DETAILED ACTION
The amendment filed on 10/31/2025 has been entered. No new matter was added.
Claims 1, 116-118, 122-124, and 128-131 were amended in the claim set filed on 10/31/2025.
Claims 115, 119, and 121 were canceled.
Claims 1, 51, 116-118,120 and 122-132 are currently pending.
Applicant’s election without traverse of Group I (encompassing claim 1, as currently amended and claims 115-132) in the reply filed on 06/11/2025 is acknowledged. Accordingly, as elected invention directed to claims 1 and 116-118,120 and 122-132 are rejected, Claim 51 is withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected group II, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 06/11/25.
Claims 1, 116-118, 120 and 122-132 are currently under examination.
Response to the Arguments
Objections to the specification in the previously mailed non-final have been withdrawn in light of applicants filling of IDS.
Applicant’s arguments regarding previous rejections of claims 121 and 131 under 35 U.S.C. 112 have been fully considered and are persuasive. The 35 U.S.C. 112 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim amendments and arguments on Pg. 9.
Applicant’s arguments regarding previous rejections of claims 1, 116-118, 120 and 122-132 under 35 U.S.C. 102 have been fully considered and are persuasive. The 35 U.S.C. 102 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim clarification, claim amendments and arguments on Pg. 9-12. However, as necessitated by amendment, and after further search and consideration, the new grounds of rejections are made under 35 U.S.C. 103 rejections as documented below, in this office action on Pg. 4-10.
Applicant’s arguments regarding previous rejections of claims 1, 116-118, 120 and 122-132 under 35 U.S.C. 103 have been fully considered and are persuasive. The 35 U.S.C. 103 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim clarification, claim amendments and arguments on Pg. 9-12. However, as necessitated by amendment, and further search and consideration, new grounds of rejections for claims 130- 132 are made, as documented below, under the 35 U.S.C. 103 rejections in this office action on Pg. 10-17.
The rejections for claims 1, 116-118, 120 and 122-132 are documented below in this Final Office Action are necessitated by claim amendments filed on 10/31/2025.
Priority
This application is a 371 of PCT/US20/60333 filed on 11/13/2020 which claims benefit of 62/935,705 filed on 11/15/2019. Accordingly, the priority date of instant claims is determined to be 11/15/2019., the filing date of 62/935,705.
Claim Objections
Claim 1 is objected to because of the following informalities: “and (ii)” should be amended to “and (iii)”. 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, 116-118, 120 and 122-129 are rejected under 35 U.S.C. 103 as being unpatentable over Smargon et al. (“Smargon”; US Patent App. Pub. No. US 20170211142 A1, July 27, 2017) in view of Zhang et al. (“Zhang”; (2018). Direct visualization of single-nucleotide variation in mtDNA using a CRISPR/Cas9-mediated proximity ligation assay. Journal of the American Chemical Society, 140(36), 11293-11301., August 20, 2018).
Smargon discloses systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA. (Abstract)
Regarding claim 1, Smargon teaches system “comprising i) a Type VI-B CRISPR-Cas effector protein, and ii) a Type VI-B CRISPR-Cas crRNA, wherein the crRNA comprises a) a guide sequence that is capable of hybridizing to a target RNA sequence, and b) a direct repeat sequence. The Type VI-B CRISPR-Cas effector protein forms a complex with the crRNA, and the guide sequence directs sequence-specific binding of the complex to the target RNA sequence, whereby there is formed a CRISPR complex comprising the Type VI-B CRISPR-Cas effector protein complexed with the guide sequence that is hybridized to the target RNA sequence” (Para. 14). Thus, Smargon teaches a nucleic acid detection system comprising: a CRISPR-Cas protein, and a CRISPR-Cas guide RNA sequence comprising a sequence capable of hybridizing to the guide RNA binding site and comprising a sequence capable of forming a complex with the CRISPR-Cas protein.
However, Smargon does not explicitly teach a two or more detection oligonucleotides, wherein each detection oligonucleotide comprises in order from 5' to 3': (i) a first target binding sequences (ii) a linking region, and(ii) a second target binding sequence, wherein the linking region comprises a guide RNA binding site, wherein, when the first target binding sequence and the second target binding sequence bind a target sequence, the 5' and 3' terminal nucleotides of the detection oligonucleotide are disposed immediately adjacent to one another or are separated by a gap region comprising between 1 and 100 nucleotides, wherein each detection oligonucleotide binds a unique target sequence of interest in the same genome, and wherein each detection oligonucleotide comprises the same guide RNA binding site.
Zhang discloses CRISPR/Cas9- mediated proximity ligation assay (CasPLA) to image SNV in mtDNA at single-molecule resolution. This method uses two Cas9 probes to target a specific mtDNA sequence, followed by proximity ligation and in situ rolling circle amplification (RCA) to reveal the spatial localization of individual wild-type and mutated mtDNAs in single cells. (Pg. 11293, Introduction, Col. 2, Para. 2)
Regarding claim 1, Zhang teaches a system wherein “this method uses two Cas9 probes to target a specific mtDNA sequence” (Pg. 11293, Col. 2, Para. 2; Scheme 1 see below). Zhang teaches a system as illustrated in Scheme 1 that depicts proximity ligation probes, with a first target binding sequence at the 5’ end, a linking region, and a second target binding sequence at the 3’ end. Zhang teaches a system as illustrated in Scheme 1 that depicts the linking region comprising a region interacting with guide RNA, thus reads on a guide RNA binding site of the detection oligonucleotide. “proximity ligation probes” reads on one or more detection oligonucleotides and the MPEP states "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05). It would be obvious to the ordinary artisan to optimize the system to use two detection oligonucleotides. Thus, Zhang teaches a system comprising detection oligonucleotides, wherein each detection oligonucleotide comprises in order from 5' to 3': (i) a first target binding sequences (ii) a linking region, and(iii) a second target binding sequence, wherein the linking region comprises a guide RNA binding site, wherein, when the first target binding sequence and the second target binding sequence bind a target sequence, the 5' and 3' terminal nucleotides of the detection oligonucleotide are disposed immediately adjacent to one another or are separated by a gap region comprising between 1 and 100 nucleotides, wherein each detection oligonucleotide binds a unique target sequence of interest in the same genome, and wherein each detection oligonucleotide comprises the same guide
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RNA binding site.
Smargon and Zhang are both considered to be analogous to the claimed invention because they are in the same field of targeting nucleic acids with CRISPR effector proteins and guide sequences. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the nucleic acid detection system comprising CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA as taught by Smargon to incorporate the system comprising CRISPR/Cas-9 (Class 2) system, detection oligonucleotides comprising a first target binding sequence, a linking region, and a second target binding sequence, and guide RNA to target a specific mtDNA sequence as taught by Zhang and provide a system comprising a CRISPR-Cas protein, detection oligonucleotides comprising a first target binding sequence, a linking sequence, and a second target binding sequence, and a guide RNA. Doing so would allow for increased signal to noise detection of probes and efficient identification and specific recognition of CRISPR-Cas system for target sequence(s).
The teachings of Smargon and Zhang are documented above in the rejection of claim 1 under 35 U.S.C. 103. Claim 116, 118, 120, 122, 125, 127-129 depends on claim 1. Claim 117 depends claim 116, which depends on claim 1. Claim 124 depends claim 118, which depends on claim 1. Claim 123 depends claim 122, which depends on claim 1. Claim 126 depends claim 125, which depends on claim 1.
Regarding claim 116, Smargon teaches a system wherein “the crRNA library consists of targets that tile the entire RNA viral genome one base pair at a time” (Para. 1202). Smargon teaches a system wherein “Targeting of putative control elements on the other hand (e.g. by tiling the region of the putative control element” (Para. 867). Thus, Smargon teaches a system wherein the target binding sequences of the plurality of detection oligonucleotides are designed to tile across distinct regions of the target sequence.
Regarding claim 117, Smargon teaches a system wherein “comprises two or more Type VI-B CRISPR-Cas crRNAs” (Para. 17). Two or more crRNAs is interpreted as comprising 2 to 50, 2 to 200, or 2 to 1000 detection oligonucleotides. Thus, Smargon teaches a system wherein the plurality of detection oligonucleotides comprise 2 to 50 detection oligonucleotides, 2 to 200 detection oligonucleotides, or 2 to 1000 detection oligonucleotides.
Regarding claim 118, Smargon teaches a system wherein “the crRNA library consists of targets that tile the entire RNA viral genome one base pair at a time” (Para. 1202). Regarding claim 119, Smargon teaches a system wherein “the crRNA library consists of targets that tile the entire RNA viral genome one base pair at a time” (Para. 1202). Smargon teaches a system wherein “wherein the crRNA comprises a) a guide sequence that is capable of hybridizing to a target RNA sequence, and b) a direct repeat sequence” (Para. 14). Smargon teaches a system wherein “the terms “CRISPR repeat,” “direct repeat,” “repeat sequence,” or “repeat” have the conventional meaning as used in the art, i.e., multiple short direct repeating sequences, which show very little or no sequence variation within a given CRISPR array” (Para. 223). Thus, Smargon teaches a system wherein the detection oligonucleotides are designed to bind target sequences tiled across a region of the genome.
Regarding claim 120, Zhang teaches a system wherein “we designed a CRISPR/Cas9 mediated proximity ligation assay” (Pg. 11293, Col. 2, Para. 2; Scheme 1 see below) Thus, Zhang teaches a system wherein the detection oligonucleotide is circularized by ligation, splinted ligation, hybridization, or proximity extension.
Regarding claim 122, Smargon teaches a system wherein “the repeats are short elements that occur in clusters that are regularly spaced by unique intervening sequences” (Para. 787). “The mRNA contained in the extracted nucleic acid sample is then detected by amplification procedures” (Para. 808). Smargon teaches a system wherein “amplification means any method employing a primer and a polymerase capable of replicating a target sequence with reasonable fidelity” (Para. 809). “Amplification procedures” are interpreted as general and comprising Forward and Reverse primers and polymerase to bind to regions of the sequence to amplify the region of interest. Thus, Smargon teaches a system wherein the linking region further comprises a forward primer binding sequence, a reverse primer binding sequence, an RNA polymerase binding sequence, and/or a barcode.
Regarding claim 123, Smargon teaches a system wherein “the expression of the guide sequence is under the control of the T7 promoter and is driven by the expression of T7 polymerase” (Para. 836). Thus, Smargon teaches a system wherein the intervening sequences comprise a T7 promoter, wherein the T7 promoter is oriented to express the CRISPR-Cas guide RNA binding site of the detection oligonucleotide.
Regarding claim 124, Smargon teaches a system wherein “target antibiotic resistance gene” (Para.1212). Thus, Smargon teaches a system wherein the region of the genome comprises an antibiotic resistance gene, a repetitive genetic element, a genomic region conserved across one or more genus or species, or a species-specific genomic region.
Regarding claims 125 and 126, Smargon teaches a system wherein “In an embodiment of the invention, the single effector protein comprises a Class 2 Type VI-B effector protein. Class 2 Type VI-B effector proteins include two subgroups, Type VI-Bl and Type VI-B2, which are also referred to as Group 29 proteins and Group 30 proteins” (Para. 10) and “Group 29 and group 30 systems comprise a large single effector… termed Cas13b (Para.11). Thus, Smargon teaches a system wherein the CRISPR-Cas protein is a Cas13 or Cas 12 and wherein the CRISPR-Cas is a Cas13 selected from Cas13a, Cas13b, Cas13c, and Cas13d; or wherein the CRISPR-Cas is a Cas12 selected from Cas12a, Cas12b, and Cas12c.
Regarding claim 127, Smargon teaches a system wherein " amplification means any method employing a primer and a polymerase capable of replicating a target sequence with reasonable fidelity. Amplification may be carried out by natural or recombinant DNA polymerases such as TaqGold™, T7 DNA polymerase, Klenow fragment of E. coli DNA polymerase, and reverse transcriptase. A preferred amplification method is PCR” (Para.773; Para. 809; Para. 811). Thus, Smargon teaches a system comprising: amplification reagents for amplifying the detection oligonucleotide; amplification reagents selected from Polymerase Chain Reaction (PCR) reagents, Recombinase Polymerase Amplification (RPA) reagents, Rolling Circle Amplification (RCA) reagents, and/or Multiple Displacement Amplification (MDA) reagents; DNA methylation enrichment agents; and/or size selection reagents to enrich for cell free DNA (cfDNA).
Regarding claim 128, Smargon teaches a system wherein “isolate and/or purify the RNA” (Para. 338) and “The mRNA contained in the extracted nucleic acid sample is then detected by amplification procedures” (Para. 808). Thus, Smargon teaches a system wherein the target sequences of interest are in cell free nucleic acids.
Regarding claim 129, Smargon teaches a system wherein “The methods and uses as described herein … may target particular cells… target cells may for instance be …cells infected by a specific (e.g. viral) pathogen, etc. (Para. 329). Thus, Smargon teaches a system wherein the genome is the genome of a pathogen.
Response to Arguments
Applicant' s arguments filed 10/31/2025 (Pg. 9-12) with respect to claims 1, 116-118, 120, 122-129 have been considered but are moot, because they do not apply to the new grounds of rejection.
Applicants’ argument: “Applicant's detection oligonucleotides are crRNAs. This is incorrect. The present amendments clarify the distinctions between Applicant's claimed detection oligonucleotides and the crRNAs present in the cited art.” (Pg. 11)
Response: As necessitated by amendment, please see the revised rejection towards claim 1 under 35 U.S.C. 103. Although the applicant suggests that the detection oligonucleotides are not crRNAs they do suggest interaction with cRNAs and thus many claims are still suggestive of the detection oligonucleotides interacting rather directly or indirectly with certain regions of the genome through guide RNA.
Claim 130 is rejected under 35 U.S.C. 103 as being unpatentable over Smargon et al. (“Smargon”; US Patent App. Pub. No. US 20170211142 A1, July 27, 2017) in view of Zhang et al. (“Zhang”; (2018). Direct visualization of single-nucleotide variation in mtDNA using a CRISPR/Cas9-mediated proximity ligation assay. Journal of the American Chemical Society, 140(36), 11293-11301., August 20, 2018).
Smargon discloses systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA. (Abstract)
Regarding claim 130, Smargon teaches system “comprising i) a Type VI-B CRISPR-Cas effector protein, and ii) a Type VI-B CRISPR-Cas crRNA, wherein the crRNA comprises a) a guide sequence that is capable of hybridizing to a target RNA sequence, and b) a direct repeat sequence. Smargon also suggests a system in which oligonucleotides are used in combination with Cas effector protein and guide RNA to detect target nucleic acids. The Type VI-B CRISPR-Cas effector protein forms a complex with the crRNA, and the guide sequence directs sequence-specific binding of the complex to the target RNA sequence, whereby there is formed a CRISPR complex comprising the Type VI-B CRISPR-Cas effector protein complexed with the guide sequence that is hybridized to the target RNA sequence” (Para. 14). Thus, Smargon teaches a nucleic acid detection system comprising: a CRISPR-Cas protein; and a guide RNA comprising a sequence capable of hybridizing to the guide RNA binding site and comprising a sequence capable of forming a complex with the CRISPR-Cas protein.
Smargon teaches a system wherein “the repeats are short elements that occur in clusters that are regularly spaced by unique intervening sequences” (Para. 787). “The mRNA contained in the extracted nucleic acid sample is then detected by amplification procedures” (Para. 808). Smargon teaches a system wherein “amplification means any method employing a primer and a polymerase capable of replicating a target sequence with reasonable fidelity” (Para. 809). “Amplification procedures” are interpreted as general and comprising Forward and Reverse primers and polymerase to bind to regions of the sequence to amplify the region of interest. Thus, Smargon suggests a system wherein the linking region of the detection oligonucleotide further comprises a forward primer binding sequence, a reverse primer binding sequence, an RNA polymerase binding sequence, and/or a barcode.
Smargon does not explicitly teach a system wherein the B) two or more detection oligonucleotides, wherein each detection oligonucleotide comprises in order from 5' to 3': (i) a first target binding sequence, (ii) a linking region, and iii) a second target binding sequence, wherein the linking region comprises: a forward primer binding sequence, a reverse primer binding sequence, an RNA polymerase binding sequence, and a guide RNA binding site, wherein, when the first target binding sequence and the second target binding sequence bind a target sequence, the 5' and 3' terminal nucleotides of the detection oligonucleotide are disposed immediately adjacent to one another or are separated by a gap region comprising between 1 and 100 nucleotides, wherein each detection oligonucleotide binds a unique target sequence of interest in the same genome, wherein each detection oligonucleotide comprises the same guide RNA binding site, and wherein the detection oligonucleotides are circularized by ligation, splinted ligation, hybridization, or proximity extension;
Zhang discloses CRISPR/Cas9- mediated proximity ligation assay (CasPLA) to image SNV in mtDNA at single-molecule resolution. This method uses two Cas9 probes to target a specific mtDNA sequence, followed by proximity ligation and in situ rolling circle amplification (RCA) to reveal the spatial localization of individual wild-type and mutated mtDNAs in single cells. (Pg. 11293, Introduction, Col. 2, Para. 2)
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Regarding claim 130, Zhang teaches a system wherein “we designed a CRISPR/Cas9 mediated proximity ligation assay” (Pg. 11293, Col. 2, Para. 2; Scheme 1 see below). Thus, Zhang teaches a system wherein the detection oligonucleotide is circularized by ligation, splinted ligation, hybridization, or proximity extension.
Regarding claim 130, Zhang teaches a system wherein “this method uses two Cas9 probes to target a specific mtDNA sequence” (Pg. 11293, Col. 2, Para. 2; Scheme 1 see above). Zhang teaches a system as illustrated in Scheme 1 that depicts proximity ligation probes, with a first target binding sequence at the 5’ end, a linking region, and a second target binding sequence at the 3’ end. Zhang teaches a system as illustrated in Scheme 1 that depicts the linking region comprising a region interacting with guide RNA, thus reads on a guide RNA binding site of the detection oligonucleotide. “proximity ligation probes” reads on one or more detection oligonucleotides and the MPEP states "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05). It would be obvious to the ordinary artisan to optimize the system to use two detection oligonucleotides. Thus, Zhang teaches a system wherein the target binding sequence of the detection oligonucleotide comprises a first target binding sequence and a second target binding sequence that are separated by intervening sequences: wherein the first target binding sequence and the second target binding sequence hybridize upon the target sequence directly adjacent to one another; or wherein the first target binding sequence and the second target binding sequence hybridize upon the target sequence such that there is at least a single nucleotide gap region between the first target binding sequence and the second target binding sequence.
Smargon and Zhang are both considered to be analogous to the claimed invention because they are in the same field of targeting nucleic acids with CRISPR effector proteins and guide sequences. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the nucleic acid detection system comprising CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA as taught by Smargon to incorporate the system comprising CRISPR/Cas-9 (Class 2) system, detection oligonucleotides comprising a first target binding sequence, a linking region, and a second target binding sequence that mediate proximity ligation, and guide RNA to target a specific mtDNA sequence as taught by Zhang and provide a system comprising a CRISPR-Cas protein, detection oligonucleotides comprising a first target binding sequence, a linking sequence, and a second target binding sequence, and a guide RNA. It would also be obvious before the effective filling date, that the linking region as taught by Zhang, would have the amplification means employing a primer and a polymerase capable of replicating a target sequence as taught by Smargon. Doing so would allow for increased signal to noise detection of probes and efficient identification and specific recognition of CRISPR-Cas system for target sequence(s).
Response to Arguments
Applicant' s arguments filed 10/31/2025 (Pg. 9-12) with respect to claim 130 have been considered but are moot, because they do not apply to the new grounds of rejection.
Claims 131-132 are rejected under 35 U.S.C. 103 as being unpatentable over Smargon et al. (“Smargon”; US Patent App. Pub. No. US 20170211142 A1, July 27, 2017) in view of Zhang et al. (“Zhang”; (2018). Direct visualization of single-nucleotide variation in mtDNA using a CRISPR/Cas9-mediated proximity ligation assay. Journal of the American Chemical Society, 140(36), 11293-11301., August 20, 2018).
Smargon discloses systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA. (Abstract)
Regarding claims 131-132, Smargon teaches system “comprising i) a Type VI-B CRISPR-Cas effector protein, and ii) a Type VI-B CRISPR-Cas crRNA, wherein the crRNA comprises a) a guide sequence that is capable of hybridizing to a target RNA sequence, and b) a direct repeat sequence. The Type VI-B CRISPR-Cas effector protein forms a complex with the crRNA, and the guide sequence directs sequence-specific binding of the complex to the target RNA sequence, whereby there is formed a CRISPR complex comprising the Type VI-B CRISPR-Cas effector protein complexed with the guide sequence that is hybridized to the target RNA sequence” (Para. 14). “Type VI-B” is considered Cas 13b. Smargon also teaches a system comprising “two or more Type VI-B CRISPR-Cas crRNAs” (Para. 17). Smargon suggests a system comprising “independent guide RNAs targeting the same gene” (Para. 949). The MPEP states "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05). It would be obvious to the ordinary artisan to optimize the system to use two or more CRISPR-Cas proteins, and two or more guide RNAs. Thus, Smargon teaches a nucleic acid detection system comprising: two or more CRISPR-Cas proteins, and two or more guide RNAs, comprising a sequence capable of hybridizing to the guide RNA binding site.
Smargon does not explicitly teach a system comprising two or more sets of detection oligonucleotides, each set comprising a plurality of detection oligonucleotides, wherein each detection oligonucleotide in a set comprises:(i)a first target binding sequence,(ii) a linking region, and(ii) a second target binding sequence, wherein the linking region comprises a guide RNA binding site, wherein, when the first target binding sequence and the second target binding sequence bind a target sequence, the 5' and 3' terminal nucleotides of the detection oligonucleotide are disposed immediately adjacent to one another or are separated by a gap region comprising between 1 and 100 nucleotides, wherein each detection oligonucleotide in a set binds a unique target sequence of interest in the same genome, and wherein each detection oligonucleotide within a set of detection oligonucleotides comprises the same guide RNA binding site that identifies the set of detection oligonucleotide.
Zhang discloses CRISPR/Cas9- mediated proximity ligation assay (CasPLA) to image SNV in mtDNA at single-molecule resolution. This method uses two Cas9 probes to target a specific mtDNA sequence, followed by proximity ligation and in situ rolling circle amplification (RCA) to reveal the spatial localization of individual wild-type and mutated mtDNAs in single cells. (Pg. 11293, Introduction, Col. 2, Para. 2)
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Regarding claim 131-132, Zhang teaches a system wherein “this method uses two Cas9 probes to target a specific mtDNA sequence” (Pg. 11293, Col. 2, Para. 2; Scheme 1 see below). Zhang teaches a system as illustrated in Scheme 1 that depicts proximity ligation probes, with a first target binding sequence at the 5’ end, a linking region, and a second target binding sequence at the 3’ end. Zhang teaches a system as illustrated in Scheme 1 that depicts the linking region comprising a region interacting with guide RNA, thus reads on a guide RNA binding site of the detection oligonucleotide. “proximity ligation probes” reads on one or more detection oligonucleotides and the MPEP states "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05). It would be obvious to the ordinary artisan to optimize the system to use two detection oligonucleotides. Thus, Zhang teaches a system comprising detection oligonucleotides, wherein each detection oligonucleotide comprises in order from 5' to 3': (i) a first target binding sequences (ii) a linking region, and(iii) a second target binding sequence, wherein the linking region comprises a guide RNA binding site, wherein, when the first target binding sequence and the second target binding sequence bind a target sequence, the 5' and 3' terminal nucleotides of the detection oligonucleotide are disposed immediately adjacent to one another or are separated by a gap region comprising between 1 and 100 nucleotides, wherein each detection oligonucleotide binds a unique target sequence of interest in the same genome, and wherein each detection oligonucleotide comprises the same guide RNA binding site.
Smargon and Zhang are both considered to be analogous to the claimed invention because they are in the same field of targeting nucleic acids with CRISPR effector proteins and guide sequences. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the nucleic acid detection system comprising CRISPR effector protein(s) and guide RNA(s) as taught by Smargon to incorporate the system comprising CRISPR/Cas-9 (Class 2) system, detection oligonucleotides comprising a first target binding sequence, a linking region, and a second target binding sequence that mediate proximity ligation, and guide RNA to target a specific region of the genome as taught by Zhang and provide a system comprising two or more CRISPR-Cas protein, two or more detection oligonucleotides comprising a first target binding sequence, a linking sequence, and a second target binding sequence, and two or more guide RNA. The MPEP states, "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05). Doing so would allow for increased signal to noise detection of probes and efficient identification and specific recognition of CRISPR-Cas system for target sequence(s).
Response to Arguments
Applicant' s arguments filed 10/31/2025 (Pg. 6) with respect to claims 131-132 have been considered but are moot, because they do not apply to the new grounds of rejection.
Conclusion of Response to Arguments
In view of the amendments, new grounds of rejections and responses to arguments are documented in this Final Office Action. No claims are in condition for allowance.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Gootenberg et al. (“Gootenberg”; (2017). Nucleic acid detection with CRISPR-Cas13a Science, 356(6336), 438-442.). Claim 125-129 (Pg. 1 and 3-4; Figure 1 and 3)
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENDRA R VANN-OJUEKAIYE whose telephone number is (571)270-7529. The examiner can normally be reached M-F 9:00 AM- 5:00 PM.
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/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682