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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 10/27/2025 has been entered.
Response to Amendment
The Amendment filed on 10/27/2025 has been entered. Claims 1, 2, 5, 6, 8-17 and 35 remain pending in the application.
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 1, 2, 5, 6, 8-17 and 35 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 1 recites “the substrate being i),” however the transitional phrase of “being” is unclear if it is opened or closed claim language. Being sounds similar to “composed of” which has been interpreted in the same manner as either “consisting of” or “consisting essentially of” (MPEP § 2111.03 (IV)). For examination purposes, “being” will be treated as “consisting essentially of.” Claims 5, 6, 8-17 and 35 are rejected by virtue of their dependence on a rejected base claim.
Claim 1 recites “the substrate being i) a material selected from the group consisting of … or ii) a multi-layered structure consisting of a based support of the material.” However, as this recitation is listed as i) or ii) it would appear that only option i) or ii) would be required. This is unclear because ii) recites that the multi-layered structure consisted of the material, but since the claim is written as either i) or ii) it is unclear what “the material” is. The examiner suggests to rewrite all of the materials under section ii) or to change how the claim is phrase so that it is clear what “the material” is. Claims 5, 6, 8-17 and 35 are rejected by virtue of their dependence on a rejected base claim.
Claim 2 recites “the substrate being i),” however the transitional phrase of “being” is unclear if it is opened or closed claim language. Being sounds similar to “composed of” which has been interpreted in the same manner as either “consisting of” or “consisting essentially of” (MPEP § 2111.03 (IV)). For examination purposes, “being” will be treated as “consisting essentially of.”
Claim 2 recites “the substrate being i) a material selected from the group consisting of … or ii) a multi-layered structure consisting of a based support of the material.” However, as this recitation is listed as i) or ii) it would appear that only option i) or ii) would be required. This is unclear because ii) recites that the multi-layered structure consisted of the material, but since the claim is written as either i) or ii) it is unclear what “the material” is. The examiner suggests to rewrite all of the materials under section ii) or to change how the claim is phrase so that it is clear what “the material” is.
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 (i.e., changing from AIA to pre-AIA ) 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
Claim(s) 1, 2, 5, 17 and 35 is/are rejected under 35 U.S.C. 103 as being unpatentable over United States Application Publication No. 2020/0024661, hereinafter Merkel in view of United States Application Publication No. 2010/0312483, hereinafter Peyser.
Regarding claim 1, Merkel teaches a flow cell (paragraph [0038]), comprising: a substrate (item 12 and 14) having a surface (the upper surface of item 14), the substrate being i) a material selected from the group consisting of epoxy siloxane, glass, acrylic, polystyrene, polypropylene, polyethylene, polybutylene, polyurethanes, polytetrafluoroethylene, acyclic olefin/cyclo-olefin polymer, a polyimide, a polyamides, silica, fused silica, aluminum silicate, silicon, boron doped p+ silicon, silicon nitride, silicon oxide, tantalum pentoxide, hafnium oxide, carbon, and a metal (all of these materials are optional and instead what is recited in part ii is utilized for the rejection), or ii) a multi-layered structure consisting of a base support (item 12) of the material (paragraph [0111]) and a resin (item 14) over the base support (figure 2F); a plurality of depression (item 16) or a lane (optional) defined in the surface; and surface chemistry (item 18) introduced in each of the plurality of depressions (item 16) or in the lane, the surface chemistry including: a polymer (item 18) attached to the substrate surface in each of the plurality of depressions or in the lane (figure 2F); a dark quencher (paragraph [0013]); and at least one primer set (item 24) attached to the polymer (figure 2F).
While it is recognized that the phrase “consisting essentially of” narrows the scope of the claims to the specified materials and those which do not materially affect the basic and novel characteristics of the claimed invention, absent a clear indication of what the basic and novel characteristics are, “consisting essentially of” is construed as equivalent to “comprising”. Further, the burden is on the applicant to show that the additional ingredients in the prior art, i.e. the dark quencher, would in fact be excluded from the claims and that such ingredients would materially change the characteristics of the applicant’s invention, See MPEP 2111.03.
Merkel fails to teach the polymer is a hydrogel and the hydrogel includes the dark quencher.
Peyser teaches a device which utilizes a polymer hydrogel and quencher covalently bonded to the hydrogel (Peyser, paragraph [0119]) so that the polymer can hold together and immobilize the quencher moiety while at the same time allowing contact with the analyte (Peyser, paragraph [0117]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have made the polymer into a hydrogel which included the dark quencher because the polymer would hold together and immobilize the quencher moiety while at the same time allowing contact with the analyte (Peyser, paragraph [0117]).
Regarding claim 2, Merkel teaches a flow cell (paragraph [0038]), comprising: a substrate (item 12 and 14) having a surface (the upper surface of item 14), the substrate being i) a material selected from the group consisting of epoxy siloxane, glass, acrylic, polystyrene, polypropylene, polyethylene, polybutylene, polyurethanes, polytetrafluoroethylene, acyclic olefin/cyclo-olefin polymer, a polyimide, a polyamides, silica, fused silica, aluminum silicate, silicon, boron doped p+ silicon, silicon nitride, silicon oxide, tantalum pentoxide, hafnium oxide, carbon, and a metal (all of these materials are optional and instead what is recited in part ii is utilized for the rejection), or ii) a multi-layered structure consisting of a base support (item 12) of the material (paragraph [0111]) and a resin (item 14) over the base support (figure 2F); a plurality of depression (item 16) or a lane (optional) defined in the surface; and surface chemistry (item 18) introduced in each of the plurality of depressions (item 16) or in the lane, the surface chemistry including: a polymer (item 18) applied to the substrate surface as a plurality of pads (figure 2E), wherein each of the plurality of pads is isolated from each other of the plurality of pads by interstitial regions (figures 2E and 2F); a dark quencher (paragraph [0013]); and at least one primer set (item 24) attached to the polymer (figure 2F).
While it is recognized that the phrase “consisting essentially of” narrows the scope of the claims to the specified materials and those which do not materially affect the basic and novel characteristics of the claimed invention, absent a clear indication of what the basic and novel characteristics are, “consisting essentially of” is construed as equivalent to “comprising”. Further, the burden is on the applicant to show that the additional ingredients in the prior art, i.e. the dark quencher, would in fact be excluded from the claims and that such ingredients would materially change the characteristics of the applicant’s invention, See MPEP 2111.03.
Merkel fails to teach the polymer is a hydrogel and the hydrogel includes the dark quencher.
Peyser teaches a device which utilizes a polymer hydrogel and quencher covalently bonded to the hydrogel (Peyser, paragraph [0119]) so that the polymer can hold together and immobilize the quencher moiety while at the same time allowing contact with the analyte (Peyser, paragraph [0117]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have made the polymer into a hydrogel which included the dark quencher because the polymer would hold together and immobilize the quencher moiety while at the same time allowing contact with the analyte (Peyser, paragraph [0117]).
Regarding claim 5, Merkel teaches wherein the polymeric hydrogel includes an acrylamide copolymer (paragraph [0139]).
Regarding claim 17, Merkel teaches wherein the dark quencher exhibits absorption at one or more wavelengths ranging from about 400 nm to about 670 nm (paragraph [0094]).
Regarding claim 35, Merkel teaches the substrate includes the plurality of depressions (item 16); each depression of the plurality of depressions has a depth ranging from about 0.1 µm to about 100 µm (paragraph [0125]); each depression of the plurality of depressions has a diameter ranging from about 0.1 µm to about 100 µm (paragraph [0126]) and an average pitch of the plurality of depressions is 500 nm or 700 nm (paragraph [0121]).
Claim(s) 6 and 13-16 is/are rejected under 35 U.S.C. 103 as being unpatentable over Merkel and Peyser as applied to claim 1 above, and further in view of WO 2010/111674, hereinafter Nikiforov.
Regarding claim 6, Merkel teaches the dark quencher is dimethylaminoazobenzenesulfonic azide (Dabsyl azide) (paragraph [0095]).
However, Merkel and Peyser fail to teach the dark quencher is dimethylaminoazobenzenesulfonic acid.
Nikiforov teaches dark quenchers with one of the being dimethylaminoazobenzenesulfonic acid (DABSYL) (Nikiforov, paragraph [00347]).
Examiner further finds that the prior art contained a device/method/product (i.e., dimethylaminoazobenzenesulfonic) which differed from the claimed device by the substitution of component(s) (i.e., dimethylaminoazobenzenesulfonic azide) with other component(s) (i.e., dimethylaminoazobenzenesulfonic acid), and the substituted components and their functions were known in the art as above set forth. An ordinarily skilled artisan at the time of invention could have substituted one known element with another (i.e., dimethylaminoazobenzenesulfonic azide with dimethylaminoazobenzenesulfonic acid), and the results of the substitution (i.e., quenching) would have been predictable.
Therefore, pursuant to MPEP §2143 (I), Examiner concludes that it would have been obvious to an ordinarily skilled artisan at the time of invention to substitute dimethylaminoazobenzenesulfonic azide of reference Merkel with dimethylaminoazobenzenesulfonic acid of reference Nikiforov, since the result would have been predictable.
Regarding claims 13 and 14, Merkel and Peyser teach all limitations of claim 1; however, they fail to teach the dark quencher is covalently attached to the polymeric hydrogel through a linking molecule which is a non-oligonucleotide linker.
Nikiforov teaches a polymer which covalently immobilizes to the surface and the hairpin oligonucleotide is link to a dye (Nikiforov paragraphs [00512] and [00606]).
Merkel is silent with regards to specific way the dark quencher is incorporated into the structure, therefore, it would have been necessary and thus obvious to look to the prior art for conventional incorporation methods. Nikiforov provides this conventional teaching showing that it is known in the art to have a polymer covalently link a dye to a surface (Nikiforov, paragraphs [00512] and [00606]). Therefore, it would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to make the dark quencher covalently linked to the dark quencher (dye) via a polymer to the polymer surface motivated by the expectation of successfully practicing the invention of Nikiforov.
Further, examiner further finds that the prior art contained a device/method/product (i.e., a dye covalently linked to a surface with a polymer) which differed from the claimed device by the substitution of component(s) (i.e., immobilizing the dye in the polymer surface) with other component(s) (i.e., covalently linking the dark quencher to the polymer surface via a polymer), and the substituted components and their functions were known in the art as above set forth. An ordinarily skilled artisan at the time of invention could have substituted one known element with another (i.e., immobilizing the dark quencher in the polymer with covalently linking the dark quencher to the surface with a polymer), and the results of the substitution (i.e., immobilizing the dark quencher) would have been predictable.
Therefore, pursuant to MPEP §2143 (I), Examiner concludes that it would have been obvious to an ordinarily skilled artisan at the time of invention to substitute immobilizing the dark quencher of reference Merkel with covalently linking the dark quencher with the polymer surface via a polymer of reference Nikiforov, since the result would have been predictable.
Modified Merkel teaches wherein the dark quencher is present in an amount ranging from about 0.25 mol% to about 50 mol% relative to a total number of moles in the polymeric hydrogel (paragraph [0096]).
Regarding claims 13 and 15, Merkel and Peyser teach all limitations of claim 1; however, they fail to teach the dark quencher is covalently attached to the polymeric hydrogel through a linking molecule which is an oligonucleotide linker.
Nikiforov teaches a hairpin oligonucleotide which covalently immobilizes to the surface and the hairpin oligonucleotide is link to a dye (Nikiforov paragraphs [00317] and [00512]).
Merkel is silent with regards to specific way the dark quencher is incorporated into the structure, therefore, it would have been necessary and thus obvious to look to the prior art for conventional incorporation methods. Nikiforov provides this conventional teaching showing that it is known in the art to have a hairpin oligonucleotide covalently link a dye to a surface (Nikiforov, paragraphs [00317] and [00512]). Therefore, it would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to make the dark quencher covalently linked to the dark quencher (dye) via a hairpin oligonucleotide to the polymer motivated by the expectation of successfully practicing the invention of Nikiforov.
Further, examiner further finds that the prior art contained a device/method/product (i.e., a dye covalently linked to a surface with a hairpin oligonucleotide) which differed from the claimed device by the substitution of component(s) (i.e., immobilizing the dye in the polymer) with other component(s) (i.e., covalently linking the dark quencher to the surface via a hairpin oligonucleotide), and the substituted components and their functions were known in the art as above set forth. An ordinarily skilled artisan at the time of invention could have substituted one known element with another (i.e., immobilizing the dark quencher in the polymer with covalently linking the dark quencher to the surface with a hairpin oligonucleotide), and the results of the substitution (i.e., immobilizing the dark quencher) would have been predictable.
Therefore, pursuant to MPEP §2143 (I), Examiner concludes that it would have been obvious to an ordinarily skilled artisan at the time of invention to substitute immobilizing the dark quencher of reference Merkel with covalently linking the dark quencher with the polymer via a hairpin oligonucleotide of reference Nikiforov, since the result would have been predictable.
Modified Merkel teaches wherein the dark quencher is present in an amount ranging from about 0.25 mol% to about 50 mol% relative to a total number of moles in the polymeric hydrogel (paragraph [0096]).
Regarding claim 16, Merkel and Peyser teach all limitations of claim 1; however, they fail to teach the dark quencher is attached to the polymeric hydrogel through a hairpin oligonucleotide.
Nikiforov teaches a hairpin oligonucleotide which immobilizes to the surface and the hairpin oligonucleotide is link to a dye (Nikiforov paragraph [00317]).
Merkel is silent with regards to specific way the dark quencher is incorporated into the structure, therefore, it would have been necessary and thus obvious to look to the prior art for conventional incorporation methods. Nikiforov provides this conventional teaching showing that it is known in the art to have a hairpin oligonucleotide linking a dye to a surface (Nikiforov, paragraph [00317]). Therefore, it would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to make the dark quencher linked to the dark quencher (dye) via a hairpin oligonucleotide to the polymer motivated by the expectation of successfully practicing the invention of Nikiforov.
Further, examiner further finds that the prior art contained a device/method/product (i.e., a dye linked to a surface with a hairpin oligonucleotide) which differed from the claimed device by the substitution of component(s) (i.e., immobilizing the dye in the polymer) with other component(s) (i.e., linking the dark quencher to the surface via a hairpin oligonucleotide), and the substituted components and their functions were known in the art as above set forth. An ordinarily skilled artisan at the time of invention could have substituted one known element with another (i.e., immobilizing the dark quencher in the polymer with linking the dark quencher to the surface with a hairpin oligonucleotide), and the results of the substitution (i.e., immobilizing the dark quencher) would have been predictable.
Therefore, pursuant to MPEP §2143 (I), Examiner concludes that it would have been obvious to an ordinarily skilled artisan at the time of invention to substitute immobilizing the dark quencher of reference Merkel with linking the dark quencher with the polymer via a hairpin oligonucleotide of reference Nikiforov, since the result would have been predictable.
Claim(s) 8-10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Merkel and Peyser as applied to claim 1 above, and further in view of WO 2021/126503, hereinafter George.
Regarding claims 8 and 9, Merkel and Peyser teach all limitations of claim 1; however, they fail to teach wherein the polymeric hydrogel has the dark quencher removably attached through a cleavable linking molecule which includes a non-covalent binding pair.
George teaches a flow cell kit in which a cleavable linking molecule is utilized for attaching the label so that the label can be removed from the structure (George, paragraph [0171]-[0172]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to utilized a non-covalent binding pair which is cleavable as the linking molecule because it would allow the dark quencher to be removed from the structure (George, paragraph [0171]-[0172]).
Regarding claim 10, modified Merkel teaches wherein the dark quencher is present in an amount ranging from about 0.25 mol% to about 50 mol% relative to a total number of moles in the polymeric hydrogel (paragraph [0096]).
Claim(s) 11-12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Merkel and Peyser as applied to claim 1 above, and further in view of WO 2017/007838, hereinafter Mastroianni.
Regarding claim 11, Merkel and Peyser teach all limitations of claim 1; however, they fail to teach wherein the polymeric hydrogel has the dark quencher incorporated into its backbone chain.
Mastroianni teaches a method of adding dyes to a polymer network in which the polymer network has the dye incorporated into its backbone chain (Mastroianni, paragraph [0089]).
Merkel is silent with regards to specific way the dark quencher is incorporated into the structure, therefore, it would have been necessary and thus obvious to look to the prior art for conventional incorporation methods. Mastroianni provides this conventional teaching showing that it is known in the art to have a dye incorporated into the polymer network backbone chain (Mastroianni, paragraph [0089]). Therefore, it would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to make the dark quencher part of the polymer backbone motivated by the expectation of successfully practicing the invention of Mastroianni.
Further, examiner further finds that the prior art contained a device/method/product (i.e., a dye incorporated into a polymer network) which differed from the claimed device by the substitution of component(s) (i.e., immobilizing the dye in the polymer) with other component(s) (i.e., the dark quencher incorporated into the backbone of the polymer), and the substituted components and their functions were known in the art as above set forth. An ordinarily skilled artisan at the time of invention could have substituted one known element with another (i.e., immobilizing the dark quencher in the polymer with adding the dark quencher part of the polymer backbone), and the results of the substitution (i.e., immobilizing the dark quencher) would have been predictable.
Therefore, pursuant to MPEP §2143 (I), Examiner concludes that it would have been obvious to an ordinarily skilled artisan at the time of invention to substitute immobilizing the dark quencher of reference Merkel with incorporating the dark quencher as part of the polymer backbone of reference Mastroianni, since the result would have been predictable.
Regarding claim 12, modified Merkel teaches wherein the dark quencher is present in an amount ranging from about 0.25 mol% to about 50 mol% relative to a total number of moles in the polymeric hydrogel (paragraph [0096]).
Response to Arguments
Applicant's arguments filed 10/27/2025 have been fully considered but they are not persuasive.
Regarding applicant’s argument that if the dark quencher is just added to the hydrogel and that the dark quencher would be in the resin as taught by Merkel as well as in the polymeric hydrogel as taught by Peyser is not found persuasive. The claim as written (and described in the 112(b) rejection above), the claim only requires the substrate made from either i) or ii) and does not require both. The dark quencher as disclosed by Merkel is present in the resin and the claim specifies that the multi-layered structure consists of a base support and a resin. The structure of Merkel as modified by Peyser, would still consist of the base support and the resin. The claim has not specified what the resin is made from (and only specifies what the base support is made from) and therefore the dark quencher is considered to be part of the resin and therefore would be able to still read on the instant claims. The examiner additionally notes that based upon the 112(b) rejections, the base support being made from the material, is being interpreted as “consisting essentially of” and therefore the dark quencher could also be present in the base support and read on still read on the instant limitations.
In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., that the dark quencher in the polymeric hydrogel may be able to quench the blue and/or green autofluorescence form the cured resin composition within 4 nm or less of its location in the depression) are not recited in the rejected claim(s). 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, 26 USPQ2d 1057 (Fed. Cir. 1993).
Regarding applicant’s argument that moving the quencher of Merkel would improperly change the principle of operation of Merkel and render Merkel unsatisfactory for its intended purpose is not found persuasive. Moving of the dark quencher from the resin to they hydrogel would not change the principle of operation of Merkel and render Merkel unsatisfactory for its intended purpose. The purpose of the dark quencher is to absorb light energy and to dissipate the energy as heat. The placement of the dark quencher would not change the principle of operation of Merkel as the dark quencher, whether it is placed in the resin or the hydrogel would still be able to absorb light energy and to dissipate the energy as heat and allow for biological analysis to occur. Additionally, the placement of the dark quencher would not change render Merkel unsatisfactory for its intended purpose as Merkel would still be able to allow for biological analysis to occur and for the dark quencher to absorb stray light energy and dissipate the energy as heat.
In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., the polymeric hydrogel pad rests on, and thus appears to protrude form, a substantially flat substrate surface) are not recited in the rejected claim(s). 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, 26 USPQ2d 1057 (Fed. Cir. 1993). The polymer coating 18 of Merkel protrudes from the surface of the resin and therefore is considered to be formed as a plurality of pads. The fact that the polymer coating is contained with the depression doesn’t prevent the ability for the polymer coating from being considered as a “pad.”
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MATTHEW D KRCHA whose telephone number is (571)270-0386. The examiner can normally be reached M-Th 7am-5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maris Kessel can be reached at (571)270-7698. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MATTHEW D KRCHA/ Primary Examiner, Art Unit 1796