DETAILED ACTION
Status of the Application
Claims 1, 6, 8, 14-17, 19-21 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment of claim 1 as submitted in a communication filed on 11/26/2025 is acknowledged.
In view of Applicant’s election of the polypeptide of SEQ ID NO: 591, claims 1, 6, 8, 14-17, 19-21 have been examined only to the extent they encompasses the Cas polypeptide of SEQ ID NO: 591.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
Claims 1, 6, 8, 14-17, 19-21 were rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention. In view of Applicant’s amendment of claim 1, this rejection is hereby withdrawn.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
Claims 1, 6, 8, 14-17, 19-21 remain rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for an in vitro method that comprises the steps of (i) contacting a sample that comprises a target RNA with a composition that comprises a Cas polypeptide, a guide RNA, labeled non-target nucleic acids which are not complementary to the guide RNA and magnesium, (ii) detecting cleavage of said non-target RNAs in the sample, and (iii) comparing the cleavage of said non-target RNAs in the sample in the presence and absence of the target RNA, does not reasonably provide enablement for an in vitro method, wherein said method consists of the steps of (a) contacting a sample with a Cas polypeptide and a guide RNA in the presence of magnesium, wherein the guide RNA forms a complex with the Cas polypeptide and directs binding of the complex to a target RNA, wherein the Cas polypeptide comprises SEQ ID NO: 591 or an amino acid sequence at least 95% sequence identical to SEQ ID NO: 591, (b) detecting cleavage of one or more non-target nucleic acids in the sample, and (c) comparing the cleavage of one or more non-target nucleic acids in the presence and in the absence of the target RNA in the sample, wherein the Cas polypeptide cleaves the target RNA and one or more non-target nucleic acids in the sample. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
This rejection has been discussed at length in prior Office actions. It is maintained for the reasons of record and those set forth below.
Applicant argues that the specification as originally filed provides clear and direct enablement for methods using compositions consisting of a Cas polypeptide, a guide RNA, and magnesium. Applicant states that paragraph [01016] of the specification explicitly discloses magnesium in the reaction conditions, while paragraph [0160] provides additional enablement by describing C2c2-mediated RNA cleavage, demonstrating multiple cleavage products and significant reduction in intensity of the target band. Applicant states that the working examples demonstrate the claimed steps. Applicant states that paragraph [1016] demonstrates step (1) by contacting a sample in the presence of magnesium, and steps (2) and (3) by the detection and analysis methodology. Applicant refers to paragraphs [200], [208], [213], [939], [996], and [999]-[1000] as explicitly supporting the detection of cleavage of non-target nucleic acids, while the comparative methodology is demonstrated throughout the experimental sections. Applicant states that the Office incorrectly distinguishes “comprises” vs. “consisting of” and that “consists of” in the context of a method does not exclude the molecular interactions that necessarily follow, such as binding and cleavage after contacting the sample with the Cas polypeptide and the guide RNA in the presence of magnesium. Applicant states that the Office incorrectly treats “comprising” as if it mandates additional components. Applicant states that when a specification describes a method “comprising” certain steps and demonstrates their functionality, it inherently discloses and enables the narrower subset “consisting of”. Applicant states that paragraphs [1016], [160], [725], and [183] along with related examples provide multiple working examples that fall squarely within the claimed scope.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection. The Examiner acknowledges the amendment made to claim 1. However, the Examiner disagrees with Applicant’s contention that the claimed invention is enabled.
Claims 1, 6, 8, 14-17, 19-21 as amended are directed to an in vitro method that consists of three steps, which are (a) contacting a sample with a Cas polypeptide and a guide RNA in the presence of magnesium, wherein the guide RNA forms a complex with the Cas polypeptide and directs binding of the complex to a target RNA, wherein the Cas polypeptide comprises SEQ ID NO: 591 or an amino acid sequence at least 95% sequence identical to SEQ ID NO: 591, (b) detecting cleavage of one or more non-target nucleic acids in the sample, and (c) comparing the cleavage of one or more non-target nucleic acids in the presence and in the absence of the target RNA in the sample, wherein the Cas polypeptide cleaves the target RNA and one or more non-target nucleic acids in the sample.
With regard to the argument that a composition that consists of a Cas polypeptide, a guide RNA, and magnesium is enabled, it is noted that a composition that only has a Cas polypeptide, a guide RNA, and magnesium cannot be used to cleave a polynucleotide, which is the use disclosed for the Cas polypeptide. There is not a single example of how one could cleave a nucleic acid with a composition where the only components are a Cas polypeptide, a guide RNA and magnesium without buffers, additional salts, cofactors, etc. Applicant is referred to paragraphs [1016], [0160] and [0183] where it is abundantly clear that cleavage of a polynucleotide is obtained with compositions that comprise a Cas polypeptide, a guide RNA and magnesium but not with compositions that consist of a Cas polypeptide, a guide RNA and magnesium. Therefore, while one could make a composition that consists only of a Cas polypeptide, a guide RNA, and magnesium, there is no disclosed use for such composition, and Applicant has not disclosed how to cleave a polynucleotide with a composition that consists only of a Cas polypeptide, a guide RNA, and magnesium.
While it is agreed that (a) paragraph [01016] describes a nuclease assay where a nuclease assay buffer is used that comprises magnesium, (b) paragraph [0160] refers to Figure 71 as disclosing the results of an assay where a C2c2 protein from Leptotrichia shahii (Cas polypeptide) was used to cleave an RNA target using two different buffers, both comprising magnesium, (c) paragraph [0183] refers to Figure 94 as disclosing that a C2c2 protein from Leptotrichia shahii processes its own array using two different buffers, both comprising magnesium, (d) paragraph, paragraph [200] refers to Figure 111 as showing that C2c2 HEPN muteins retain targeted binding activity by means of an electrophoretic mobility shift assay, (e) paragraph [208] refers to Figures 119A-119E as showing that the two HEPN domains of a C2c2 are necessary for crRNA-guided ssRNA cleavage but not for crRNA-guided ssRNA binding, including the results of an electrophoretic mobility shift assay where C2c2 was contacted with a target RNA and a non-target RNA, (f) paragraph [213] refers to Figures 124A-124B where the results of a biochemical assay for assaying non-specific RNase activity on non-crRNA-targeted collateral RNA molecules are shown, (g) paragraph [939] refers to an assay to identify PAM nucleotides, (h) paragraph [0996] describes that C2c2 cleaves the target RNA outside of the crRNA binding site at varying distances depending on flanking sequence and describes in vitro cleavage reactions that included, in addition to LshC2c2, crRNA and its target RNA, one of four unrelated RNA molecules without any complementarity to the crRNA guide, and (h) paragraphs [999]-[1000] refer to targeting assays with (I) gRNAs directed to EGFP and (II) gRNAs directed against endogenous target genes in HEK293 cells and gRNAs which do not target these endogenous genes, none of these paragraphs, or the remainder of the specification provide enablement for a method that consists only of the three steps recited or disclose cleavage with a composition that consists solely of a Cas polypeptide, a guide RNA and magnesium. Paragraphs [1016], [160], [183], [939], [999], [1000] describe assays where there are no non-target nucleic acids involved. Please note that while the methods referred to by these paragraphs may require one of the steps recited in the method, and use compositions that require additional components beyond a Cas polypeptide, a guide RNA and magnesium to observe cleavage, none of the methods disclosed in these paragraphs require solely the three steps recited.
With regard to the argument that the Office incorrectly distinguishes “comprises” vs. “consisting of” and that “consists of” in the context of a method does not exclude the molecular interactions that necessarily follow, such as binding and cleavage after contacting the sample with the Cas polypeptide and the guide RNA in the presence of magnesium, it is noted that the Examiner has interpreted the term “consisting of” as closed language in accordance with MPEP § 2111.03(II) which states that the transitional phrase "consisting of" excludes any element, step, or ingredient not specified in the claim. The examiner has not argued that molecular interactions that follow after a particular action can occur, such as binding and cleavage. Instead, the Examiner has repeatedly argued that binding and cleavage cannot occur if only certain elements are present. In the instant case, one cannot observe binding and cleavage if only a Cas polypeptide, a guide RNA and magnesium are present. This is evidenced by the specification itself, including paragraph [1016], that discloses the requirement of additional components, temperature and pH for binding and cleavage to occur.
The claimed method is limited solely to three steps, namely (a) contacting a sample with a Cas polypeptide, a guide RNA and magnesium, (b) detecting cleavage of one or more non-target nucleic acids in the sample, and (c) comparing the cleavage of one or more non-target nucleic acids in the presence and absence of the target RNA. As indicated above, as disclosed by the specification, the mere contact of a sample with a composition that consists only of a Cas polypeptide, a guide RNA and magnesium is not enough to obtain cleavage. Moreover, even if the required step is the contact of a sample with a composition that comprises a Cas polypeptide, a guide RNA and magnesium, one would require additional steps to be able to detect the cleavage of non-target nucleic acids in the sample, such as maintaining the proper temperature (37 C) for a certain period of time, quenching the reaction, denaturing, as well as all the steps needed to prepare a sample that has the cleaved non-target nucleic acids so that the detectable label can be measured/visualized. Those examples in the specification that refer to the use of non-target nucleic acids and detection of their cleavage require fluorescent labeling. In that situation, the sample containing the non-target nucleic acids after exposure to the Cas polypeptide is loaded to a gel, which is then run through an electrophoresis process, followed by exposing said gel to an instrument that would provide an image that shows the detectable label. The step of contacting a sample with a Cas polypeptide, a guide RNA and magnesium is not enough to be able to detect cleavage of non-target nucleic acids in a sample. This is evidenced by paragraphs [208] and [213]. Furthermore, the step of comparing the cleavage of non-target nucleic acids in the presence and absence of the target RNA would require additional steps, which would include all the steps needed in an assay with a sample that lacks the target RNA and has the non-target nucleic acids under the same conditions as those used with the sample that has the target RNA and the non-target nucleic acids in addition to all the steps required to detect the presence or absence of cleaved non-target nucleic acids. In view of the fact that additional components and steps are needed and the specification fails to explicitly or implicitly disclose or suggest a method that cleaves non-target nucleic acids target RNA, detects cleavage of non-target nucleic acids, and compares cleavage of non-target nucleic acids in the presence and absence of a target RNA nucleic acids with only the three steps recited one cannot reasonably conclude that the method recited by the claims is enabled by the teachings of the specification.
While Applicant asserts that paragraphs [1016], [160], [725], and [183] along with related examples provide multiple working examples that fall squarely within the claimed scope, it is noted that (a) paragraph [0725] of the specification refers to detection methods, radiolabels, fluorescent markers and enzymatic labels without making any mention of magnesium or non-target nucleic acids, and (b) none of paragraphs [1016], [160], and [183] refer to the use of non-target nucleic acids that comprise a detectable label, let alone describe or suggest a method where the only steps required are those recited in the claims.
Therefore, contrary to Applicant’s assertions, the claimed invention is not fully supported by the originally filed disclosure and the enablement requirements have not been met.
Claims 1, 6, 8, 14-17, 19-21 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This rejection is necessitated by the introduction of new matter.
As set forth in MPEP 2163 (I)(B), new or amended claims which introduce elements or limitations which are not supported by the as-filed disclosure violate the written description requirement. See, e.g., In re Lukach, 442 F.2d 967, 169 USPQ 795 (CCPA 1971) (subgenus range was not supported by generic disclosure and specific example within the subgenus range); In re Smith, 458 F.2d 1389, 1395, 173 USPQ 679, 683 (CCPA 1972) (a subgenus is not necessarily described by a genus encompassing it and a species upon which it reads). Claims 1, 6, 8, 14-17, 19-21 as amended are directed to an in vitro method that consists of three steps, which are (a) contacting a sample with a Cas polypeptide and a guide RNA in the presence of magnesium, wherein the guide RNA forms a complex with the Cas polypeptide and directs binding of the complex to a target RNA, wherein the Cas polypeptide comprises SEQ ID NO: 591 or an amino acid sequence at least 95% sequence identical to SEQ ID NO: 591, (b) detecting cleavage of one or more non-target nucleic acids in the sample, and (c) comparing the cleavage of one or more non-target nucleic acids in the presence and in the absence of the target RNA in the sample, wherein the Cas polypeptide cleaves the target RNA and one or more non-target nucleic acids in the sample.
While the Examiner has found support for a method as claimed that comprises the steps of (i) contacting a sample that comprises a target RNA with a composition that comprises a Cas polypeptide, a guide RNA, labeled non-target nucleic acids which are not complementary to the guide RNA, and magnesium, (ii) detecting cleavage of said non-target RNAs in the sample, and (iii) comparing the cleavage of said non-target RNAs in the sample in the presence and absence of the target RNA, the Examiner is unable to find support for a method that consists of three steps, which are (a) contacting a sample with a Cas polypeptide and a guide RNA in the presence of magnesium, wherein the guide RNA forms a complex with the Cas polypeptide and directs binding of the complex to a target RNA, wherein the Cas polypeptide comprises SEQ ID NO: 591 or an amino acid sequence at least 95% sequence identical to SEQ ID NO: 591, (b) detecting cleavage of one or more non-target nucleic acids in the sample, and (c) comparing the cleavage of one or more non-target nucleic acids in the presence and in the absence of the target RNA in the sample, wherein the Cas polypeptide cleaves the target RNA and one or more non-target nucleic acids in the sample.
Thus, there is no indication that a method that consists of three steps, which are (a) contacting a sample with a Cas polypeptide and a guide RNA in the presence of magnesium, wherein the guide RNA forms a complex with the Cas polypeptide and directs binding of the complex to a target RNA, wherein the Cas polypeptide comprises SEQ ID NO: 591 or an amino acid sequence at least 95% sequence identical to SEQ ID NO: 591, (b) detecting cleavage of one or more non-target nucleic acids in the sample, and (c) comparing the cleavage of one or more non-target nucleic acids in the presence and in the absence of the target RNA in the sample, wherein the Cas polypeptide cleaves the target RNA and one or more non-target nucleic acids in the sample was within the scope of the invention as conceived by Applicant at the time of the invention. Accordingly, Applicant is required to cancel the new matter in the response to this Office Action.
Applicant argues that the specification provides extensive written description support for the claimed method through multiple paragraphs describing the exact elements now claimed. Applicant refers to paragraph [01016] in support of the argument that the specification demonstrate the claimed approach by describing a Cas polypeptide and a guide RNA performed in the presence of magnesium, inherently supporting a method consisting of the procedural steps of contacting a sample with the composition in the presence of magnesium and detecting the results. Applicant further argues that the specification demonstrates that performing the methods in the presence of magnesium results in RNA cleavage as shown in paragraph [01016]. Applicant also refers to paragraph [0183] as providing enablement since it shows that LshC2c2 cleaves arrays containing magnesium. Applicant states that the term “non-target nucleic acids” has established written description support. Applicant refers to paragraphs [00331], [0996] as providing support to the cleavage of non-target nucleic acids by a C2c2 protein. Applicant states that paragraphs [01016], [0160], [0725] and [0183] explicitly describe methods performed in the presence of magnesium.
Applicant’s arguments have been fully considered but not deemed persuasive to avoid the instant rejection. The Examiner acknowledges the amendments made to claim 1. However, the Examiner disagrees with Applicant’s contention that the method of amended claim 1 is fully supported by the specification as originally filed. The Examiner acknowledges that (a) paragraph [01016] describes a nuclease assay where a nuclease assay buffer is used that comprises magnesium, (b) paragraph [0160] refers to Figure 71 as disclosing the results of an assay where a C2c2 protein from Leptotrichia shahii (Cas polypeptide) was used to cleave an RNA target using two different buffers, both comprising magnesium, and (c) paragraph [0183] refers to Figure 94 as disclosing that a C2c2 protein from Leptotrichia shahii processes its own array using two different buffers, both comprising magnesium. It is noted that contrary to Applicant’s assertions, paragraph [0725] of the specification refers to detection methods, radiolabels, fluorescent markers and enzymatic labels but does not mention magnesium. The Examiner also acknowledges that (i) paragraph [0331] indicates that C2c2 in a complex with crRNA is activated upon binding to target RNA and subsequently cleaves nearby single stranded RNAs which are not the target RNA, and (ii) paragraph [0996] describes that C2c2 cleaves the target RNA outside of the crRNA binding site at varying distances depending on flanking sequence and describes in vitro cleavage reactions that included, in addition to LshC2c2, crRNA and its target RNA, one of four unrelated RNA molecules without any complementarity to the crRNA guide. However, the issue in the instant case is whether the specification as originally filed describes a method where the only steps allowed are (a) contacting a sample with a Cas polypeptide and a guide RNA in the presence of magnesium, wherein the guide RNA forms a complex with the Cas polypeptide and directs binding of the complex to a target RNA, wherein the Cas polypeptide comprises SEQ ID NO: 591 or an amino acid sequence at least 95% sequence identical to SEQ ID NO: 591, (b) detecting cleavage of one or more non-target nucleic acids in the sample, and (c) comparing the cleavage of one or more non-target nucleic acids in the presence and in the absence of the target RNA in the sample, wherein the Cas polypeptide cleaves the target RNA and one or more non-target nucleic acids in the sample, and whether one could obtain cleavage of a polynucleotide solely with a Cas polypeptide, a guide RNA and magnesium. It is reiterated herein that the specification provides support for a composition that comprises a Cas polypeptide, a guide RNA, non-target nucleic acids which are not complementary to the guide RNA, and magnesium, and for a method that comprises the recited steps but there is no indication in the specification of a composition that consists of a Cas polypeptide, a guide RNA and magnesium, or a method where the only steps allowed (i.e., consisting of) are the recited steps, or any suggestion in the specification that a method that consists of the three steps recited is a preferred embodiment of the genus of methods that comprise the recited steps, or that a method that consists of the three steps recited was within the scope of the invention as conceived by Applicant at the time of the invention.
Conclusion
No claim is in condition for allowance.
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 extension fee 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 date of this final action.
Applicant is advised that any Internet email communication by the Examiner has to be authorized by Applicant in written form. See MPEP § 502.03 (II). Without a written authorization by Applicant in place, the USPTO will not respond via Internet email to any Internet correspondence which contains information subject to the confidentiality requirement as set forth in 35 U.S.C. 122. Sample written authorization language can be found in MPEP § 502.03 (II). An Authorization for Internet Communications in a Patent Application or Request to Withdraw Authorization for Internet Communications form (SB/439) can be found at https://www.uspto.gov/patent/forms/ forms-patent-applications-filed-or-after-september-16-2012, which can be electronically filed.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to DELIA M RAMIREZ, Ph.D., whose telephone number is (571) 272-0938. The examiner can normally be reached on Monday-Friday from 8:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert B. Mondesi, can be reached at (408) 918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/DELIA M RAMIREZ/Primary Examiner, Art Unit 1652
DR
March 6, 2026