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 claims 1 and 21 as submitted in a communication filed on 7/13/2026 is acknowledged.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 7/13/2026 has been entered.
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Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.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(a) or First Paragraph (pre-AIA )
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 six steps, which are (a) contacting a sample with a Cas polypeptide, a guide RNA, Mg2+, a pH buffer and a salt, 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) incubating the contacted sample at a temperature and for a time sufficient to allow cleavage of the target RNA, (c) quenching the incubated sample with a protease, a cation chelator, or both, (d) denaturing the quenched sample, (e) detecting cleavage of one or more labeled non-target nucleic acids in the sample by gel electrophoresis, fluorescence detection or both, and (f) comparing the cleavage of the one or more labeled 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 Mg2+, (ii) incubating the contacted sample to allow cleavage of a target RNA, and (iii) detecting cleavage of said non-target RNAs in the sample, the Examiner is unable to find support for a method that consists of six steps, which are (a) contacting a sample with a Cas polypeptide, a guide RNA, Mg2+, a pH buffer and a salt, 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) incubating the contacted sample at a temperature and for a time sufficient to allow cleavage of the target RNA, (c) quenching the incubated sample with a protease, a cation chelator, or both, (d) denaturing the quenched sample, (e) detecting cleavage of one or more labeled non-target nucleic acids in the sample by gel electrophoresis, fluorescence detection or both, and (f) comparing the cleavage of the one or more labeled 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 six steps, which are (a) contacting a sample with a Cas polypeptide, a guide RNA, Mg2+, a pH buffer and a salt, 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) incubating the contacted sample at a temperature and for a time sufficient to allow cleavage of the target RNA, (c) quenching the incubated sample with a protease, a cation chelator, or both, (d) denaturing the quenched sample, (e) detecting cleavage of one or more labeled non-target nucleic acids in the sample by gel electrophoresis, fluorescence detection or both, and (f) comparing the cleavage of the one or more labeled 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.
With regard to the previous written description rejection, Applicant argues that the Office’s analysis misreads the cited paragraphs. Applicant states that paragraphs [001016], [00160] and [00183] do not use the term “comprising”. Applicant states that the grounds of rejection is on the premise that the specification supports only a “comprises” formulation and that a closed three step claim is therefore new matter. Applicant states that the paragraphs relied upon provide a working buffer that has specific components at specific concentrations. Applicant states that the recited buffer supports possession of that buffer formulation, not just the broader genus of buffers that include magnesium. Applicant states that the same is true for the recited steps and states that paragraph [001016] recites the incubating, quenching, denaturing, and detection operations as steps performed in the working examples. Applicant states that the written description analysis did not address the collateral cleavage section of the specification under the heading “C2c2 cleaves collateral RNA in addition to crRNA-targeted ssRNA” (paragraph [00996]) that allegedly describes the components and steps of the claimed method. Applicant states that Figure 124A confirms that those non-complementary RNA molecules carry a detectable label and that paragraph [00331] disclose the mechanism that drives the comparison recited in step (f). Applicant submits that paragraph [001016] provides a nuclease assay buffer that comprises Mg2+, pH buffer and salt of step (a) the steps of quenching, denaturing and detecting. Applicant states that the nuclease assay protocol of paragraph [001016] provides a buffer that maps precisely onto the contacting of step (a) and that the same paragraph describes incubation, quenching, denaturing and resolving of the cleavage products by fluorescence imaging, thus mapping steps (c)-(e). Applicant states that one of skill in the art would understand that the collateral cleavage experiments were conducted in that buffer and under the protocol of paragraph [001016]. Applicant states that Figures 124A, 140A and 140B independently corroborate the disclosure. Applicant states that the experiment described in Figure 140B is the comparison recited in step (f) where the same reaction performed in the presence and absence of the target RNA with cleavage of the labeled non-target nucleic acids as the readout. Applicant is of the opinion that every step of the claimed method is described together in paragraphs [00996] and [001016] and is corroborated by Figures 124A, 140A and 140B.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection. The Examiner acknowledges the amendments made to the claims. However, the Examiner disagrees that the specification adequately describes the claimed method.
With regard to the argument that paragraphs [001016], [11160] and [00183] do not use the term “comprising” and that the grounds of rejection is on the premise that the specification supports only a “comprises” formulation and that a closed three sept claim is therefore new matter, it is noted that the use of “comprising” by the Examiner on page 10 of the Office action of 3/11/2026 was intended to indicate that the solutions disclosed in these paragraphs have a Cas polypeptide, a guide RNA and magnesium. It is believed that the term “comprising” is completely accurate and proper because as correctly pointed out by Applicant, these paragraphs refer to solutions that have additional elements. If the solutions have additional elements beyond a Cas polypeptide, a guide RNA and magnesium, as is the case in paragraphs [001016], [00160] and [00183], the term “comprising” is merely indicating the fact that the solutions disclosed in these paragraphs have other elements.
With regard to the argument that the paragraphs relied upon provide a working buffer that has specific components at specific concentrations and that the recited buffer supports possession of that buffer formulation, not just the broader genus of buffers that include magnesium, it is noted that while these paragraphs provide buffers fully defined with regard to their components and concentrations, the instant claims refer to a subgenus of buffers that encompass more than those buffers disclosed in paragraphs [001016], [00160] or [00183]. There is no indication in the specification that a subgenus of compositions comprising a Cas polypeptide, a guide RNA, Mg2+, any pH buffer having any pH, and any salt were within the scope of the invention as conceived by Applicant at the time of the invention.
With regard to the argument that these paragraphs also support the recited steps and that paragraph [001016] recites the incubating, quenching, denaturing, and detection operations as steps performed in the working examples, it is reiterated herein that paragraphs [01016], [0160] and [0183] make no mention whatsoever of a non-target nucleic acid, let alone a labeled non-target nucleic acid or the cleavage of a non-target nucleic acid. It should also be noted that while paragraph [01016] discloses nuclease assays performed with a labeled target single stranded RNA, a C2c2 protein from L shahii and crRNA, wherein the assays require a nuclease assay buffer that comprises Tris-HCl, NaCl and MgCl2, the composition of step (a) requires a genus of Cas polypeptides, a genus of nucleic acid components, a genus of pH buffers having any pH, and a genus of salts. In addition, the assay of paragraph [01016] comprises incubating for a specific period of time at a specific temperature, quenching with proteinase K and EDTA for a specific period of time at a specific temperature, denaturing with urea using a denaturing buffer as a specific temperature for a specific period of time, and analysis using gel electrophoresis under specific conditions. The claims do not require a labeled target RNA and require a genus of temperatures, periods of times to perform the recited steps, any protease, any cation chelator and any denaturing agent. Therefore, one cannot reasonably conclude that paragraphs [001016], [0160] or [0183] provide support for a method that consists solely of the recited six steps, including the step of contacting a sample with a Cas polypeptide, a guide RNA, Mg2+, any pH buffer having any pH, and any salt.
With regard to the argument that the written description analysis did not address the collateral cleavage section of the specification under the heading “C2c2 cleaves collateral RNA in addition to crRNA-targeted ssRNA” (paragraph [00996]) that allegedly describes the components and steps of the claimed method, it is noted that contrary to Applicant’s assertions, the Examiner specifically referred to this paragraph on page 10 of the Office action of 3/11/2026, item 8, and stated that this paragraph along with others cited by Applicant did not address the issue, which was whether the specification as originally filed describes a method with solely three steps, as previously presented. Even taking into consideration the amendments made to the claims, it is not believed that paragraph [00996] provides support to the claimed method. Paragraph [00996] states the following:
[00996] In contrast to Cas9 and Cpf1, which cleave DNA within the crRNA-target heteroduplex at a defined position, reverting into an inactive state after cleavage, C2c2 cleaves the target RNA outside of the crRNA binding site at varying distances depending on flanking sequence, presumably within exposed ssRNA loop regions (FIG. 118D-I). This observed flexibility in cleavage distance lead us to consider the possibility of cleavage of nearby non-target ssRNAs upon C2C2 target binding and activation. Accordingly, C2c2 could cause PCD through a two-part mechanism: a priming stage in which C2c2-crRNA complexes bind to target sites and cleave ssRNA in a crRNA-guided fashion and a second stage in which primed C2c2 cleaves non-targeted, collateral RNA non-specifically. To test this hypothesis, we carried out 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 (FIG. 124A). These experiments showed that, whereas the LshC2c2-crRNA complex did not mediate cleavage of any of the four collateral RNAs in the absence of the target RNA, all four were efficiently degraded in the presence of the target RNA (FIG. 124B and FIG. 140A). Furthermore, R597A and R1278A HEPN mutants were unable to cleave collateral RNA (FIG. 140B). These results indicate a HEPN-dependent mechanism whereby C2c2 in a complex with crRNA is activated upon binding to target RNA and subsequently cleaves any nearby ssRNA targets. Such promiscuous RNA cleavage may cause cellular toxicity, resulting in the observed growth rate inhibition. These findings imply that, in addition to their role in direct suppression of RNA viruses, type VI CRISPR-Cas systems could function as mediators of a distinct variety of PCD/dormancy induction that is specifically triggered by the cognate invader genomes (FIG. 125). Under this scenario, dormancy would slow the infection and supply additional time for adaptive immunity to succeed; when adaptive immunity fails, the suicidal role of C2c2 would prevail and spread of the infection would be limited. Such a mechanism falls within the previously proposed scheme of coupling between adaptive immunity and PCD during the CRISPR-Cas defensive response (K. S. Makarova, V. Anantharaman, L. Aravind, E. V. Koonin, Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. Biol Direct 7, 40 (2012)).
While it is agreed that this paragraph discloses 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 also discloses that for cleavage of the unrelated RNA molecules to occur, C2c2 in a complex with crRNA is activated upon binding to target RNA, there is absolutely no mention whatsoever of Mg2+, any pH buffer and any salt, incubation, quenching, or denaturing. In addition, it is noted that even if the argument is made that Figure 124B discloses a denaturing gel showing cleavage products in the absence of a target RNA, it is noted that to show cleavage products in the absence of a target RNA, one would require additional steps such as removing the target RNA from the sample, contacting the sample lacking a target RNA with the Cas polypeptide as well as detecting the presence or absence of cleavage of the non-target nucleic acids. The method of the claims does not allow for those additional steps such that the comparison step could be carried out because the method of the claims is limited solely to the recited six steps. Therefore, Figure 124B does not provide support to step (f) as currently recited.
With regard to the argument that Figure 124A confirms that those non-complementary RNA molecules carry a detectable label and that paragraph [00331] disclose the mechanism that drives the comparison recited in step (f), it is noted that while it is agreed that Figure 124A shows that collateral RNA comprises a detectable label, it is not believed that that paragraph [00331] discloses the mechanism that drives the comparison recited in step (f). Paragraph [00331] states the following
[00331] In certain embodiments C2c2 in a complex with crRNA is activated upon binding to target RNA and subsequently cleaves any nearby ssRNA targets (i.e. “collateral” or “bystander” effects). C2c2, once primed by the cognate target, can cleave other (non-complementary) RNA molecules. Such promiscuous RNA cleavage could potentially cause cellular toxicity, or otherwise affect cellular physiology or cell status.
As shown above, while paragraph [00331] describes that activation of the C2c2-cRNA complex upon binding to the target RNA allows the cleavage of non-complementary RNA molecules, there is no mention whatsoever in this paragraph of a comparison step between cleavage of non-target nucleic acids in the presence or absence of a target RNA, or a method as currently recited.
With regard to the argument that one of skill in the art would understand that the collateral cleavage experiments were conducted in that buffer and under the protocol of paragraph [001016], it is noted that the specification provides several cleavage assays that use different types of buffers. See paragraphs [00160] and [00183] discussed in the prior Office action. Therefore, one cannot reasonably conclude that the collateral cleavage experiments where carried out using the buffer and protocol of paragraph [001016]. It is reiterated herein that the protocol of paragraph [001016] makes no mention whatsoever of a non-target nucleic acid or cleavage of a non-target nucleic acid. With regard to the argument that Figures 124A, 140A and 140B independently corroborate the disclosure, it is noted that neither Figures 124A, 140A or 140B nor the captions of these Figures disclose the buffer used, the presence of Mg2+, a pH buffer, or a salt, let alone the specific steps recited in the claims. With regard to the argument that Figure 140B is the comparison of step (f), it is noted that the comparison of Figure 140B requires additional steps which would include, for example contacting the Cas polypeptide with the non-target nucleic acids without any target RNA, as well as detecting the presence or absence of cleavage of the non-target nucleic acid in the absence of a target RNA. The method of the claims does not allow for those additional steps such that the comparison step could be carried out because the method of the claims is limited solely to the recited six steps. As such, it is not believed that Figure 140B is the comparison step (f) of the claimed method.
Therefore, contrary to Applicant’s assertions, a method that consists of six steps, which are (a) contacting a sample with a Cas polypeptide, a guide RNA, Mg2+, a pH buffer and a salt, 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) incubating the contacted sample at a temperature and for a time sufficient to allow cleavage of the target RNA, (c) quenching the incubated sample with a protease, a cation chelator, or both, (d) denaturing the quenched sample, (e) detecting cleavage of one or more labeled non-target nucleic acids in the sample by gel electrophoresis, fluorescence detection or both, and (f) comparing the cleavage of the one or more labeled 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, is not described in paragraphs [00996] and [001016] or corroborated by Figures 124A, 140A and 140B.
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 Mg2+, (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 six steps, wherein said steps are (a) contacting a sample with a Cas polypeptide, a guide RNA, Mg2+, a pH buffer and a salt, 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) incubating the contacted sample at a temperature and for a time sufficient to allow cleavage of the target RNA, (c) quenching the incubated sample with a protease, a cation chelator, or both, (d) denaturing the quenched sample, (e) detecting cleavage of one or more labeled non-target nucleic acids in the sample by gel electrophoresis, fluorescence detection or both, and (f) comparing the cleavage of the one or more labeled 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.
Applicant argues that the enablement rejection rests on mischaracterization of the cited paragraphs. Applicant states that none of paragraphs [001016], [00160], or [00183] refer to compositions that comprise a Cas polypeptide, a guide RNA and magnesium. Applicant states that paragraph [001016] recites a nuclease assay buffer having a specific recipe while paragraphs [00160] and [00183] each recite a buffer with specified components at specific concentrations. Applicant states that claim 1 has been amended to refer to each of those items in the order the protocol of paragraph [001016] performs them. Applicant states that step (a) now recites contacting in the presence of Mg2+, a pH buffer, and a salt, aligning with the composition components the Office alleges on the previous Office action. Applicant states that all the steps recited in claim 1 aligns with what was indicated in the prior Office action.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection. The Examiner acknowledges the amendments made to claim 1, including the additional steps added. However, the Examiner disagrees with Applicant’s contention that the claimed method is fully enabled by the teachings of the specification.
With regard to the arguments that (i) the enablement rejection rests on mischaracterization of the cited paragraphs and that none of paragraphs [001016], [00160], or [00183] refer to compositions that comprise a Cas polypeptide, a guide RNA and magnesium, (ii) paragraph [001016] recites a nuclease assay buffer having a specific recipe, and (iii) paragraphs [00160] and [00183] each recite a buffer with specified components at specific concentrations, it is noted that the use of “comprising” by the Examiner on page 4 of the Office action of 3/11/2026 was intended to indicate that the solutions disclosed in these paragraphs have a Cas polypeptide, a guide RNA and magnesium. The term “comprising” is completely accurate and proper because as correctly pointed out by Applicant, these paragraphs refer to solutions that have additional elements. If the solutions have additional elements beyond a Cas polypeptide, a guide RNA and magnesium, as is the case in paragraphs [001016], [00160] and [00183], the term “comprising” is merely indicating the fact that the solutions disclosed in these paragraphs have other elements.
With regard to the argument that claim 1 has been amended to refer to each of those items in the order the protocol of paragraph [001016] performs them and that step (a) now requires Mg2+, a pH buffer, and a salt, aligning with the composition components the Office alleges on the previous Office action, it is noted that while it is agreed that paragraph [01016] discloses nuclease assays performed with a labeled target single stranded RNA, a C2c2 protein from L shahii and crRNA, wherein the assays require a nuclease assay buffer that comprises Tris-HCl, NaCl and MgCl2, the composition of step (a) requires a genus of Cas polypeptides, a genus of nucleic acid components, a genus of pH buffers having any pH, and a genus of salts. While the claims require any pH buffer, and any salt, it is unclear if any composition that comprises any Cas9 polypeptide having the recited structural features, any nucleic acid component, Mg2+, any pH buffer having any pH, and any salt would be enzymatically active and cleave a target RNA required by the claims. In addition, while the claims require a comparison step of the cleavage of the non-target nucleic acids in the presence and absence of the target RNA in the sample, it is noted that one could not make the recited comparison without additional steps which would include the removal of the target RNA from the sample and contacting the sample without the target RNA with the Cas polypeptide as well as detecting whether or not cleavage occurs in said sample lacking the target RNA. Therefore, for the reasons of record and those set forth above, one cannot reasonably conclude that an in vitro method, wherein said method consists of six steps, wherein said steps are (a) contacting a sample with a Cas polypeptide, a guide RNA, Mg2+, a pH buffer and a salt, 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) incubating the contacted sample at a temperature and for a time sufficient to allow cleavage of the target RNA, (c) quenching the incubated sample with a protease, a cation chelator, or both, (d) denaturing the quenched sample, (e) detecting cleavage of one or more labeled non-target nucleic acids in the sample by gel electrophoresis, fluorescence detection or both, and (f) comparing the cleavage of the one or more labeled 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, is fully enabled by the teachings of the specification.
Conclusion
No claim is in condition for allowance.
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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
August 13, 2026
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