Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1, 3, 5, 7-8, 16-19, 23-25, 28, 31, 35, 41, 53-55, and 57 are pending and currently under examination.
Response to Amendment
The Amendment filed 9/15/25 has been entered. Claims 1, 3, 5, 7-8, 16-19, 23-25, 28, 31, 35, 41, 53-55, and 57 are currently pending. Applicant’s amendments to claims 1, 3, 18, 35, 55, and 57 have overcome the objection and 112(b) and 112(d) rejections previously set forth in the Non-Final Office Action mailed 5/14/25.
Response to Arguments
Applicant’s arguments, see pages 10-15, filed 9/15/25, with respect to the rejections of claims 1, 3, 5, 7-8, 16-19, 23-25, 28, 31, 35, 41, 53-55, and 57 under 35 USC 103 have been fully considered and are found unpersuasive, and the 103 rejections documented in the Non-Final mailed 5/14/25 have been revised to address claim amendments filed 9/15/25 in this Final Office Action. More detailed responses to Applicant’s arguments are provided at the end of each maintained rejection.
Claim Objections
Claims 1, 7, 18, 28, 31, 35, 41, 55, and 57 are objected to because of the following informalities:
Per MPEP 608.01(m), “Periods may not be used elsewhere in the claims except for abbreviations.” It is recommended to use parentheses instead (e.g., claim 1 a) a detection CRISPR system…).
Appropriate correction is required.
Claim Rejections - 35 USC § 103
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.
Claims 1, 3, 5, 7-8, 16-19, 23-24, 28, 31, 35, 41, and 53-54 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Dai et al. (2019; NPL citation 8 on IDS filed 4/28/22; "Exploring the Trans-Cleavage Activity of CRISPR-Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor". Angew. Chem. Int. Ed. 2019, 58, 17399 – 17405. DOI: 10.1002/anie.201910772) in view of Chun et al. (2014; US 2014/0073534 A1; USPGPub citation 2 on IDS filed 4/28/22; publication of US application 14/114,253 which claims the priority of foreign applications KR 10-2011-0043332 filed 5/4/11, KR 10-2011-0068888 filed 7/12/11, and PCT/KR2011/009311 filed 12/2/11) and Liu et al. (2010; NPL citation V in PTO-892 filed 5/14/25; "Toward a Universal 'Adhesive Nanosheet' for the Assembly of Multiple Nanoparticles Based on a Protein-Induced Reduction/Decoration of Graphene Oxide". J. AM. CHEM. SOC. 9 VOL. 132, NO. 21. https://doi.org/10.1021/ja100938r).
This rejection is necessitated by claim amendments filed 9/15/25.
(i) Dai et al. teaches “This study introduces a new strategy for the development
of electrochemical biosensors by using electrochemistry to probe the CRISPR cleavage activity (E-CRISPR)” (first sentence of “Conclusion” section). Dai et al. teaches limitations relevant to claims 1, 3, 5, 7-8, 41, and 53.
Relevant to claims 1, 3, 5, and 53, Dai et al. Figure 1 and associated caption teaches “Principle of E-CRISPR. A) Cas12a (cpf1) performs crRNA-guided trans-cleavage of nonspecific ssDNA, initiated by the cis-cleavage of specific DNA. B) Nonspecific ssDNA reporter with methylene blue tag immobilized on the gold electrode. C) In the presence of the target, Cas12a-crRNA would initiate the trans-cleavage of the nonspecific ssDNA reporter, resulting in a low electrochemical current of methylene blue.”
The Dai et al. E-CRISPR reads on claim 1 A nucleic acid detection system comprising: a. a detection CRISPR system comprising an effector protein and one or more guide nucleic acid strands designed to bind to corresponding target nucleic acid molecules; b. an effector nucleic acid strand… d. an electrode comprising: i. a conductive surface.
The effector protein and one or more guide nucleic acid strands correspond to the Dai et al. Cas12a-crRNA duplex; the effector nucleic acid strand corresponds to the Dai et al. ssDNA; the electrode comprising: i. a conductive surface corresponds to the Dai et al. gold electrode.
This teaching also reads on claims 3, 5, and 53. The Dai et al. Cas12a reads on claim 3 the CRISPR system effector protein is selected from the group consisting of… Cas12a; and claim 5 the CRISPR system effector protein is a DNA targeting protein or an RNA targeting protein. As seen in Figure 1 and disclosed within the caption, Dai et al. teaches target nucleic acids, reading on claim 53 the system further comprises a target nucleic acid.
Relevant to claims 7-8 and 41, Dai et al. teaches “A nonspecific ssDNA reporter is designed with a methylene blue (MB) electrochemical tag for signal transduction and a thiol moiety to tether on the sensor surface in order to acquire the signal electrically (Figure 1B)" (last sentence of page 1, column 2; continued to first sentence of page 2, column 1).
This teaching reads on claim 7 the effector strand further comprises: a. a functional group for immobilization on the conductive surface…; b. at least one electroactive label; and claim 8 the functional group is at the 5'-end of the effector strand or the 3'-end of the effector strand; and claim 41 the system further comprises an electroactive mediator precipitating composition comprising:… b. an electroactive mediator selected from the group consisting of… methylene blue.
(ii) Dai et al. does not teach specifics regarding detector nucleic acid strands or nucleic acid modifications relevant to claims 1, 16-19, 23-24, and 35. However, these limitations were known in the prior art and taught by Chun et al.
Chun et al. teaches “Detection of Target Nucleic Acid Sequences by PO Cleavage and Hybridization” (Title).
Relevant to claim 1, Chun et al. teaches “The present invention detects the target nucleic acid sequence by use of in which the PO (Probing Oligonucleotide) hybridized with the target nucleic acid sequence is cleaved and the cleavage of the PO is detected by hybridization with the CO (Capturing Oligonucleotide). In the present invention, an uncleaved PO is hybridized with the CO immobilized onto the solid substrate" (Abstract). Chun et al. further teaches that “The single label on the PO may be described as a reporter molecule. The single label used includes, but is not limited to… electrochemical labels and metal labels” (page 8, paragraph 0146).
The Chun et al. PO corresponds to the detector strand. These teachings read on claim 1 c. a detector nucleic acid strand sufficiently complementary to the effector nucleic acid strand to enable nucleic acid hybridization, and conjugated with at least one electroactive label.
Relevant to claims 16-18 and 23-24, Chun et al. page 8, paragraph 0142 teaches that “The PO and CO may be comprised of naturally occurring dNMPs. Alternatively, the PO and CO may be comprised of modified or non-natural nucleotide such as PNA (peptide nucleic acid, see PCT Publication No. WO 92/20702) and LNA (locked nucleic acid, see PCT Publication Nos…)”.
This teaching reads on claim 16 the effector strand comprises a nucleic acid modification that inhibits or reduces cleavage of the effector strand by the CRISPR system effector protein; claim 17 the nucleic acid modification that inhibits or reduces cleavage of the effector strand by the CRISPR system effector protein is a peptide nucleic acid (PNA); claim 18 the detector strand further comprises… b. a nucleic acid modification; claim 23 the detector strand comprises a nucleic acid modification that inhibits or reduces cleavage of the detector strand by the CRISPR system effector protein; and claim 24 the nucleic acid modification that inhibits or reduces cleavage of the detector strand by the CRISPR system effector protein is a peptide nucleic acid.
Relevant to claim 19, Chun et al. page 7, paragraph 0131 teaches "According to a preferred embodiment, the PO is the 3'-tagged PO and the CO is immobilized onto the solid substrate through its 5'-end (FIG. 4). Preferably, the PO is the 5'-tagged PO and the CO is immobilized onto the solid substrate through its 3'-end (FIG. 5)". This teaching reads on claim 19 the functional group for conjugating with the electroactive label is at the 5'-end of the detector strand or at the 3'-end of the detector strand.
Relevant to claim 35, Chun et al page 8, paragraph 0146 teaches “The single label on the PO may be described as a reporter molecule. The single label used includes, but is not limited to… enzymatic labels (e.g., alkaline phosphatase..." This teaching reads on claim 35 the electroactive label comprises: a. an enzyme selected from… alkaline phosphatase (AP).
(iii) Dai et al. and Chun et al. are silent to specifics regarding nanocomposite coatings relevant to claims 1, 28, 31, and 54. However, these limitations were known in the prior art and taught by Liu et al.
Liu et al. discloses “In this communication, we report on a protein-based, environmentally friendly one-step reduction/decoration strategy to produce protein-conjugated graphene oxide (GO) and reduced graphene oxide (RGO) nanosheets with pH-dependent solubility” (first sentence of page 7279, column 1).
Relevant to claims 1, 28, 31, and 54, Liu et al. Scheme 1 and caption teaches “Protein-Based Decoration and Reduction of Graphene Oxide, Leading to a General Nanoplatform for Nanoparticle Assembly”.
As seen in Liu et al. Scheme 1, the nanosheets comprise a mixture of a conducting element (gold (Au) nanoparticles) and heat-denatured proteinaceous material (55-90°C Bovine Serum Albumin (BSA)). The reduced graphene sheets are arranged in a hexagonal lattice, forming a three-dimensional, porous matrix.
This teaching reads on claim 1 ii. a nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of said conductive surface; claim 28 the conducting element comprises: a. conductive and semi-conductive particles, rods, fibers, nano-particles or polymers; b. gold; or c. an allotrope of carbon atoms arranged in a hexagonal lattice; claim 31 the allotrope of carbon is:… b. … reduced graphene oxide comprising carboxylated reduced graphene oxide; and claim 54 the nanocomposite coating comprises a three dimensional, porous matrix.
Although Dai et al. does not teach specifics regarding detector nucleic acid strands, nucleic acid modifications, or nanocomposite coatings, it would have been prima facie obvious to the skilled artisan to include these limitations as taught by Chun et al. and Liu et al. Dai et al. and Chun et al. are analogous disclosures to the instant nucleic acid detection system. Liu et al. discloses an analogous nanocomposite coating to the coating of the instant invention.
The skilled artisan would be motivated to include the Chun et al. detector nucleic acid strands and nucleic acid modifications within the Dai et al. methodology because Chun et al. teaches that they “have made intensive researches to develop novel approaches to detect target sequences with more improved accuracy and convenience, inter alia, in a multiplex manner…The present protocols with dramatically enhanced target specificity are well adopted to solid phase reactions, and ensures multiple detection of target sequences with more improved accuracy and convenience” (paragraph 0014).
Additionally, the skilled artisan would be motivated to include the Liu et al. nanocomposite coatings within the Dai et al. electrochemical biosensors because Liu et al. teaches that “GO [graphene oxide], RGO [reduced graphene oxide], and their derivatives are emerging materials capable of delivering attractive electronic, catalytic, mechanical, optical, and magnetic properties” (page 7279, column 1, first sentence of paragraph 2). Liu et al. further teaches that “Proteins such as bovine serum albumin (BSA) are also good reductants due to their Tyr residues as investigated before. These properties allowed us to use BSA as both a reductant and a stabilizer to prepare BSA-GO/RGO conjugates” (page 7279, column 1, last two sentences of paragraph 4). Liu et al. teaches that “In conclusion, we have demonstrated that GO can be readily reduced and decorated by BSA, resulting in an extremely versatile and highly efficient self-assembly platform to create graphene-based hybrid materials” (page 7281, column 1, first sentence of paragraph 4).
Thus, the skilled artisan would find it obvious to combine Dai et al. E-CRISPR system with the Chun et al. detector nucleic acid strands and nucleic acid modifications, and Liu et al. nanocomposite coating in order to enable a more accurate, convenient, and versatile nucleic acid detection system. The skilled artisan would have a reasonable expectation of success based on the disclosures of Dai et al. in view of Chun et al. and Liu et al.
Applicant’s Arguments
Applicant argues that “The Examiner however fails to articulate, with any rational underpinnings where and how Dai, Chun and Liu teach or suggest the feature of ‘a nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of’ the conductive surface of the electrode” (Remarks 9/15/25, page 10, paragraph 2).
Applicant further argues that “the Examiner also fails to articulate any reason or motivation for coating a conductive surface of Dai’s electrode, let alone coating it with Liu’s protein conjugated GO and RGO nanosheets” (Remarks 9/15/25, page 12, paragraph 1).
Applicant further argues that “the claimed systems and methods provide unexpected sensitivity, including attomolar (10-18 M) sensitivity” and that “to date, there were no reports of such a sensitive Cas-mediated detection system with an electrical readout (see e.g., par [00262])” (Remarks 9/15/25, page 12, paragraph 2).
Response to Applicant’s Arguments
The Examiner respectfully disagrees with the assertion of no articulation of the nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of the conductive surface of the electrode. Excerpts of the Non-Final mailed 5/14/25 include:
Liu et al. discloses “In this communication, we report on a protein-based, environmentally friendly one-step reduction/decoration strategy to produce protein-conjugated graphene oxide (GO) and reduced graphene oxide (RGO) nanosheets with pH-dependent solubility” (first sentence of page 7279, column 1).
Relevant to claims 1, 28, 31, and 54, Liu et al. Scheme 1 and caption teaches “Protein-Based Decoration and Reduction of Graphene Oxide, Leading to a General Nanoplatform for Nanoparticle Assembly”.
As seen in Liu et al. Scheme 1, the nanosheets comprise a mixture of a conducting element (gold (Au) nanoparticles) and heat-denatured proteinaceous material (55-90°C Bovine Serum Albumin (BSA)). The reduced graphene sheets are arranged in a hexagonal lattice, forming a three-dimensional, porous matrix. (emphasis added)
These excerpts demonstrate that the Examiner did articulate ‘a nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of’ the conductive surface of the electrode”.
Additionally, the “motivation for coating a conductive surface of Dai’s electrode…with Liu’s protein conjugated GO and RGO nanosheets” can be found within the below excerpt of the Non-Final mailed 5/14/25:
Additionally, the skilled artisan would be motivated to include the Liu et al. nanocomposite coatings within the Dai et al. electrochemical biosensors because Liu et al. teaches that “GO [graphene oxide], RGO [reduced graphene oxide], and their derivatives are emerging materials capable of delivering attractive electronic, catalytic, mechanical, optical, and magnetic properties” (page 7279, column 1, first sentence of paragraph 2). Liu et al. further teaches that “Proteins such as bovine serum albumin (BSA) are also good reductants due to their Tyr residues as investigated before. These properties allowed us to use BSA as both a reductant and a stabilizer to prepare BSA-GO/RGO conjugates” (page 7279, column 1, last two sentences of paragraph 4). Liu et al. teaches that “In conclusion, we have demonstrated that GO can be readily reduced and decorated by BSA, resulting in an extremely versatile and highly efficient self-assembly platform to create graphene-based hybrid materials” (page 7281, column 1, first sentence of paragraph 4). (emphasis added)
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., sensitivity) 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 instant claims as written do not recite the unexpected sensitivity results or detection ranges/limits. Furthermore, although par [00262] states that “To date, there are no reports of such a sensitive Cas-mediated detection system with an electrical readout”, there are no side-by-side comparisons to indicate which step(s) of the claimed assay renders it unexpectedly more sensitive than the combined teachings of cited prior arts. As a result, this argument is considered as unpersuasive.
Claims 25, 55, and 57 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Dai et al. (2019; NPL citation 8 on IDS filed 4/28/22; "Exploring the Trans-Cleavage Activity of CRISPR-Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor". Angew. Chem. Int. Ed. 2019, 58, 17399 – 17405. DOI: 10.1002/anie.201910772) in view of Chun et al. (2014; US 2014/0073534 A1; USPGPub citation 2 on IDS filed 4/28/22; publication of US application 14/114,253 which claims the priority of foreign applications KR 10-2011-0043332 filed 5/4/11, KR 10-2011-0068888 filed 7/12/11, and PCT/KR2011/009311 filed 12/2/11) and Liu et al. (2010; NPL citation V in PTO-892 filed 5/14/25; "Toward a Universal 'Adhesive Nanosheet' for the Assembly of Multiple Nanoparticles Based on a Protein-Induced Reduction/Decoration of Graphene Oxide". J. AM. CHEM. SOC. 9 VOL. 132, NO. 21. https://doi.org/10.1021/ja100938r) as applied to claims 1, 3, 5, 7-8, 16-19, 23-24, 28, 31, 35, 41, and 53-54 above, and further in view of Dai et al. Supplemental Information (2019; NPL citation U in PTO-892 filed 5/14/25; Supplemental Information; "Exploring the Trans-Cleavage Activity of CRISPR-Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor". Angew. Chem. Int. Ed. 2019, 58, 17399 – 17405. DOI: 10.1002/anie.201910772).
The teachings of Dai et al. in view of Chun et al. and Liu et al. are applied to instantly rejected claims 25, 55, and 57 as they were applied to claims 1, 3, 5, 7-8, 16-19, 23-24, 28, 31, 35, 41, and 53-54 as rendering obvious a nucleic acid detection system.
Dai et al. in view of Chun et al. and Liu et al. is silent to specifics regarding electrochemical cells (claim 25) and applying a voltage to measure currents (claims 55 and 57). However, these limitations were known in the prior art and taught by Dai et al. Supplemental Information.
Relevant to claim 25, Dai et al. Supplemental Information contains Supplemental Figure S1, which depicts the Dai et al. sensor comprised of reference electrode, counter electrode, working electrode, insulating layer, and Ag conducting pad. The Dai et al. sensor reads on claim 25 the electrode is comprised in an electrochemical cell.
Relevant to claims 55 d. and 57 c., Dai et al. Supplemental Figure S2 and caption teaches that voltage was applied to the electrode within the E-CRISPR assays, with Supplemental Figure S2 panel B depicting current measurement generated from the electrode. The figure and caption read on claim 55 d. applying a voltage to the electrode and measuring a current generated from electrode; and claim 57 c. applying a voltage to the electrode and measuring a current generated from electrode.
It would have been prima facie obvious to the skilled artisan to include the Dai et al. electrochemical cell and application of a voltage to measure currents within the methodology rendered obvious by Dai et al. in view of Chun et al. and Liu et al. The skilled artisan would recognize that Dai et al. Supplemental Information is analogous to the instant nucleic acid detection, as it is a supplemental extension of the Dai et al. disclosure of the E-CRISPR system.
The skilled artisan would be motivated to use the Dai et al. electrode, electrochemical cell system, and current measurement, as Dai et al. Supplemental Information Figure S1 caption teaches that “The stability and reproducibility of the sensor was evaluated previously… The fabrication method and design of the sensors allows mass-production of single-use disposable sensors with a cost around $1.5/sensor. Therefore, this sensor platform is suitable for the development of a portable, cost-effective, electrochemical sensing system as a potential point-of-care diagnostic platform.”
The skilled artisan would have a reasonable expectation of success based on the disclosures of Dai et al. in view of Chun et al. and Liu et al., and further in view of Dai et al. Supplemental Information.
Applicant’s Arguments
Applicant argues that “Dai Supplementary does not cure the deficiencies in the combination of Dai, Chun and Liu as directed to the feature of ‘a nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of’ the conductive surface of the electrode” (Remarks 9/15/25, page 12, paragraph 1).
Response to Applicant’s Argument
As discussed in the above Response to Applicant’s Arguments relevant to claims 1, 3, 5, 7-8, 16-19, 23-24, 28, 31, 35, 41, and 53-54, Dai et al. in view of Chun et al. and Liu et al. renders obvious ‘a nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of’ the conductive surface of the electrode. Dai et al. Supplemental is not relied upon for this limitation, and as such, is not required to “cure the deficiencies in the combination of Dai, Chun and Liu”.
Claim Rejections - 35 USC § 103
Claims 1, 3, 5, 7-8, 16-19, 23-25, 28, 31, 35, 41, 53-55, and 57 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Church et al. (2018; US 2018/0320226 A1; USPGPub citation 5 on IDS filed 4/28/22; publication of US application 15/504,421 which claims the priority of provisional application 62/039,341 filed 8/19/14) in view of Chun et al. (2014; US 2014/0073534 A1; USPGPub citation 2 on IDS filed 4/28/22; publication of US application 14/114,253 which claims the priority of foreign applications KR 10-2011-0043332 filed 5/4/11, KR 10-2011-0068888 filed 7/12/11, and PCT/KR2011/009311 filed 12/2/11) and Liu et al. (2010; NPL citation V in PTO-892 filed 5/14/25; "Toward a Universal 'Adhesive Nanosheet' for the Assembly of Multiple Nanoparticles Based on a Protein-Induced Reduction/Decoration of Graphene Oxide". J. AM. CHEM. SOC. 9 VOL. 132, NO. 21. https://doi.org/10.1021/ja100938r).
This rejection is necessitated by claim amendments filed 9/15/25.
(i) Church et al. teaches “Methods of detecting, probing, mapping and directed sequencing of target nucleic acids are provided using a guide RNA and a Cas9 protein” (Abstract). Church et al. teaches limitations relevant to claims 1, 3, 5, 25, 53, 55 and 57.
Relevant to claims 1, 3, 5, 53, 55, and 57, Church et al. Abstract teaches “Methods for detecting the binding of the guide RNA/Cas9 complex to a target nucleic acid where the guide RNA includes a 3’ tail sequence that can hybridize to a probe are provided. Methods for detecting the binding of the guide RNA/Cas9 complex to a target nucleic acid where the complex is physically detected are provided.”
This teaching reads on claim 1 A nucleic acid detection system comprising: a. a detection CRISPR system comprising an effector protein and one or more guide nucleic acid strands designed to bind to corresponding target nucleic acid molecules; claim 3 the CRISPR system effector protein is selected from the group consisting of Cas9; claim 5 the CRISPR system effector protein is a DNA targeting protein or an RNA targeting protein; claim 53 the system further comprises a target nucleic acid; claim 55 A method for detecting a nucleic acid, the method comprising: a. contacting a target nucleic acid with a detection CRISPR system, wherein the CRISPR detection system comprises an effector protein and one or more guide nucleic acid strands designed to bind to or hybridize with the target nucleic acid molecules; and claim 57 A method for detecting a nucleic acid, the method comprising: a. contacting a target nucleic acid with a detection CRISPR system, wherein the CRISPR detection system comprises an effector protein, one or more guide nucleic acid strands designed to bind to the target nucleic acid molecules.
Relevant to claims 1, 25, 55, and 57, Church et al. paragraph 0006 teaches “According to certain aspects, the complex may be detected by detecting the physic-chemical property of the complex, such as electrostatic charge… Such methods include detecting the complex using nanopore detection methods”. Church et al. paragraphs 0090-0092 teach nanopore applications within their invention. Particularly relevant, Church et al. paragraph 0093 teaches “In addition to a nanopore, the present disclosure envisions the use of a nanogap which is known in the art as being a gap between two electrodes where the gap is about a few nanometers in width…”
These teachings read on claim 1 d. an electrode comprising: i. a conductive surface; claim 25 the electrode is comprised in an electrochemical cell; claim 55 b. contacting the CRISPR detection system from (a) with an electrode, wherein the electrode comprises: i. a conductive surface; and claim 57 b. contacting the detector strand from (a) with an electrode, wherein the electrode comprises: i. a conductive surface.
Further relevant to claims 55 and 57, Church et al. paragraph 0093 teaches “It is to be understood that one of skill will readily envision different embodiments of molecule or moiety identification and sequencing based on movement of a molecule or moiety through an electric field and creating a distortion of the electric field representative of the structure passing through the electric field.”
This teaching reads on claims 55 d and 57 c applying a voltage to the electrode and measuring a current generated from electrode
(ii) Church et al. does not teach specifics regarding effector/detector nucleic acid strands or nucleic acid modifications relevant to claims 1, 7-8, 16-19, 23-24, 35, 41, 55, and 57. However, these limitations were known in the prior art and taught by Chun et al.
Chun et al. teaches “Detection of Target Nucleic Acid Sequences by PO Cleavage and Hybridization” (Title).
Relevant to claims 1, 55, and 57, Chun et al. teaches “The present invention detects the target nucleic acid sequence by use of in which the PO (Probing Oligonucleotide) hybridized with the target nucleic acid sequence is cleaved and the cleavage of the PO is detected by hybridization with the CO (Capturing Oligonucleotide). In the present invention, an uncleaved PO is hybridized with the CO immobilized onto the solid substrate" (Abstract). Chun et al. further teaches that “The single label on the PO may be described as a reporter molecule. The single label used includes, but is not limited to… electrochemical labels and metal labels” (page 8, paragraph 0146).
The Chun et al. CO corresponds to the effector nucleic acid strand and the PO corresponds to the detector strand. These teachings read on claim 1 b. an effector nucleic acid strand; c. a detector nucleic acid strand sufficiently complementary to the effector nucleic acid strand to enable nucleic acid hybridization, and conjugated with at least one electroactive label; claim 55 iii. an effector nucleic acid strand immobilized on the conductive surface; c. contacting the electrode with a detector nucleic acid strand, wherein the detector nucleic acid strand is sufficiently complementary to the effector nucleic acid strand to enable nucleic acid hybridization, the effector nucleic acid strand and is conjugated with at least one electroactive label; and claim 57 a detector nucleic acid strand, wherein the detector strand is conjugated with at least one electroactive label…iii. an effector nucleic acid strand immobilized on the conductive surface, wherein the effector strand is substantially complementary to the detector strand.
Relevant to claims 7-8, Chun et al. page 7, paragraph 0132 teaches “The CO is immobilized directly or indirectly (preferably indirectly) through its 5'-end or 3'-end onto the surface of the solid substrate… For example, alkyl or aryl compounds with amine functionality, or alkyl or aryl compounds with thiol functionality serve as linkers for CO immobilization."
This teaching reads on claim 7 the effector strand further comprises: a. a functional group for immobilization on the conductive surface; and claim 8 the functional group is at the 5'-end of the effector strand or the 3'-end of the effector strand.
Relevant to claims 16-18 and 23-24, Chun et al. page 8, paragraph 0142 teaches that “The PO and CO may be comprised of naturally occurring dNMPs. Alternatively, the PO and CO may be comprised of modified or non-natural nucleotide such as PNA (peptide nucleic acid, see PCT Publication No. WO 92/20702) and LNA (locked nucleic acid, see PCT Publication Nos…)”.
This teaching reads on claim 16 the effector strand comprises a nucleic acid modification that inhibits or reduces cleavage of the effector strand by the CRISPR system effector protein; claim 17 the nucleic acid modification that inhibits or reduces cleavage of the effector strand by the CRISPR system effector protein is a peptide nucleic acid (PNA); claim 18 the detector strand further comprises… b. a nucleic acid modification; claim 23 the detector strand comprises a nucleic acid modification that inhibits or reduces cleavage of the detector strand by the CRISPR system effector protein; and claim 24 the nucleic acid modification that inhibits or reduces cleavage of the detector strand by the CRISPR system effector protein is a peptide nucleic acid.
Relevant to claim 19, Chun et al. page 7, paragraph 0131 teaches "According to a preferred embodiment, the PO is the 3'-tagged PO and the CO is immobilized onto the solid substrate through its 5'-end (FIG. 4). Preferably, the PO is the 5'-tagged PO and the CO is immobilized onto the solid substrate through its 3'-end (FIG. 5)". This teaching reads on claim 19 the functional group for conjugating with the electroactive label is at the 5'-end of the detector strand or at the 3'-end of the detector strand.
Relevant to claims 35 and 41, Chun et al page 8, paragraph 0146 teaches “The single label on the PO may be described as a reporter molecule. The single label used includes, but is not limited to… enzymatic labels (e.g., alkaline phosphatase..." This teaching reads on claim 35 the electroactive label comprises: a. an enzyme selected from… alkaline phosphatase (AP).
The skilled artisan would recognize that the Chun et al. “alkaline phosphatase” would have dephosphorylating enzymatic activity against claim 41 electroactive mediator precipitating composition comprising: a. a reporter enzyme substrate selected from the group consisting of… phosphorylated peptides, phosphorylated proteins, phosphorylated molecules.
(iii) Church et al. and Chun et al. are silent to specifics regarding nanocomposite coatings relevant to claims 1, 28, 31, and 54. However, these limitations were known in the prior art and taught by Liu et al.
Liu et al. discloses “In this communication, we report on a protein-based, environmentally friendly one-step reduction/decoration strategy to produce protein-conjugated graphene oxide (GO) and reduced graphene oxide (RGO) nanosheets with pH-dependent solubility” (first sentence of page 7279, column 1).
Relevant to claims 1, 28, 31, and 54, Liu et al. Scheme 1 and caption teaches “Protein-Based Decoration and Reduction of Graphene Oxide, Leading to a General Nanoplatform for Nanoparticle Assembly”.
As seen in Liu et al. Scheme 1, the nanosheets comprise a mixture of a conducting element (gold (Au) nanoparticles) and heat-denatured proteinaceous material (55-90°C Bovine Serum Albumin (BSA)). The reduced graphene sheets are arranged in a hexagonal lattice, forming a three-dimensional, porous matrix.
This teaching reads on claim 1 ii. a nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of said conductive surface; claim 28 the conducting element comprises: a. conductive and semi-conductive particles, rods, fibers, nano-particles or polymers; b. gold; or c. an allotrope of carbon atoms arranged in a hexagonal lattice; claim 31 the allotrope of carbon is:… b. … reduced graphene oxide comprising carboxylated reduced graphene oxide; and claim 54 the nanocomposite coating comprises a three dimensional, porous matrix.
Although Church et al. does not teach specifics regarding detector nucleic acid strands, nucleic acid modifications, or nanocomposite coatings, it would have been prima facie obvious to the skilled artisan to include these limitations as taught by Chun et al. and Liu et al. Church et al. and Chun et al. are analogous disclosures to the instant nucleic acid detection system. Liu et al. discloses an analogous nanocomposite coating to the coating of the instant invention.
The skilled artisan would be motivated to include the Chun et al. detector nucleic acid strands and nucleic acid modifications within the Church et al. methodology because Chun et al. teaches that they “have made intensive researches to develop novel approaches to detect target sequences with more improved accuracy and convenience, inter alia, in a multiplex manner…The present protocols with dramatically enhanced target specificity are well adopted to solid phase reactions, and ensures multiple detection of target sequences with more improved accuracy and convenience” (paragraph 0014).
Additionally, the skilled artisan would be motivated to include the Liu et al. nanocomposite coatings within the Church et al. detection methodology because Liu et al. teaches that “GO [graphene oxide], RGO [reduced graphene oxide], and their derivatives are emerging materials capable of delivering attractive electronic, catalytic, mechanical, optical, and magnetic properties” (page 7279, column 1, first sentence of paragraph 2). Liu et al. further teaches that “Proteins such as bovine serum albumin (BSA) are also good reductants due to their Tyr residues as investigated before. These properties allowed us to use BSA as both a reductant and a stabilizer to prepare BSA-GO/RGO conjugates” (page 7279, column 1, last two sentences of paragraph 4). Liu et al. teaches that “In conclusion, we have demonstrated that GO can be readily reduced and decorated by BSA, resulting in an extremely versatile and highly efficient self-assembly platform to create graphene-based hybrid materials” (page 7281, column 1, first sentence of paragraph 4).
Thus, the skilled artisan would find it obvious to combine Church et al. CRISPR-mediated nucleic acid detection system with the Chun et al. detector nucleic acid strands and nucleic acid modifications, and Liu et al. nanocomposite coating in order to enable a more accurate, convenient, and versatile nucleic acid detection system. The skilled artisan would have a reasonable expectation of success based on the disclosures of Church et al. in view of Chun et al. and Liu et al.
Applicant’s Arguments
Applicant argues that “the Examiner has provided no articulated reasoning or rational underpinnings to modify the conductive surface of Church’s electrode in order to meet the feature of ‘a nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of’ the conductive surface of the electrode” (Remarks 9/15/25, page 14, paragraph 4) and that “the claimed systems and methods provide unexpectedly sensitive detection of target nucleic acids, which one of skill in the art could not have predicted on the basis of the cited references” (Remarks 9/15/25, page 14, paragraph 5).
Response to Applicant’s Arguments
The Examiner respectfully disagrees with the assertion of no articulation of the nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of the conductive surface of the electrode. Excerpts of the Non-Final mailed 5/14/25 include:
Liu et al. discloses “In this communication, we report on a protein-based, environmentally friendly one-step reduction/decoration strategy to produce protein-conjugated graphene oxide (GO) and reduced graphene oxide (RGO) nanosheets with pH-dependent solubility” (first sentence of page 7279, column 1).
Relevant to claims 1, 28, 31, and 54, Liu et al. Scheme 1 and caption teaches “Protein-Based Decoration and Reduction of Graphene Oxide, Leading to a General Nanoplatform for Nanoparticle Assembly”.
As seen in Liu et al. Scheme 1, the nanosheets comprise a mixture of a conducting element (gold (Au) nanoparticles) and heat-denatured proteinaceous material (55-90°C Bovine Serum Albumin (BSA)). The reduced graphene sheets are arranged in a hexagonal lattice, forming a three-dimensional, porous matrix. (emphasis added)
These excerpts demonstrate that the Examiner did articulate ‘a nanocomposite coating comprising a mixture of a conducting element and a denatured proteinaceous material coated on at least a part of’ the conductive surface of the electrode”.
Additionally, the motivation for coating the conductive surface can be found within the below excerpt of the Non-Final mailed 5/14/25:
Additionally, the skilled artisan would be motivated to include the Liu et al. nanocomposite coatings within the Dai et al. electrochemical biosensors because Liu et al. teaches that “GO [graphene oxide], RGO [reduced graphene oxide], and their derivatives are emerging materials capable of delivering attractive electronic, catalytic, mechanical, optical, and magnetic properties” (page 7279, column 1, first sentence of paragraph 2). Liu et al. further teaches that “Proteins such as bovine serum albumin (BSA) are also good reductants due to their Tyr residues as investigated before. These properties allowed us to use BSA as both a reductant and a stabilizer to prepare BSA-GO/RGO conjugates” (page 7279, column 1, last two sentences of paragraph 4). Liu et al. teaches that “In conclusion, we have demonstrated that GO can be readily reduced and decorated by BSA, resulting in an extremely versatile and highly efficient self-assembly platform to create graphene-based hybrid materials” (page 7281, column 1, first sentence of paragraph 4). (emphasis added)
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., sensitivity) 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 instant claims as written do not recite the unexpected sensitivity results or detection ranges/limits. Furthermore, although par [00262] states that “To date, there are no reports of such a sensitive Cas-mediated detection system with an electrical readout”, there are no side-by-side comparisons to indicate which step(s) of the claimed assay renders it unexpectedly more sensitive than the combined teachings of cited prior arts. As a result, this argument is considered as unpersuasive.
Conclusion
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.
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/SARAH JANE KENNEDY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682