines 32-40). Bent teaches the activation of disulfide linkages within a bead (interpreted as activating a surface of a solid support including a bead, claim 6) (col 58, lines 4-5). Bent teaches the post-production functionalization of the bead with the oligonucleotide including through controlling loading ratios of species in beads (interpreted as activating a surface or a solid support, claim 6) (col 58, lines 43-45).
Regarding claim 7, Bent teaches that nucleic acid molecule 802 can comprise a specific priming sequence 812, such as an mRNA specific priming sequence (e.g., poly-T sequence), a targeted priming sequence, and/or a random priming sequence, wherein the nucleic acid molecule 802 can comprise an anchoring sequence 814 to ensure that the specific priming sequence 812 hybridizes at the sequence end (e.g., of the mRNA), such that the anchoring sequence 814 can include a random short sequence of nucleotides, such as a 1-mer, 2-mer, 3-mer or longer sequence, which can ensure that a poly-T segment is more likely to hybridize at the sequence end of the poly-A tail of the mRNA (interpreted as further comprising an amplification primer; and where the polyT sequence is a capture sequence; and oligonucleotides further comprise dinucleotides or trinucleotides, claims 6 and 7) (col 56, lines 17-28).
Regarding claim 25, Bent teaches that nucleic acid molecule 802 can comprise a specific priming sequence 812, such as an mRNA specific priming sequence (e.g., poly-T sequence), a targeted priming sequence, and/or a random priming sequence, wherein the nucleic acid molecule 802 can comprise an anchoring sequence 814 to ensure that the specific priming sequence 812 hybridizes at the sequence end (e.g., of the mRNA), such that the anchoring sequence 814 can include a random short sequence of nucleotides, such as a 1-mer, 2-mer, 3-mer or longer sequence, which can ensure that a poly-T segment is more likely to hybridize at the sequence end of the poly-A tail of the mRNA (interpreted as further comprising an amplification primer; and where the capture sequence is an oligo-dT, claim 25) (col 56, lines 17-28).
Regarding claim 36 (in part), Bent teaches that the attachment can be reversible, such that when the disulfide bond is broken (e.g., in the presence of a reducing agent), the attached species is released from the bead; and in other cases, an acrydite moiety can comprise a reactive hydroxyl group that can be used for attachment (interpreted as a hydroxyl group, claim 36) (col 55, lines 12-17).
Bent teaches that precursors comprising a functional group that is reactive or capable of being activated such that it becomes reactive can be polymerized with other precursors to generate gel beads comprising the activated or activatable functional group, wherein the functional group can then be used to attach additional species (e.g., disulfide linkers, primers, other oligonucleotides, etc.) to the gel beads, where some precursors comprising a carboxylic acid (COOH) group can co-polymerize with other precursors to form a gel bead that also comprises a COOH functional group; an acrylic acid (a species comprising free COOH groups), acrylamide, and bis(acryloyl)cystamine can be copolymerized together to generate a gel bead comprising free COOH groups, such that the COOH groups of the gel bead can be activated (e.g., via 1-Ethy 1-3-(3-dimethylaminopropyl)carbodiimide (EDC) and N-Hydroxysuccinimide (NHS) or 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM)) such that they are reactive (e.g., reactive to amine functional groups where EDC/NHS or DMTMM are used for activation), wherein the activated COOH groups can then react with an appropriate species (e.g., a species comprising an amine functional group where the carboxylic acid groups are activated to be reactive with an amine functional group) comprising a moiety to be linked to the bead (interpreted as activating the surface using an agent including carbodiimide, claim 36) (col 57, lines 26-51).
Regarding claim 37, Bent teaches that the methods of the present disclosure can be used to generate barcode molecules comprising one or more amino acids, peptides, proteins, PEG moieties, hydrocarbon chains, and/or other moieties (interpreted as a PEG linker; and comprising amine, hydroxyl, thiol, and methoxy groups, claim 37) (col 16, lines 56-59). Bent teaches that a first molecule (e.g., a first nucleic acid molecule) can be provided that is capable of attaching to a starter sequence attached to a bead, wherein the first molecule can be a nucleic acid molecule and/or can comprise an amino acid, peptide, polyethylene glycol (PEG) moiety, hydrocarbon chain, or another moiety (interpreted as a PEG linker; and comprising amine, hydroxyl, thiol, and methoxy groups, claim 37) (col 18, lines 15-20). Bent teaches that the polymer or gel can include one or more of disulfide cross-linked poly-acrylamide, agarose, alginate, polyvinyl alcohol, polyethylene glycol (PEG)-diacrylate, PEG-acrylate, PEG-thiol, PEG-azide, PEG-alkyne, other acrylates, chitosan, hyaluronic acid, collagen, fibrin, gelatin, or elastin, where the polymer or gel can comprise any other polymer or gel (interpreted as different functional groups including amine, hydroxyl, thiol and methoxy, claim 37) (col 50, lines 9-16).
Regarding claim 38, Bent teaches that biological samples in partitions can be subjected to various processes, such as chemical processes or physical processes, wherein samples in partitions can be subjected to heating or cooling, or chemical reactions, such as to yield species that can be qualitatively or quantitatively processed (interpreted as analyzing released oligos to confirm yield, claim 38) (col 1, lines 39-43). Bent teaches that a barcode can be added to a fragment of a deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) sample before, during, and/or after sequencing of the sample, such that barcodes can allow for identification and/or quantification of individual sequencing-reads (interpreted as analyzing released oligos to confirm yield; and sequence fidelity, claim 38) (col 12, lines 65-67; and col 13, lines 1-2).
Regarding claim 39, Bent teaches that Figure 32 shows a process in which fluorescent probes were used to examine the effects of exonuclease treatment (interpreted as hybridizing a fluorescent probe to a portion of the oligonucleotides; and assess oligonucleotide density and distribution, claim 39) (col 12, lines 17-20; and Figure 32).
Regarding claim 40, Bent teaches that beads can be provided as a population or plurality of beads having a relatively monodisperse size distribution; and providing relatively consistent amounts of reagents within partitions, maintaining relatively consistent bead characteristics, such as size; and that a support used in a method of the present disclosure can be, such as a well, matrix, rod, container, or beads, can have any useful features and characteristics, such as any useful size, fluidity, solidity, density, porosity, and composition (interpreted as sorting or filtering the population of solid supports based on size gates to select beads having a uniform density of oligonucleotides, claim 40) (col 17, lines 43-46; and col 53, lines 39-43).
Bent does not specifically exemplify using CDI, cyanogen bromide, tresyl chloride, or divinyl sulfone (claim 36, in part).
Bent meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Response to Arguments
Applicant’s arguments filed May 19, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) amended claim 6 recites a sequential method comprising 3 distinct steps: (a) activating a surface of solid supports with reactive groups to provide an activated surface; (b) reacting the activated surface with a heterobifunctional spacer; and (c) synthesizing or attaching oligonucleotides to the second functional group, where Bent’s agents do not activate the surface of an already formed solid surface; they are not separate heterobifunctional spacer molecules reacted with an already activated surface after bead formation (Applicant Remarks, pg. 10, third full paragraph through pg. 12, first full paragraph); and (b) Bent does not teach the ordered architecture of in order, a universal sequence, an origin-specific barcode, a unique molecular identifier, and a nucleic acid capture sequence (Applicant Remarks, pg. 12, last full paragraph through pg. 13, third full paragraph).
Regarding (a), although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26USPQ2d 1057 (Fed. Cir. 1993). Additionally, MPEP § 2112.01(I) states that,
where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
Applicant’s assertion that Fan does not teach the activation of the surface of an already-formed solid support; they are not separate heterobifunctional spacer molecules reacted with an already activated surface after bead formation, is not found persuasive. Regarding already formed solid support -
Bent teaches:
Acrylic acid (a species comprising free COOH groups), acrylamide, and bis(acryloyl)cystamine can be copolymerized together to generate a gel bead comprising free COOH groups, such that the COOH groups of the gel bead can be activated such as via EDC and NHS or DMTMM such that they are reactive (e.g., reactive to amine functional groups where EDC/NHS or DMTMM are used for activation), wherein the activated COOH groups can then react with an appropriate species (e.g., a species comprising an amine functional group where the carboxylic acid groups are activated to be reactive with an amine functional group) comprising a moiety to be linked to the bead (corresponding to generating a solid surface, then activating the surface of a support, claim 6) (col 57, lines 37-51).
Acrydite moieties can be modified with thiol groups capable of forming a disulfide bond or can be modified with groups already comprising a disulfide bond, wherein the thiol or disulfide (via disulfide exchange) can be used as an anchor point for a species to be attached; and/or an acrydite moiety can comprise a reactive hydroxyl group that can be used for attachment (interpreted as forming reactive groups on an activated surface of a support) (col 55, lines 6-17).
The functionalization of beads for attachment of nucleic acid molecules such as oligonucleotides can be achieved through a wide range of different approaches, including activation of chemical groups within a polymer, incorporation of active or activatable functional groups in the polymer structure, or attachment at the pre-polymer or monomer stage in bead production (corresponding to activating a surface of a support, claim 6) (col 55, lines 18-24).
The activation of disulfide linkages within a bead (interpreted as activating a surface or a solid support, claim 6) (col 58, lines 4-5).
The post-production functionalization of the bead with the oligonucleotide including through controlling loading ratios of species in beads (interpreted as activating a surface or a solid support, claim 6) (col 58, lines 43-45).
Regarding a heterobifunctional spacer - Bent teaches:
A support (e.g., a bead) can comprise a starter sequence functionalized thereto (e.g., as described herein), wherein a starter sequence (e.g., a partial read sequence) can be attached to the support via, for example, a disulfide linkage (interpreting a disulfide linkage and/or a starter sequence as a heterobifunctional spacer) (col 17, lines 49-53).
Figure 8 shows releasable linkage such as a disulfide linker 806 coupled to a bead 804 (col55, lines 61-63).
Bent clearly teaches activation of the surface of a solid support to provide an activated surface including activating a surface and reacting the activated surface with a heterobifunctional spacer. Thus, the claims remain rejected.
Regarding (b), Applicant’s assertion that Bent does not teach the ordered architecture of in order, a universal sequence, an origin-specific barcode, a unique molecular identifier, and a nucleic acid capture sequence, is not found persuasive. Referring to Figure 8, shown in part below):
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802 Nucleic acid molecule (col 55, line 59).
804 Bead (col 55, line 61).
806 Releasable linkage coupled to the bead 804 (interpreted as the linker) (col 55, line 61).
808 Functional sequence (col 56, lines 2-3), where a functional sequence can be a universal primer
sequence (interpreted as a universal sequence) (col 21, lines 39-40); such as a P5 sequence for
Illumina sequencing systems (interpreted as a universal sequence) (col 56, lines 2-7).
810 Barcode sequence including a bead-specific barcode, a partition-specific barcode (col 56, lines 8-14).
812 Specific priming sequence, such as an mRNA priming sequence (col 56, lines 17-19).
814 Anchoring sequence to ensure that the specific priming sequence hybridizes mRNA (interpreted as a
nucleic acid capture sequence) (col 56, lines 20-23).
816 UMI - where the UMI can provide a unique identifier of the starting mRNA molecules captured,
allowing quantitation of the number of original expressed RNA (interpreted as comprising a UMI; and UMIs as origin-specific barcode) (col 56, lines 35-37; and col 57, lines 7-9).
Bent clearly teaches the architecture, in order, as recited in instant claim 6. Thus, the claims remain rejected.
Claim Rejections - 35 USC § 103
The rejection of claims 6, 7, 25 and 36-40 is maintained under 35 U.S.C. 103 as being unpatentable over Bent et al. (hereinafter “Bent”) (US Patent No. 10745742, issued August 18, 2020; filed December 21, 2018; effective filing date November 15, 2017; of record) in view of Stephanie Lopina (hereinafter “Lopina”) (Thesis, Massachusetts Institute of Technology, 1996, 1-167; of record) as evidenced by Biosynthesis (Biosynthesis, 2015, 1-11; of record).
The teachings of Bent as applied to claims 6, 7, 25 and 37-40 are described supra.
Bent does not specifically exemplify using CDI, cyanogen bromide, tresyl chloride, or divinyl sulfone (claim 36, in part).
Regarding claim 36 (in part), Lopina teaches that appropriate ligands were covalently coupled to poly(ethylene oxide) substrates producing materials that elicit a desired cellular response, wherein hydroxyl groups on the PEO chains provided the site for attaching ligands, such that the hydroxyls are first activated, providing a leaving group which will then couple to the desired ligand (interpreted as a functional group is a hydroxyl group, claim 36) (pg. 70, first full paragraph). Lopina teaches that activated supports have long been used to immobilize antibodies for immunoaffinity chromatography (Shaltiel, 1976; Hjerten, 1981); that various activation agents have been used including N-hydroxy-succinimide (NHS) (Cuatrecasas, 1972), hydrazide (O'Shannessey, 1990), carbonyldiimidazole (CDI) (Bethel, 1979), 1,4-butanedioldiglydicyl ether (BDGE) (Sundberg, 1974); divinyl sulphone (DVS) (Porath, 1975); cyanogen bromide (CNBr) (March, 1974), tosyl chloride (Nilsson, 1984); and tresyl chloride (Nilsson, 1981; Nilsson, 1984), where it’s reactivity makes tresyl chloride attractive for use in substrate activation (Crossland, 1971) (interpreted as CDI, CNBr, tresyl chloride, and divinyl sulfone, claim 36) (pg. 70, second full paragraph), wherein CDI activation of a solid support is known in the art for the conjugation of oligonucleotides as evidenced by Biosynthesis (pg. 4, Figure 1). Lopina teaches that PEO hydrogels provide a pure poly(ethylene oxide) surface for derivatization, offering the most biologically inert scaffold possible, such that through radiation crosslinking of star PEO and linear/oligomer mixtures, PEO hydrogels with a range of ligand tether lengths and hydroxyl concentrations are possible (interpreted as PEO heterobifunctional spacers, claims 6 and 36) (pg. 77, first full paragraph).
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 derivatizing hydrogels as exemplified by Lopina, it would have been prima facie obvious before the effective filing date of the claimed invention to modify the method for the production of supports such as gel beads comprising differential functionalization for the attachment of tags, barcode molecules, UMI, capture sequences, and/or primers as disclosed by Bent to include activating agents such as CDI, CNBr, tresyl chloride, and divinyl sulfone as taught by Lopina with a reasonable expectation of success in activating, functionalizing, and/or derivatizing polymer supports including hydrogel beads; and/or for the efficient attachment of nucleic acid molecules such as oligonucleotides to supports including hydrogel beads.
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 as obvious over the art.
Response to Arguments
Applicant’s arguments filed May 19, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) Bent does not teach activating a surface of solid supports with reactive groups to provide an activated surface or reacting the activated surface with a heterobifunctional spacer whose first functional group covalently couples directly to the reactive groups of the activated surface. Bent also does not disclose the ordered oligonucleotide architecture recited in amended claim 6, and Lopina does not cure the deficiencies of Bent (Applicant Remarks, pg. 14, entire page).
Regarding (a), it is noted that none of the references has to teach each and every claim limitation. If they did, this would have been anticipation and not an obviousness-type rejection. One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Please see the Examiner’s response to Applicant’s arguments discussed supra including the teachings of Bent. Additionally,
Lopina teaches:
PEO hydroxyl end-groups were activated with tresyl chloride chemistry to provide a leaving group for efficient ligand coupling through amines or thiols (interpreted as activating a surface for treatment with a heterobifunctional spacer) (Abstract, third full paragraph).
Tresyl chloride activation of terminal hydroxyl groups in PEO hydrogels was carried out (interpreted as activating a surface for treatment with a heterobifunctional spacer) (pg. 77, last full paragraph).
The terminal hydroxyl groups of gels were modified with 1-amino-1-deoxy sugars (glucose or galactose) or the RGD adhesion peptide (interpreted as heterobifunctional spacers) (pg. 78, second full paragraph).
Activation agents for the generation of activated supports include, for example: N-hydroxy-succinimide (NHS), hydrazide, carbonyldiimidazole (CDI), 1,4-butanediol, diglycidyl ether (BDGE), sulphone (DVS), cyanogen bromide (CNBr), tosyl chloride, and tresyl chloride (pg. 70, second full paragraph).
The combined references of Bent and Lopina teach all of the limitations of the claims including activating a surface and reacting the activated surface with a heterobifunctional spacer. Thus, the claims remain rejected.
The Examiner suggests that Applicant amend claim 6 to recite specific solid supports, methods and reagents for surface activation, heterobifunctional spacers, and gating methods that improve the number of viable beads comprising an improved number of capture sites as compared to commercially available beads (instant Specification, paragraphs [0159]-[0163]).
Conclusion
Claims 6, 7, 25 and 36-40 are rejected.
THIS ACTION IS MADE FINAL. 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.
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/AMY M BUNKER/Primary Examiner, Art Unit 1684
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