1DETAILED 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 .
Applicants’ reply to the August 11, 2025 Office Action, filed February 11, 2026, is acknowledged. Applicants’ previously canceled claims 1-57. Applicants amend claims 71-72. Claims 58-77 are pending in this application and are under examination.
Any objection or rejection of record in the previous Office Action, mailed August 11, 2025, which is not addressed in this action has been withdrawn in light of Applicants’ amendments and/or arguments. This action is FINAL.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 58-69 are rejected under 35 U.S.C. 103 as being unpatentable over Reeks et al. (452 Biochemical Journal 223-230 (2013), and cited in the Information Disclosure Statement filed April 21, 2022), as evidenced by Simeonov (8(9) Expert Opinion on Drug Discovery 1071-1082 (2013), and cited in the Information Disclosure Statement filed April 21, 2022), in view of Doudna et al. (U.S. Patent Application Publication No. 2014/068797, published March 6, 2014, and cited in the Information Disclosure Statement filed April 21, 2022).
Regarding claims 58 and 64, Reeks discloses CRISPR-Cas6 enzyme proteins and complexes with crRNA sequences to detect and degrade invading DNA or RNA (abstract and page 223, column 1, first paragraph). Reeks discloses that CRISPR enzymes include Cas9 (page 223, paragraph bridging columns 1 and 2). Simeonov discloses the use of differential scanning fluorometry (DSF) to determine stability of proteins in a temperature-ramp regime (abstract). Simeonov discloses that DSF can be used to determine the melting temperature (Tm) of proteins to determine the impact of mutations, storage conditions, and use of stabilizers of proteins (page 1071, first paragraph). Simeonov further discloses that the DSF method is also known as the Thermofluor method, and when used with SYPROOrange™, is a thermal shift assay (page 1072, column 2, first and second full paragraphs and Table 1). Thus, Reeks’ assay is deemed to be a thermal shift assay using DSF.
Regarding claims 59, 65, and 75, Reeks discloses that the stability of the CRISPR protein can be determined using a thermofluor assay, which is interpreted as being a thermal shift assay using SYPROOrange™, where the melting point is determined as the temperature is raised from 25 °C to 95 °C (page 225, column 1, first full paragraph).
Regarding claims 60, 66, and 76, Simeonov discloses that DSF can be used to determine the melting temperature (Tm) of proteins to determine the impact of mutations, storage conditions, and use of stabilizers of proteins (page 1071, first paragraph). Simeonov further discloses that the DSF method is also known as the Thermofluor method, and when used with SYPROOrange™, is a thermal shift assay (page 1072, column 2, first and second full paragraphs and Table 1). Thus, Reeks’ assay is deemed to be a thermal shift assay using DSF.
Regarding claims 61, 67, and 77, Reeks discloses that the inflection point of the thermal profile was determined to be the melting point (page 225, column 1, first full paragraph).
Regarding claims 62 and 68, Reeks discloses that the melting point of a monomeric protein was 68 °C, while the melting point of a dimeric protein is 75 °C (page 226, paragraph bridging columns 1 and 2 and Figure 3).
Reeks, as evidenced by Simeonov, fails to disclose or suggest screening for or determining the stability of CRISPR-Cas9/guide RNA complexes. Reeks, as evidenced by Simeonov, fails to disclose or suggest use of a variety of reference molecules or Tm reference values. Reeks, as evidenced by Simeonov, fails to disclose using the proportion of Cas9 molecule and gRNA molecule relative to the complex being evaluated.
Doudna discloses that the stability of guide RNAs is enhanced by the presence of Cas9 (paragraph [0691]). Doudna discloses that the Cas9 can be from S. pyogenes (paragraph [0749]). Doudna discloses that the CRISPR-Cas9/guide RNA complex is stabilized by basepairing between the crRNA and the DNA target (paragraph [0749]).
It would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to substitute Doudna’s CRISPR-Cas9/guide RNA complexes, including those obtained from S. pyogenes, for Reeks’ Cas6 protein in an assay for determining stability or screening for a CRISPR/guide RNA complex because these are both well-known CRISPR enzymes/complexes, as evidenced by Simeonov. Thus, one of ordinary skill in the art would have a predictable and reasonable expectation of success in substituting Doudna’s Cas9/guide RNA complex for Reeks’ Cas enzyme.
Further, it would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to employ a reference molecule of either a Cas9 molecule or complex with the same or different guide RNAs, or having a specified proportion of Cas9 to gRNA relative to the test complex, or Tm in the screening/stability determination assays, including a Tm range and conditions of complex formation, which may be pre-determined, for a desired CRISPR-Cas9/guide RNA complex, as disclosed and suggested by Reeks, as evidenced by Simeonov, and Doudna because this allows for accuracy and reproducibility of an assay, where control and reference standards are routinely used in order to provide such accurate and reproducible results.
Claims 70-77 are rejected under 35 U.S.C. 103 as being unpatentable over Reeks, as evidenced by Simeonov, in view of Doudna as applied to claims 58-69 above, and further in view of Wu et al. (32(7) Nature Biotechnology 670-676. Online Methods (2014), and cited in the Information Disclosure Statement filed April 21, 2022).
Reeks, as evidenced by Simeonov, in view of Doudna disclose methods of screening Cas9/gRNA complexes, and determination of stability thereof, using thermal assays and melting temperatures
Reeks, as evidenced by Simeonov, in view of Doudna fail to disclose or suggest determining the stability of a Cas9/gRNA complex using binding assays. Reeks, as evidenced by Simeonov, in view of Doudna fail to disclose or suggest the specific binding assays employed.
Regarding claim 70, Wu discloses that inactive Cas9 can be loaded with guide RNAs in mouse embryonic stem cells (abstract). Wu discloses a two-stage model of Cas9 binding and cleavage (abstract).
Regarding claim 71, Wu discloses that the ability of a Cas9/gRNA complex to target sites can be measured, which is interpreted as including measuring the binding of the complex components (paragraph bridging pages 670 and 671 and Figure 1).
Regarding claim 72, Wu discloses the use of libraries as control samples, which is interpreted as being able to determine a relative binding value of a Cas9/gRNA Page 671, column 1, second full paragraph to column 2, second full paragraph).
Regarding, claims 73-74, Wu discloses testing the binding ability of the Cas9/gRNA complex by use of in vitro gel shift assays (a kinetic assay to determine binding activity (page 671, column 2, first full paragraph, Figure 2, and Online Methods, Gel Shift Assy).
It would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to use Wu’s gel shift assay to determine the binding ability of the Cas9/gRNA complex in order to determine the stability of the complex according to Reeks, as evidenced by Simeonov, and Doudna. One of ordinary skill in the art would have had a predictable and reasonable expectation of success in using Wu’s assay, in conjunction with the thermal stability assay of Reeks, as evidenced by Simeonov, and Doudna because by measuring the binding ability of a Cas9/gRNA complex can provide information as to the ability of the complex to act on a target sequence, whether inducing cleavage, insertions, or deletions of sequences.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 58-69 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of U.S. Patent No. 11,180,793.
Although the claims at issue are not identical, they are not patentably distinct from each other because both the ‘793 patent and the instant application claim methods of screening for and determining the stability of Cas9/gRNA complexes using melting point determinations and comparisons with reference Cas9/gRNA complexes. Both the ‘793 patent and the instant application claim methods of determining the stability of such complexes using thermal assays, including differential scanning fluorimetry, differential scanning calorimetry, or isothermal titration calorimetry. Because the claims for the ’793 patent and the instant application claim the same methods having the same steps, the claims are not deemed to be patentably distinct.
Claims 70-77 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of U.S. Patent No. 11,180,793 in view of Wu et al. (32(7) Nature Biotechnology 670-676. Online Methods (2014), and cited in the Information Disclosure Statement filed April 21, 2022).
The ‘793 patent claims methods of screening for and determining the stability of Cas9/gRNA complexes.
The ‘793 patent does not claim methods of determining binding activity of the Cas9/gRNA complex.
Regarding claim 70, Wu discloses that inactive Cas9 can be loaded with guide RNAs in mouse embryonic stem cells (abstract). Wu discloses a two-stage model of Cas9 binding and cleavage (abstract).
Regarding claim 71, Wu discloses that the ability of a Cas9/gRNA complex to target sites can be measured, which is interpreted as including measuring the binding of the complex components (paragraph bridging pages 670 and 671 and Figure 1).
Regarding claim 72, Wu discloses the use of libraries as control samples, which is interpreted as being able to determine a relative binding value of a Cas9/gRNA Page 671, column 1, second full paragraph to column 2, second full paragraph).
Regarding, claims 73-74, Wu discloses testing the binding ability of the Cas9/gRNA complex by use of in vitro gel shift assays (a kinetic assay to determine binding activity (page 671, column 2, first full paragraph, Figure 2, and Online Methods, Gel Shift Assy).
It would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to use Wu’s gel shift assay to determine the binding ability of the Cas9/gRNA complex in order to determine the stability of the complex according to the ‘793 patent. One of ordinary skill in the art would have had a predictable and reasonable expectation of success in using Wu’s assay, in conjunction with the thermal stability assay of the ‘793 patent because by measuring the binding ability of a Cas9/gRNA complex can provide information as to the ability of the complex to act on a target sequence, whether inducing cleavage, insertions, or deletions of sequences.
Response to Amendments and Arguments
Regarding the rejections under 35 U.S.C. § 103, Applicant's arguments have been fully considered but they are not deemed to be persuasive.
To begin, Applicants appear to be attacking the cited prior art references individually. However, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. In re Keller, 642 F.2d 413 208 USPQ 871 (CCPA 1981); In re Merck & Co., Inc., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Here, the combination of Reeks (as evidenced by Simeonov) and Doudna taken together and as a whole is deemed to render the claimed invention obvious. While Reeks does disclose a thermofluor assay for protein stability using a CRISPR-Cas6 protein, Reeks also does disclose Cas9 as being a CRISPR protein. Further, Simeonov’s disclosure provides for Reeks’ assay is deemed to be a thermal shift assay using DSF. And while Doudna does not disclose using a thermal shift assay, Doudna does disclose Cas9. And taken together, and as a whole, it is the combination of Reeks (as evidenced by Simeonov) and Doudna that would have led one of ordinary skill in the art to apply the thermal shift assay to a protein and guide RNA, with the expectation that the protein thermofluor assay could be applied successfully to a Cas9-guide RNA complex. The motivation to apply the thermofluor assay to the Cas9-guide RNA complex is the same as what’s found in Reeks – to determine the stability of a protein (Cas6) or a protein-RNA complex (Cas9-guide RNA).
Regarding Applicants’ assertion of impermissible hindsight, it is noted that “[a]ny judgment on obviousness is in a sense necessarily a reconstruction based on hindsight reasoning, but so long as it takes into account only knowledge which was within the level of ordinary skill in the art at the time the claimed invention as made and does not include knowledge gleaned only from applicant’s disclosure, such a reconstruction is proper.” In re McLaughlin, 443, F.2d 1392, 1395, 170 USPQ 209, 212 (CCPA 1971). Here, the thermofluor assay was known to be applicable to Cas6 proteins to determine stability, as shown by Reeks, as evidenced by Simeonov. And Reeks notes that Cas9 is a known CRISPR protein. Doudna provides for the Cas9-guide RNA complex. And one of ordinary skill in the art, having Reeks (and Simeonov) and Doudna in front of them would have found it reasonable to apply the thermofluor assay to the Cas9-guide RNA complex to determine the stability of such a complex. At the very least, one of ordinary skill in the art would have found it obvious to try applying the thermofluor assay of Reeks (as evidenced by Simeonov) to the Cas9-guide RNA complex of Doudna. “[A] person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely that produce [was] not of innovation but of ordinary skill and common sense. It that instance the fact that a combination was obvious to try might show that it was obvious under § 103.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 421, 82 USPQ2d 1385m 1397 (2007).
In addition, Applicants have not provided any objective, factually-supported evidence that the thermofluor assay of Reeks (as evidenced by Simeonov) would not function for a Cas9 protein, as required by the claims. Applicants have provided only arguments of counsel. And arguments of counsel cannot take the place of factually supported objective evidence. See, e.g., In re Huang, 100 F.3d 135,139-40, 40 USPQ2d 1685, 1689 (Fed. Cir. 1996); In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984).
It is noted that Wu (regarding claims 70-77) is cited for the disclosure of a gel shift assay to determine the binding ability of the Cas9/gRNA. While Wu does not disclose determination of melting temperature or stability, these limitations are disclosed and suggested by the combination of Reeks (as evidenced by Simeonov) and Doudna, as discussed above. Wu is not cited for disclosure of those limitations.
For all these reasons, and those listed above, the combination of Reeks (as evidenced by Simeonov) and Doudna (with or without Wu) is deemed to render the claimed invention obvious.
Regarding the non-statutory double patenting rejections over U.S. Patent No. 11,180,793, Applicants request that these rejections be held in abeyance until the claims are otherwise indicated as allowable. Therefore, these rejections are maintained.
Conclusion
THIS ACTION IS MADE FINAL. 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 NANCY J LEITH whose telephone number is (313)446-4874. The examiner can normally be reached Monday - Thursday 8:00 AM - 6:30 PM.
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NANCY J. LEITH
Primary Examiner
Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636