DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. Applicant’s election without traverse of Group I in the reply filed on February 11, 2026 is acknowledged.
Claims 1-2, 6, 13, 20-21, 23, 29-31, 35-39, 44, 53-54, 61, 75, and 78 are currently pending.
Claims 35-39, 44, 53-54, 75, and 78 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on February 11, 2026.
Claim Rejections - 35 USC § 102
3. The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 6, 13, 20, 21, and 31 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhang (WO 2019/071051 Pub 4/11/2019).
Regarding Claim 1 Zhang discloses a nucleic acid detection system comprising a CRISPR system, one or more guide RNAs designed to bind to corresponding target molecules, a reporter construct, and optional amplification reagents to amplify target nucleic acid molecules in a sample. The reporter construct is a molecule that comprises an oligonucleotide component (DNA or RNA) that can be cleaved by an activated CRISPR effector protein. The composition of the oligonucleotide component may be generic i.e. not the same as a target molecule. The reporter construct is configured so that it prevents or masks generation of a detectable positive signal when in the uncleaved configuration, but allows or facilitates generation of a positive detectable signal when cleaved (para 0143). Zhang teaches that amplification reactions may include dNTPs, nucleic acid primers, and a polymerase (para 0269). Zhang teaches the concept of a “one pot” reaction combining RPA-DNA amplification, T7 polymerase conversion of DNA to RNA and C2c2 detection (para 0450, Table 10). Thus Zhang teaches a system for detecting a target nucleic acid, comprising a buffer comprising:
i. amplification reagents (primers and polymerase) for an amplification reaction targeting the target nucleic acid; and
ii. detection reagents (a programmable nuclease, a non-naturally occurring guide nucleic acid, and reporters).
Zhang teaches that the non-naturally occurring guide nucleic acid comprises a sequence that hybridizes to a segment of the target nucleic acid or DNA amplicons thereof. Zhang teaches that the amplification reagents are present in amounts effective to amplify the target nucleic acid in a test sample to produce DNA amplicons of the target nucleic acid. Zhang teaches that the programmable nuclease and non-naturally occurring guide nucleic acid form a complex in the buffer that is activated upon binding one of the DNA amplicons to induce detectable transcollateral cleavage of the reporters.
Regarding Claim 6 Zhang teaches that target nucleic acids may be amplified prior to activating the CRISPR effector protein. Zhang teaches that the amplification can be isothermal amplification (para 0264). Zhang further discloses the reagents necessary for recombinase polymerase amplification (RPA), which is an isothermal amplification method (para 0432). Thus Zhang teaches a system wherein the amplification reagents comprise reagents for isothermal amplification.
Regarding Claim 13 Zhang teaches that the CRISPR-Cas effector protein may be a Cas12 protein, such as Cpf1 or C2cl (para 0010). Cas12 is a type V CRISPR/Cas effector protein.
Regarding Claim 20 Zhang teaches that amplification reactions may include dNTPs, primers, and polymerases (para 0269). Zhang further discloses that target RNA may be converted to cDNA using a reverse transcriptase (para 0266). Thus Zhang teaches a reverse transcriptase, an oligonucleotide primer, and dNTPs for reverse transcribing the target nucleic acid.
Regarding Claim 21 Zhang teaches a cell lysis component in order to break open or lyse a cell for analysis (para 0269). Thus Zhang teaches a lysis buffer.
Regarding Claim 31 Zhang teaches a substrate may be a flexible materials substrate, such as a paper substrate or a flexible polymer based substrate (para 0008). Zhang further teaches that reporting constructs comprise a first molecule and a second molecule connected by an RNA or DNA nucleic acid linker. Use of an RNA or DNA linker will depend on whether the CRISPR effector protein(s) used have RNA or DNA collateral activity. The first and second molecule are generally part of a binding pair, where the other binding partner is affixed to the lateral flow substrate. The systems further comprise a detection agent that specifically binds the second molecule and further comprises a detectable label (para 0143). Thus Zhang teaches a polymer matrix (substrate) that is complexed with the reporters.
Claim Rejections - 35 USC § 103
4. 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.
5. Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang (WO 2019/071051 Pub 4/11/2019) in view of Harrington (WO 2020/142739 Pub 7/9/2020 and Filed 1/3/2020) and Harrington (WO 2020/142754 Pub 7/9/2020 and Filed 1/3/2020).
The teachings of Zhang are presented above.
Zhang does not teach a system wherein (a) at least 1 nM of the reporters undergo transcollateral cleavage within one hour of addition of at least 5000 copies of the target nucleic acid to the system; (b) at least 5 nM of the reporters undergo transcollateral cleavage within one hour of addition of at least 5000 copies of the target nucleic acid to the system; (c) at least 10 nM of the reporters undergo transcollateral cleavage within one hour of addition of at least 5000 copies of the target nucleic acid to the system; (d) at least 1 nM of the reporters undergo transcollateral cleavage within one hour of addition of at least 1000 copies of the target nucleic acid to the system; or (e) at least 1 nM of the reporters undergo transcollateral cleavage within one hour of addition of at least 1000 copies of the target nucleic acid to the system.
However Harrington ‘739 teaches a system wherein the concentration of the ssDNA-FQ reporter can be from 1 nM to 10 nM (para 0204). Harrington ‘739 further discloses programmable nucleases with a high turnover rate. Programmable nucleases with a high turnover rate have a turnover rate of at least 90-100 cleaved detector molecules per minute (para 0095).
Additionally Harrington ‘754 teaches that samples comprise at least 1000-5000 copies of target nucleic acid (para 00269).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the system of Zhang such that the recited number of reporters undergo transcollateral cleavage within one hour of the addition of the recited copies of the target nucleic acid as suggested by Harrington ‘739 and ‘754. One of skill in the art would have been motivated to make the claimed system for the benefit of producing a superior system that can detect different amounts of target nucleic acids in a short amount of time.
6. Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang (WO 2019/071051 Pub 4/11/2019) in view of Nyan (CID 2014:59 (1 July 2014)).
The teachings of Zhang are presented above.
Zhang does not teach a system wherein the buffer comprises a pH of 7.25 to 8.75, at least 5 mM of a buffering agent, at least 7.5 mM potassium acetate, at least 1 mM magnesium acetate, and at least 0.5% glycerol.
However Nyan teaches a novel thermostable reaction buffer, the mannitol-acetate buffer (MAB; pH 7.8) was formulated and used for the LAMP reaction. MAB consisted of 2% D-mannitol; 0.2% Triton X-100; 0.5M L-proline; 10 mM Tris acetate; 1.6 mM magnesium acetate; 15 mM potassium acetate; 40 mM Tris hydrochloride; 20 mM potassium chloride; 20 mM ammonium sulfate; 6 mM magnesium sulfate; and 2 mM each deoxynucleotide triphosphate (page 17). Nyan additionally discloses nucleic acid from the clinical specimens was concentrated by the addition of 0.5 M ammonium-acetate and 0.05 mg/mL glycerol (page 17).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the system of Zhang wherein the buffer comprises a pH of 7.25 to 8.75, at least 5 mM of a buffering agent, at least 7.5 mM potassium acetate, at least 1 mM magnesium acetate, and at least 0.5% glycerol as suggested by Nyan. One of skill in the art would have been motivated to make a buffer that comprises a pH of 7.25 to 8.75, at least 5 mM of a buffering agent, at least 7.5 mM potassium acetate, at least 1 mM magnesium acetate, and at least 0.5% glycerol since Nyan teaches that this reaction buffer can be used for LAMP assays.
Further, to have determined the optimum concentration of reagents in the buffer would have been obvious to one of ordinary skill in the art and well within the skill of the art. As discussed in MPEP 2144.05(b), “(w)here 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. In re Aller, 220 F.2d 454, 105 USPQ 233, 235 (CCPA 1955).
MPEP 2144.05(b):
“Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. "[W]here 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." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955)”
“A particular parameter must first be recognized as a result-effective variable, i.e., a variable which achieves a recognized result, before the determination of the optimum or workable ranges of said variable might be characterized as routine experimentation. In re Antonie, 559 F.2d 618, 195 USPQ 6 (CCPA 1977).”
7. Claim 29 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang (WO 2019/071051 Pub 4/11/2019) in view of Yan (Mol BioSys 2014 10 970-1003).
The teachings of Zhang are presented above.
Zhang does not teach a system further comprising a circular template with internal complementarity formed from a single polynucleotide strand, wherein: (a) the circular template comprises a first portion with complementarity to one of the one or more oligonucleotide primers and a second portion with complementarity to a portion of the target nucleic acid; (b) the internal complementarity comprises part of the first portion and part of the second portion; (c) the second portion has a total length that is longer than a combined length of the first portion and second portion that are within the internal complementarity; and (d) the circular template undergoes a conformational change upon hybridization to the target nucleic acid to expose the first portion to hybridization to the oligonucleotide primer.
However Yan discloses target sequence recycled rolling circle amplification (TR-RCA). For TR-RCA, the circular DNA template that is required for the amplified sensing is already circularized but the primer-binding site is ‘‘sequestered’’ in the duplex region of the dumbbell. Upon target binding, the duplex region opens up to enable the primer to bind for the RCA process to begin. TR-RCA has been used to detect fM target (page 980).
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Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the system of Zhang in view of the teachings of Yan. One of skill in the art would have been motivated to make a system with a circular template with internal complementarity formed from a single polynucleotide strand since Yan teach that such configurations have been used to detect fM target (page 980).
8. Claim 30 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang (WO 2019/071051 Pub 4/11/2019) in view of Yan (Mol BioSys 2014 10 970-1003) and Kenten (WO 2021/236584 Filed 5/18/2021 with priority back to 63/032,031 Filed 5/29/2020)
The teachings of Zhang are presented above.
Zhang does not teach a system further comprising circular template, wherein:(a) the circular template comprises a first portion with complementarity to one of the one or more oligonucleotide primers and a second portion with complementarity to the target nucleic acid; (b) the oligonucleotide primer complementary to the first portion comprises a blocking motif at its 3' end; and (c) the oligonucleotide primer complementary to the first portion undergoes cleavage to remove the blocking motif by the programmable nuclease in the presence of the target nucleic acid.
However Yan discloses target sequence recycled rolling circle amplification (TR-RCA). For TR-RCA, the circular DNA template that is required for the amplified sensing is already circularized but the primer-binding site is ‘‘sequestered’’ in the duplex region of the dumbbell. Upon target binding, the duplex region opens up to enable the primer to bind for the RCA process to begin. TR-RCA has been used to detect fM target (page 980).
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Additionally Kenten discloses an oligonucleotide detection reagent that comprises, in 5' to 3' order, a targeting agent complement (TAC), an amplification primer, a nuclease cleavage site, and an amplification blocker. A Cas 13 complex binds a nucleic acid of interest, thereby activating collateral cleavage activity of the Cas 13. The Cas 13 collaterally cleaves one or more copies of the oligonucleotide detection reagent, thereby generating one or more first cleaved oligonucleotides, each comprising the TAC and the amplification primer. The first cleaved oligonucleotide(s) are subjected to extension and detection (0013).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the system of Zhang in view of the teachings of Yan. One of skill in the art would have been motivated to make a system with a circular template with internal complementarity formed from a single polynucleotide strand since Yan teach that such configurations have been used to detect fM target (page 980). Further it would have been obvious to modify the primer of Yan such that it contains a blocking group at the 3’ end that gets cleaved by a programmable nuclease in the presence of the target as suggested by Kenten. One of skill in the art would have been motivated to make the claimed primer for the benefit of being able to control when the rolling circle amplification process starts.
9. Claim 61 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang (WO 2019/071051 Pub 4/11/2019) in view of Bokelmann (medRxiv preprint doi: https://doi.org/10.1101/2020.08.04.20168617 August 6, 2020).
The teachings of Zhang are presented above.
Zhang does not teach a system that further comprises thermostable inorganic pyrophosphatase (TIPP).
However Bokelmann teaches performing isothermal amplification in the presence of thermostable inorganic pyrophosphatase (TIPP) (pages 4, 8, 15).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the system of Zhang by adding thermostable inorganic pyrophosphatase (TIPP) as suggested by Bokelmann. One of skill in the art would have been motivated to add thermostable inorganic pyrophosphatase (TIPP) to an isothermal amplification system since Bokelmann teaches thermostable inorganic pyrophosphatase increases reaction speed (page 4)
10. Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMANDA HANEY whose telephone number is (571)272-8668. The examiner can normally be reached Monday-Friday, 8:15am-4:45pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Shen can be reached at 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AMANDA HANEY/Primary Examiner, Art Unit 1682
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