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 .
Response to Amendment
This action is in response to the papers filed October 31, 2025. Applicant's remarks and amendments have been fully and carefully considered but are not found to be sufficient to put the application in condition for allowance. Any rejections or objections not reiterated herein have been withdrawn. This action is made FINAL.
Applicant's election of Group I (a composition comprising programmable nuclease and a non-naturally occurring guide nucleic acid) in the response filed March 28, 2025 is reiterated for the record. Claims 36 and 184-187 were withdrawn by the office in the action mailed July 1, 2025, pursuant to 37 CFR 1.142(b) as being drawn to nonelected subject matter, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on March 28, 2025.
It is acknowledged that Applicant cancelled claim 30 in the response filed October 31, 2025.
Claims 1-5, 9, 10, 12, 13, 16-18, 21, 23, 25, 27-29, 31-36, and 184-198 are currently pending. Claims 1-5, 9, 10, 12, 13, 16-18, 21, 23, 25, 27-29, 31-35, and 188-198 are currently under examination.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed applications, Application Nos. 62/863,166 (06/18/2019), 62/894,515 (08/30/2019), 62/795,463 (01/22/2019), 62/788,706 (01/04/2019) and 62/788,704 (01/04/2019) fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. None of the recited references teaches a programmable nuclease having at least 90% sequence identity to SEQ ID NO: 11 and a non-naturally occurring guide nucleic acid. Accordingly, the claims are not entitled to the benefit of the earlier applications.
Therefore, the filing date to which the instant claims are entitled is 1 August 2019, the filing date of Provisional Application 62/881,801.
Double Patenting
The non-statutory 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 non-statutory 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.
(I). Claims 1-5, 9-10, 12-13, 16-17, and 31-32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 6, 9, 13, 20-21, 25 and 26 of U.S. Patent No. 11,174,470 B2, hereinafter referred to as patent ‘470. Although the claims at issue are not identical, they are not patentably distinct from each other because:
Instant claim 1 limitations “A composition comprising a programmable nuclease having at least 90% sequence identity to SEQ ID NO: 11 and a non-naturally occurring guide nucleic acid” are read on by patent ‘470 claim 1 limitations “A composition comprising: a) a programmable nuclease having a turnover rate of at least 0.1 cleaved detector nucleic acid molecules per minute, and b) a non-naturally occurring guide nucleic acid capable of hybridizing to a segment of a target nucleic acid”, and patent ‘470 claim 25 limitation “The composition of claim 1, wherein the programmable nuclease comprises an amino acid sequence at least 95% identical to SEQ ID NO: 11.”
Instant claim 2 limitation “further comprising a detector nucleic acid.” is read on by patent ‘470 claim 9 limitation “The composition of claim 1, further comprising the detector nucleic acid.”
Instant claim 3 limitations “wherein the programmable nuclease recognizes a protospacer adjacent motif of 5 '-YYN-3 ' and instant claim 5, limitations “wherein the protospacer adjacent motif is 5'-YYN-3'” are read on by patent ‘470 claim 2 limitations “The composition of claim 1, wherein the programmable nuclease recognizes a protospacer adjacent motif of YYN, wherein the Y is a C nucleotide or a T nucleotide, and wherein the N is any nucleotide”.
Instant claim 4 limitations “further comprising a target nucleic acid, wherein when a region of said non-naturally occurring guide nucleic acid hybridizes to a portion of said target nucleic acid adjacent to a protospacer adjacent motif” are read on by patent ‘470 claim 13 limitation “The composition of claim 1, further comprising the target nucleic acid.” and patent ‘470 claim 1 limitation “b) a non-naturally occurring guide nucleic acid capable of hybridizing to a segment of a target nucleic acid,” --- “wherein, if the non-naturally occurring guide nucleic acid hybridizes to the segment of the target nucleic acid, the programmable nuclease is activated to non- specifically cleave a detector nucleic acid,” and patent ‘470 claim 2 limitation “The composition of claim 1, wherein the programmable nuclease recognizes a protospacer adjacent motif of YYN”.
Instant claim 4 limitations, “said programmable nuclease cleaves detector nucleic acids at a rate of at least about 0.1 cleaved detector nucleic acid molecules per minute” are read on by patent ‘470 claim 1 limitation “a) a programmable nuclease having a turnover rate of at least 0.1 cleaved detector nucleic acid molecules per minute”.
Instant claim 9 limitation “wherein the programmable nuclease comprises three partial RuvC domains” is read on by patent ‘470 claim 1 limitation b) “wherein the programmable nuclease comprises (i) three partial RuvC domains”.
Instant claim 10 limitations “wherein the programmable nuclease comprises a RuvC-I subdomain, a RuvC-II subdomain, and a RuvC-III subdomain” is read on by patent ‘470 claim 6 limitation “The composition of claim 1, wherein the three partial RuvC domains comprise a RuvC-I subdomain, a RuvC-II subdomain, and a RuvC-III subdomain.”
Instant claim 12 limitation “The composition of claim 1, wherein the programmable nuclease has at least 95% sequence identity to SEQ ID NO: 11” is read on by patent ‘470 claim 25 limitation “The composition of claim 1, wherein the programmable nuclease comprises an amino acid sequence at least 95% identical to SEQ ID NO: 11.”
Instant claim 13 limitation “The composition of claim 1, wherein the programmable nuclease is SEQ ID NO: 11” is read on by patent ‘470 claim 26 limitation “The composition of claim 1, wherein the programmable nuclease comprises an amino acid sequence of SEQ ID NO: 11.”
Instant claim 16 limitations “The composition of claim 1, wherein the composition further comprises a buffer” and Instant claim 17 limitations “wherein the buffer comprises a buffering agent, a salt, a crowding agent, a detergent, or any combination thereof” are read on by patent ‘470 claim 20 limitations “The composition of claim 1, further comprising a buffer comprising a buffering agent, a salt, a crowding agent, a detergent, or any combination thereof.”
Instant claim 31 limitations “The composition of claim 17, wherein a pH of the composition is from 7 to 8” and instant claim 32 limitations “wherein a pH of the buffer is approximately 7.5. are read on by patent ‘470 claim 21 limitation “--- and wherein the buffer has a pH of from 7 to 8”.
(II). Claims 1 and 189-190 are rejected on the ground of non-statutory double patenting as being unpatentable over claim 104 and 105 of co-pending Application No. 18/585,306.
This is a provisional non-statutory double patenting rejection.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Instant claim 1 limitations “A composition comprising a programmable nuclease having at least 90% sequence identity to SEQ ID NO: 11 and a non-naturally occurring guide nucleic acid” are read on by Application No. 18/585,306 claim 104 limitations “A composition comprising an effector protein and an engineered guide nucleic acid, wherein the effector protein comprises an amino acid sequence that is at least 90% identical to any one of SEQ ID NOs: 1-1614 and 3195-3302.” The specification of Application No. 18/585,306 defines an effector protein as “The effector protein may be a Cas protein (i.e., an effector protein of a CRISPR-Cas system)” [27]. The specification of Application No. 18/585,306 further discloses “A programmable nuclease, such as a clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) protein, may be coupled to a guide nucleic acid that imparts activity or sequence selectivity to the programmable nuclease” [3]. Therefore, an effector protein is a programmable nuclease as recited in instant claim 1. The specification of Application No. 18/585,306 discloses SEQ ID NO: 422, which aligns to instant claim 1, SEQ ID NO:11.
Instant claim 189 limitation “wherein the guide RNA comprises a sequence that is 80% homologous to SEQ ID NO:512”, and instant claim 190 limitation “wherein the non-naturally occurring guide nucleic acid has at least 60% sequence identity to SEQ ID NO:512”, is read on by Application No. 18/585,306 claim 105 limitation “The composition of claim 104, wherein the amino acid sequence of the effector protein is at least 90% identical to a sequence selected from Column A1 of TABLE 1;and at least a portion of the engineered guide nucleic acid comprises a nucleobase sequence that is at least 90% identical to a sequence selected from Column B1 of TABLE 1, wherein the sequence from Column A1 and the sequence from Column B1 are in the same row of TABLE 1”, which refers to Table 1, column B1 SEQ ID NO: 2021 and SEQ ID NO: 2012 (pg., 58 of the reference application specification).
(III). Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 36 of co-pending Application No. 17/817,889.
This is a provisional nonstatutory double patenting rejection.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Instant claim 1 limitations “A composition comprising a programmable nuclease having at least 90% sequence identity to SEQ ID NO: 11 and a non-naturally occurring guide nucleic acid” are read on by Application No. 17/817,889 claim 1 limitations “ii) a composition comprising a programmable nuclease and a non- naturally occurring guide nucleic acid that hybridizes to a segment of the target nucleic acid, wherein the programmable nuclease cleaves the detector nucleic acid upon hybridization of the non-naturally occurring guide nucleic acid to the segment of the coronavirus target nucleic acid” and Application No. 17/817,889 claim 36 limitations “(e) the programmable nuclease has at least 80%, at least 85%, at least 90%, at least 92%,at least 95%, at least 97%, or at least 99% sequence identity to any one of SEQ ID NO:18 - SEQ ID NO: 60; (f) the programmable nuclease comprises a sequence selected from SEQ ID NO: 18 - SEQ ID NO: 60.” SEQ ID NO: 28 of Application No. 17/817,889 corresponds to SEQ ID NO: 11 of the instant application.
(IV). Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 66 of co-pending Application No. 18/336,718.
This is a provisional nonstatutory double patenting rejection.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Instant claim 1 limitations “A composition comprising a programmable nuclease having at least 90% sequence identity to SEQ ID NO: 11 and a non-naturally occurring guide nucleic acid” are read on by Application No. 18/336,718 claim 66 limitations
“A composition comprising a CRISPR-associated protein, or a nucleic acid encoding the CRISPR-associated protein, and a guide nucleic acid molecule,” and “wherein the CRISPR-associated protein comprises an amino acid sequence that is at least 95% identical to any one of SEQ ID NOs: 1-220, 244, and 248-262.” This reads on Instant claim 1 because the specification of the instant application teaches “The methods described herein use a programmable nuclease, such as the CRISPR/Cas system, to detect a target nucleic acid.” (pg. 51 [00249]), and because SEQ ID NO: 11 of Instant claim 1 corresponds to SEQ ID NO: 11 of Application No. 18/336,718.
(V). Claim 1-2 and 12 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 109 of co-pending Application No. 17/555,236.
This is a provisional nonstatutory double patenting rejection.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Instant claim 1 limitations “A composition comprising a programmable nuclease having at least 90% sequence identity to SEQ ID NO: 11 and a non-naturally occurring guide nucleic acid” and instant claim 2 limitation “The composition of claim 1, further comprising a detector nucleic acid” are read on by Application No. 17/555,236 claim 1 limitation “c) a detection reagent chamber fluidically connected to the detection chamber via a resistance channel, the detection reagent chamber comprising a programmable nuclease, a guide nucleic acid, and a labeled detector nucleic acid, wherein the labeled detector nucleic acid is capable of being cleaved upon binding of the guide nucleic acid to a segment of a target nucleic acid” and Application No. 17/555,236 claim 109 limitation “The microfluidic cartridge of claim 1, wherein the programmable nuclease: (e) has at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, or at least 99% sequence identity to any one of SEQ ID NO: 27 - SEQ ID NO: 37.”
Instant claim 12 limitation “the composition of claim 1, wherein the programmable nuclease has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%,at least 97%, or at least 99% sequence identity to SEQ ID NO: 11” is read on by Application No. 17/555,236 claim 109 limitation “The microfluidic cartridge of claim1, wherein the programmable nuclease: (e) has at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, or at least 99% sequence identity to any one of SEQ ID NO: 27 - SEQ ID NO: 37.”
Application No. 17/555,236 SEQ ID NO: 37 corresponds to instant claim 1 SEQ ID NO: 11.
(VI). Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 72 of co-pending Application No. 18/431,664.
This is a provisional nonstatutory double patenting rejection.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Instant claim 1 limitations “A composition comprising a programmable nuclease having at least 90% sequence identity to SEQ ID NO: 11 and a non-naturally occurring guide nucleic acid” is read on by Application No. 18/431,664 claim 72 limitation “wherein the programmable nuclease comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, or at least 99% identical to SEQ ID NO: 266 ”. Application No. 18/431,664 SEQ ID NO: 266 corresponds to instant claim 1 SEQ ID NO:11.
Response to Arguments
Rejection over patent ‘470
In the response filed October 31, 2025, Applicant stated that they traversed the nonstatutory double patenting rejection over US Patent No. 11,174,470 B2 and requested that the rejection be held in abeyance until the claims are otherwise in condition for allowance.
The request has been fully considered. MPEP 804(I)(B)(1) states that “[a] complete response to a nonstatutory double patenting (NSDP) rejection is either a reply by applicant showing that the claims subject to the rejection are patentably distinct from the reference claims, or the filing of a terminal disclaimer in accordance with 37 CFR 1.321 in the pending application(s) with a reply to the Office action (see MPEP § 1490 for a discussion of terminal disclaimers)... As filing a terminal disclaimer, or filing a showing that the claims subject to the rejection are patentably distinct from the reference application’s claims, is necessary for further consideration of the rejection of the claims, such a filing should not be held in abeyance.”
Because Applicant did not file a terminal disclaimer or properly traverse the rejection by filing a showing that the claims subject to the rejection are patentably distinct from the reference application’s claims, the rejections are maintained.
Provisional rejections
In the response filed October 31, 2025, Applicant requested that the provisional double-patenting rejections be held in abeyance until the claims are otherwise in condition for allowance. Applicant argued that if the provisional double patenting rejections were the only outstanding rejections, MPEP 804(I)(B)(1)(b)(i) provides that as the instant application has the earlier patent term filing date, the provisional double patenting rejections should be withdrawn in the instant application.
The request has been fully considered. MPEP 804(I)(B)(1) states that “[a] complete response to a nonstatutory double patenting (NSDP) rejection is either a reply by applicant showing that the claims subject to the rejection are patentably distinct from the reference claims, or the filing of a terminal disclaimer in accordance with 37 CFR 1.321 in the pending application(s) with a reply to the Office action (see MPEP § 1490 for a discussion of terminal disclaimers). Such a response is required even when the nonstatutory double patenting rejection is provisional. As filing a terminal disclaimer, or filing a showing that the claims subject to the rejection are patentably distinct from the reference application’s claims, is necessary for further consideration of the rejection of the claims, such a filing should not be held in abeyance.”
Applicants did not file a terminal disclaimer or file a showing that the claims subject to the rejection are patentably distinct from the reference application’s claims. Therefore, and because the provisional double patenting rejections are not the only outstanding rejections, the rejections are maintained.
Conclusion
No claims are allowed.
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/C.M.J./Examiner, Art Unit 1682
/AMANDA HANEY/Primary Examiner, Art Unit 1682
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