DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 02/12/2026 has been entered.
Claims Status
Claims 1-3, 5-9, & 18-20 filed on 02/12/2026 are pending. Claims 10-16 are withdrawn from consideration as being drawn to a non-elected invention. The new claim 20 in the reply filed on 02/12/2026 is acknowledged. It is noted, as discussed in the previous office action dated 11/13/2025, that the reply filed on 02/12/2026 continues to indicate that claim 9 has been previously cancelled, however, the claims filed on 02/12/2026 indicate that claim 9 is previously presented and not cancelled. All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant application. Response to Applicant’s argument follow. This action is Non-FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
Claim Rejections - 35 USC § 103
Claim(s) 1, 3, 8, 9, & 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Rouillon (Rouillon et al.; eLife, Vol. 7, pages 1-22, July 2018), as cited in the IDS dates 12/16/2021, in view of Gootenberg (Gootenberg et al.; Science, Vol. 360, pages 1-14, April 2018).
Regarding amended claim 1, Rouillon teaches a Solfolobus solfataricus (S. solfataricus), which encodes for two Type III effector systems including a Cmr Type III-B complex and a Csm Type III-D complex, and further teaches Csm/III-D CRISPR complex (Type III CRISPR-associated effector protein) that generates cOA in response to target RNA binding to a CRISPR RNA (crRNA), activating a CARF-domain nuclease Csx1 for RNA degradation (pg. 3 1st full paragraph lines 1-7; pg. 6 & 8 paragraph bridging pg. 6 & pg. 8 lines 1-4) and further monitoring cOA production (an enzyme or substrate which directly or indirectly determines the level of cOA) (pg. 2-3 paragraph bridging pg. 2 & pg. 3 lines 1-6; pg. 8 1st full paragraph lines 1-7; Figure 4).
Rouillon does not teach the system comprises an amplification system for amplification of a target nucleic acid.
Gootenberg teaches a system for detecting target nucleic acids comprising pre-amplification (an amplification system for amplification of a target nucleic acid) and a CRISPR type-III effector nuclease system which is activated by cyclic adenylate molecules (Type III CRISPR-Cas system) (pg. 3 1st full paragraph lines 1-6; pg. 3 2nd full paragraph lines 1-14). Gootenberg also teaches that the system comprising pre-amplification of the target nucleic acids (amplification system for amplification of a target nucleic acid) and a CRISPR type-III effector nuclease system enables amplified signal detection and quantitative accuracy of the assay (pg. 3 1st full paragraph lines 1-6; pg. 3 2nd full paragraph lines 1-14).
Rouillon and Gootenberg are considered to be analogous to the claimed invention because they are all in the same field of Type III CRISPR-Cas systems. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified a Type III CRISPR-Cas system in Rouillon to incorporate an amplification system with the CRISPR type-III effector nuclease system as taught in Gootenberg because Gootenberg teaches that the amplification system enables pre-amplification of target nucleic acids leading to amplified signal detection and quantitative accuracy in the system.
Regarding claim 3, Rouillon teaches the type III CRISPR system is from the heat-loving microbe Solfolobus solfataricus that is found in volcanic springs (from a thermophylic organism) (pg. 2 3rd full paragraph lines 1-8; pg. 2-3 paragraph bridging pg. 2 & pg. 3 lines 1-4; pg. 3 1st full paragraph lines 1-7).
Regarding claims 8 & 19, pg. 7-8 of the specification teaches the term “cOA-dependent, non-specific effector ribonuclease” refers to ribonucleases which degrade RNA non-specifically using a HEPN active site which are activated by binding of a cOA messenger using their CARF domain and further that examples of these ribonucleases include Csx1 and Csm6.
Rouillon teaches the type III CRISPR system activates the CARF-domain nuclease Csx1 (cOA-dependent, non-specific effector endoribonuclease) in response to generation of cOA from target RNA binding (pg. 2 6th full paragraph lines 1-6 & 13-15; pg. 3 1st full paragraph lines 1-7; pg. 3-4 paragraph bridging pg. 3 & pg. 4 lines 2-3).
Regarding amended claim 9, Rouillon teaches incubating Csx1 with cOA activator and P-5’- labelled substrate RNA (detectable substrate) in Csx1 buffer so that RNA cleavage could be visualized by phosphorimaging followed by denaturing gel electrophoresis (pg. 19 1st full paragraph lines 1-8).
Claim(s) 2, 18, & 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Rouillon (Rouillon et al.; eLife, Vol. 7, pages 1-22, July 2018), as cited in the IDS dates 12/16/2021, and Gootenberg (Gootenberg et al.; Science, Vol. 360, pages 1-14, April 2018), as being applied to claims 1, 3, 8, 9, & 19 above, and further in view of Ramia (Ramia et al.; Cell Reports, Vol. 9, pages 1610-1617, December 2014).
The teachings of Rouillon and Gootenberg with respect to claim 1 are discussed above.
Regarding claims 2, 18, & 20, Rouillon does not teach that the Type III Cas is a Type IIIB Cmr (see claims 2 & 18) or that the Type III Cas is a Type III Cas7 lacking cleavage activity (see claim 20).
Ramia teaches mutations of Cmr4 (Type IIIB Cas) on target RNA cleavage activity and crRNA-binding/Cmr complex formation in which cleavage was abolished by the D26A mutation (pg. 1614 column 1 1st full paragraph lines 9-12 & 23-26). Ramia also teaches that while the Cmr4 D26A mutation resulted in the loss of target RNA cleavage (Type III Cas lacks cleavage activity), this mutation did not lead to a loss if crRNA association/Cmr complex assembly (Type III Cas7 lacking cleavage activity is Cmr4 ) (pg. 1614 column 1 2nd full paragraph lines 4-15; Figure 4).
Rouillon, Gootenberg, and Ramia are considered to be analogous to the claimed invention because they are all in the same field of Type III CRISPR-Cas systems. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified a Type III CRISPR-Cas system that does not lack cleavage activity in Rouillon to incorporate the use of a Type IIIB Cmr Cas that lacks cleavage activity as taught in Ramia because Ramia teaches that the Cmr4 D26A mutation abolishes cleavage activity without effecting the crRNA association/Cmr complex assembly.
Claim(s) 5-7 is/are rejected under 35 U.S.C. 103 as being unpatentable over Rouillon (Rouillon et al.; eLife, Vol. 7, pages 1-22, July 2018), as cited in the IDS dates 12/16/2021, and Gootenberg (Gootenberg et al.; Science, Vol. 360, pages 1-14, April 2018), as being applied to claims 1, 3, 8, 9, & 19 above, and further in view of Niewoehner (Niewoehner et at.; Nature, Vol. 548, pages 543-548, August 2017), as cited in the IDS dated 12/16/2021, and Pegan (Pegan, Tian, Sershon, & Mesecar; Combinatorial Chemistry & Hight Throughput Screening, Vol. 13, pages 27-38, March 2009).
The teachings of Rouillon and Gootenberg with respect to claim 1 are discussed above.
Regarding amended claim 5 & claim 6, Rouillon and Gootenberg does not teach an enzyme or substrate that directly or indirectly determines the level of cOA comprises an enzyme or substrate which determines the level of pyrophosphate (PPi) or inorganic pyrophosphate from a thermophylic organism.
Niewoehner teaches type III CRISPR-Cas systems bind target RNA by the interference complex leading to its Cas10 subunit to covert ATP into a cOA product (abstract lines 1-3 & 6-8) and further teaches the mechanism of cOA synthesis by Cas10 leads to the formation of inorganic pyrophosphate (PPi) (pg. 547 column 2 1st full paragraph lines 1-12 & 17-28; Extended Data Figure 10).
Niewoehner does not teach detecting levels of inorganic pyrophosphate (PPi) generated by cOA which determines the level of cOA.
Pegan teaches a method for optimizing the malachite green assay that is a universal assay for measuring the presence of inorganic pyrophosphate concentrations for the majority of enzymes that release phosphate or pyrophosphate (abstract lines 1-7). Pegan also teaches that the malachite green assay for inorganic pyrophosphate detection showed the most potential between assays that could be used universally for any enzyme that releases PPi or Pi due to its lost cost and ability to become a high-throughput screening tool (pg. 28 paragraph bridging column 1 & 2 lines 1-4; pg. 29 paragraph bridging column 1 & 2 lines 1-23; Table 1).
Rouillon, Gootenberg, Niewoehner, and Pegan are considered to be analogous to the claimed invention because they are all in the same field of target detection methods. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified detecting levels of cOA in a Type III CRISPR-Cas system in Rouillon to incorporate determining the level of pyrophosphate or inorganic pyrophosphate with the malachite green assay as taught in Pegan, as Niewoehner teaches inorganic pyrophosphate (PPi) is generated from cOA synthesis, because Pegan teaches that the malachite green assay is low cost and the most potential for use as a high-throughput screening tool for detecting inorganic pyrophosphate released from enzymes.
Regarding claim 7, Rouillon teaches the type III CRISPR system is from the heat-loving microbe Solfolobus solfataricus that is found in volcanic springs (from a thermophylic organism) (pg. 2 3rd full paragraph lines 1-8; pg. 2-3 paragraph bridging pg. 2 & pg. 3 lines 1-4; pg. 3 1st full paragraph lines 1-7).
Response to Arguments
The response traverses the rejection. The response asserts that the present invention is focused on a detection system that uses a Type III CRISPR-Cas system for detection of target nucleic acids and that the claimed subject matter is thus distinguishable from that of Rouillon and Ramia because both Rouillon and Ramia are concerned solely with academic research to characterize Type III CRISPR-Cas systems and that neither Rouillon or Ramia suggests or even hints at that a Type III CRISPR-Cas system would be useful in a detection system as presently claimed. These arguments have been thoroughly reviewed but were not found persuasive as claim 1, as currently amended, is drawn to a system comprising an effector complex comprising type III CRISPR-associated protein (Cas) and at least one CRISPR RNA (crRNA) that binds to the target nucleic acid molecule in which Rouillon teaches a Solfolobus solfataricus (S. solfataricus), which encodes for two Type III effector systems including a Cmr Type III-B complex and a Csm Type III-D complex, and further teaches Csm/III-D CRISPR complex (Type III CRISPR-associated effector protein) that generates cOA in response to target RNA binding to a CRISPR RNA (crRNA) (detection system for target nucleic acid) (pg. 2-3 paragraph bridging pg. 2 & pg. 3 lines 1-6; pg. 8 1st full paragraph lines 1-7; Figure 4). Therefore, Rouillon teaches an effector complex comprising type III CRISPR-associated protein (Cas) as recited in b) of claim 1 is currently amended. Further, Applicant’s arguments rely on language solely recited in preamble recitations in claim(s) 1. When reading the preamble in the context of the entire claim, the recitation "a clustered regularly interspaced short palindromic repeats (CRISPR) based ribonucleic acid detection system comprising:" is not limiting because the body of the claim describes a complete invention and the language recited solely in the preamble does not provide any distinct definition of any of the claimed invention’s limitations. Thus, the preamble of the claim(s) is not considered a limitation and is of no significance to claim construction. See Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See MPEP § 2111.02.
The response also asserts that neither Rouillon nor Ramia discloses a detection system that comprises an amplification system as presently claimed and, accordingly, the amended claims are unobvious over Rouillon and Ramia. Further, the response asserts that the role of the amplification system in the detection system is to improve detection of target nucleic acids by improving sensitivity and/or accelerating the detection process through pre-amplifying the target nucleic acid and that is would not be obvious for the skilled person to modify either Rouillon or Ramia to introduce an amplification system. Specifically, the response asserts that Rouillon and Ramia disclose Tyle III CRISPR-Cas complexes that were used solely in experiments to analyze the structure and enzyme kinetics of the Tyle III CRISPR-Cas systems and that the introduction of an amplification system would be undesirable in Rouillon and Ramia as it would be incompatible with the purpose of Rouillon and Ramia to generate structural data and conduct studies on enzyme kinetics. Further, the response asserts that in Ramia and Rouillon the target RNA was provided as a controlled amount of pre-prepared target RNA and therefore the amplification of the target RNA is incompatible with the systems and approaches used in Rouillon and Ramia and would frustrate the principle of operation of the structural and kinetic studies of Rouillon and Ramia. These arguments have been thoroughly reviewed but were not found persuasive. First, the prior art of Rouillon and Gootenberg, as applied to claim 1 as necessitated by amendment, appreciates an amplification system with a Type III CRISPR-Cas system as Gootenberg teaches a system for detecting target nucleic acids comprising pre-amplification (an amplification system for amplification of a target nucleic acid) and a CRISPR type-III effector nuclease system which is activated by cyclic adenylate molecules (Type III CRISPR-Cas system) (pg. 3 1st full paragraph lines 1-6; pg. 3 2nd full paragraph lines 1-14). Further, an intended purpose of Rouillon is to bind target RNA and monitor cOA production, as discussed further above, and Gootenberg also teaches that the system comprising pre-amplification of the target nucleic acids (amplification system for amplification of a target nucleic acid) and a CRISPR type-III effector nuclease system enables amplified signal detection and quantitative accuracy of the assay (pg. 3 1st full paragraph lines 1-6; pg. 3 2nd full paragraph lines 1-14). Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified a Type III CRISPR-Cas system in Rouillon to incorporate an amplification system with the CRISPR type-III effector nuclease system as taught in Gootenberg because Gootenberg teaches that the amplification system enables pre-amplification of target nucleic acids leading to amplified signal detection and quantitative accuracy in the system as discussed further above. Second, applicants arguments cannot take place of evidence in the record.
The response also asserts that neither Niewoehner nor Pegan cures the deficiencies of Rouillon and Ramia for similar reasons as described above for Rouillon and Ramia and therefore, the amended claims are unobvious over Rouillon, Ramia, Niewoehner, and Pegan. These arguments have been thoroughly reviewed but were not found persuasive for the reasons set forth above.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Conclusion
Claims 1-3, 5-9, & 18-20 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY C BUCHANAN whose telephone number is (703)756-1315. The examiner can normally be reached Monday-Friday 8:00am-5:00pm ET.
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/BAILEY BUCHANAN/Examiner, Art Unit 1682
/JEHANNE S SITTON/Primary Examiner, Art Unit 1682
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