DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Response to Amendment/Status of Claims
Receipt of Arguments/Remarks filed on 08/28/2026 is acknowledged. Claim 158 was cancelled. Claims 142,143,145-149,157,160 and 161 were amended. Claims 142-157 and 159-161 are pending and under examination.
Withdrawn Objections and Rejections
Applicant’s arguments and amendments, see page 11, filed 08/28/2026, with respect to the nucleotide sequences appearing in the drawings and specification not identified by sequence identifiers as well as the objection to the specification for containing an embedded hyperlink in paragraph 0098, have been fully considered and are persuasive due to providing replacement drawings with sequence identifiers in Figs. 4C,5B,10B-10C,11B-11C,12A-12E, and 13C and providing sequence identifiers in the specification in paragraphs 0196,0209 and 0210 and removing the embedded hyperlink. The objections to the drawings and specification has been withdrawn.
Applicant’s arguments and amendments, see pages 11-12, filed 08/28/2026, with respect to the objection to claims 142,147-149 and 157, have been fully considered and are persuasive due to amending claims 142,147,148 and 157 to recite “capable of” rather than “configured to” and amending claim 149 correcting the typo. The objections to claims 142,147-149 and 157 have been withdrawn.
Applicant’s arguments and amendments, see page 12, filed 08/28/2026, with respect to the 35 U.S.C. 112(b) rejection of claims 145,146,160 and 161 have been fully considered and are persuasive due to amending claims 145 and 146 to remove the phrase “non-degenerate nucleotides of“, and the amendment to claims 160 and 161 such that the recited sequence corresponds to the correct component. The 35 U.S.C. 112(b) rejection of claims 145,146,160 and 161 has been withdrawn.
Applicant’s arguments and amendments, see page 12, filed 08/28/2026, with respect to the rejection(s) of claim(s) 143 and 158 under 35 U.S.C. 112(d) have been fully considered and are persuasive as claim 158 has been canceled, and claim 143 has been amended to remove the phrase “a sequence having”. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of the amendment to claim 142 limiting the endonuclease to having at least 95% identity to SEQ ID NO: 30, with claim 143 still reciting the endonuclease has at least 90% identity to SEQ ID NO: 30 which is broader. See the 35 U.S.C. 112(d) rejection below.
Applicant’s arguments and amendments, see page 13, filed 08/28/2026, with respect to the 35 U.S.C. 102(a)(2) rejection of claims 142,143 and 145-161 have been fully considered and are persuasive due to amending claims 142 and 148 to require at least 95% sequence identity to SEQ ID NO: 30 which was not taught by Watters et al. The 35 U.S.C. 102(a)(2) rejection of claims 142,143 and 145-161 has been withdrawn.
Priority
This application is a CON of 18/173,722, filed 02/23/2023 (Abandoned) which is a CON of PCT/US2021/047195, filed 08/23/2021 which claims benefit of 63/069,703, filed 08/24/2020 and claims benefit of 63/186,698, filed 05/10/2021 and claims benefit of 63/232,593, filed 08/12/2021.
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 application, Application No. 63/069,703, 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. There is no support in 63/069,703, filed 08/27/2020 for the instant recited sequences (SEQ ID NOs: 30-33,111,123 or 124) in instant claims 142-161.
Claim Interpretation
Regarding claims 145,146,148,150,152-156,160 and 161, the recitation of “a sequence having at least X% identity to SEQ ID NO: X”, or “a polypeptide comprising a sequence having at least X% identity to SEQ ID NO: X”, or “a polypeptide comprising SEQ ID NO: X” is interpretated as only requiring two or more amino acids of the recited sequence in the case of an amino acid sequence or two or more nucleotides of the recited sequence in the case of a nucleic acid sequence. “A sequence” or “A polypeptide” encompasses two or more amino acids or nucleotides of any portion of the recited sequences. Paragraph 0098 of the instant specification states “The term "sequence identity" or "percent identity" in the context of two or more nucleic acids or polypeptide sequences, generally refers to two (e.g., in a pairwise alignment) or more (e.g., in a multiple sequence alignment) sequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence over a local or global comparison window, as measured using a sequence comparison algorithm”.
Response to Arguments
Applicant's arguments filed 08/28/2026 regarding the Examiners interpretation of claims 143,145,146,148,150-156,160 and 161 regarding the recitation of “a sequence” have been fully considered but they are not persuasive.
Applicant argues on page 13 that the recitation of “a sequence having at least X% identity to SEQ ID NO: X” in the context of the instant claims cannot reasonably be interpreted as covering identity between only “two or more amino acids or nucleotides” of the recited sequence, and such interpretation is inconsistent with the specification’s definition of “sequence identity” referring to “two (e.g., in a pairwise alignment) or more (e.g., in a multiple sequence alignment) sequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum corresponding over a local or global comparison window (paragraph 0098). Under the Examiner’s interpretation, “a sequence” sharing only two nucleotides over the entire length of SEQ ID NO: X would meet a 100% identity threshold, no matter the length of the sequences, and this is not consistent with the common understanding of sequence identity and would render the claimed percentage identity thresholds meaningless as any two amino acids sharing identity would satisfy any percentage threshold. The broadest reasonable interpretation must be consistent with the specification as it would be interpreted by one of ordinary skill in the art, and reserves the right to further argue claim interpretation in subsequent prosecution.
This is not found persuasive. The interpretation of the definition of “sequence identity” as defined in the instant specification is not in question, it is the broadest reasonable interpretation of “a sequence” which the Examiner maintains as only requiring two or more amino acids in the case of an amino acid sequence or two or more nucleotides of the recited sequence in the case of a nucleic acid sequence, and therefore reads on a fragment of the sequence. The affected claims could be amended to remove “a sequence” so that the scope of the claims is consistent with what Applicant is arguing, for example as was done in claim 143.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 143 and 150 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 143 depends on claim 142, and claim 142 was amended to require that the endonuclease comprising a RuvC domain, wherein said endonuclease is a Class II, type V endonuclease having at least 95% identity to SEQ ID NO: 30 and previously required 80% identity. Claim 143 was not amended to modify the percent identity to SEQ ID NO: 30 and still only requires 90% sequence identity to SEQ ID NO: 30 which is broader than the claim upon which is depends. Therefore, claim 143 does not further limit the subject matter of the claim upon which it depends.
Likewise, claim 150 depends on claim 148 and claim 148 was amended to require the Class II, type V Cas effector comprising a polypeptide having at least 95% sequence identity to SEQ ID NO: 30, while claim 150 only requiring at least 90% sequence identity to SEQ ID NO: 30 which is broader.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 142-157 and 159-161 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 59,67-73,75-77,112 and 113 of copending Application No. 18/840,723 (‘723) (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because claims 59,67-73,75-77,112 and 113 of ‘723 recite a system for transposing a cargo nucleotide sequence into a target nucleic acid site in a target nucleic acid comprising a) a Cas effector complex configured to hybridize to the target nucleic acid site and comprising i) a class 2, type V Cas effector comprising a polypeptide having a sequence having at least 80% sequence identity to SEQ ID NO: 30; and ii) an engineered guide polynucleotide comprising a sequence having at least 80% sequence identity to SEQ ID NO: 111;b) a Tn7 type transposase complex configured to bind the Cas effector complex and comprising TnsB, TnsC, and TniQ components, the TnsB, TnsC, or TniQ component comprising a sequence having at least 80% identity to SEQ ID NOs: 31-33; and c) a double-stranded nucleic acid configured to interact with the Tn7 type transposase complex and comprising in 5' to 3' order: i) a left-hand recombinase sequence comprising a sequence having at least 80% sequence identity to SEQ ID NO: 123, ii) the cargo nucleotide sequence; and iii) a right-hand recombinase sequence comprising a sequence having at least 80% identity to SEQ ID NO: 124.
Instant claims 142-147 recite an engineered nuclease system comprising: an endonuclease comprising a RuvC domain, wherein said endonuclease is a Class II, type V endonuclease having at least 95% identity to SEQ ID NO: 30, and an engineered guide ribonucleic acid (RNA), wherein said engineered guide RNA capable of forming a complex with said endonuclease and said engineered guide RNA comprises a spacer sequence capable of hybridizing to a target nucleic acid sequence, and instant claims 145,146,155 and 156 recite wherein said engineered guide RNA comprises a sequence having at least 80% or 90% sequence identity to SEQ ID NO: 111.
Instant claims 148-157 and 159-161 also recite a system for transposing a cargo nucleotide sequence to a target nucleic acid site comprising: a first double-stranded nucleic acid comprising said cargo nucleotide sequence capable of interacting with a Tn7 type transposase complex; a Cas effector complex comprising a class II, type V Cas effector and an engineered guide polynucleotide capable of hybridizing to said target nucleic acid site; and said Tn7 type transposase complex, wherein said Tn7 type transposase complex is capable of binding said Cas effector complex, wherein said Tn7 type transposase complex comprises a TnsB component, a TnsC component, and a TniQ component, wherein: (a) said Class II, type V Cas effector comprises a polypeptide having at least 95% sequence identity to SEQ ID NO: 30; or b) said TnsB component, said TnsC component, and said TniQ component each comprise a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 31-33. Claims 155-156 further recite the engineered guide polynucleotide comprising a sequence having at least 80% or 90% sequence identity to SEQ ID NO: 111. Claims 160-161 further recite at least 80% sequence identity to SEQ ID NOs: 123 and 124.
Therefore, the claims of ‘723 recite a system having the same components of the instant claims and recite the same sequences of the instant claims: SEQ ID NOs: 30, 111, 31-33,123 and 124 and therefore are not patentably distinct.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant requested that the provisional nonstatutory double patenting rejections be held in abeyance until at least one claim of the application is deemed allowable.
While the instant application is earlier filed (08/23/21) than the ‘723 application, the provisional nonstatutory double patenting rejection is not the only rejection remaining in the application, and therefore, the double patenting rejection is maintained until the provisional nonstatutory double patenting rejection is the only rejection remaining. See MPEP 804.
Claims 142-157 and 159-161 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 82,90-92,94-96,99-101,138-142,148-150 of copending Application No. 18/840,729 (‘729) (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because claims 82,90-92,94-96,99-101,138-142,148-150 of ‘729 recite a system for transposing a cargo nucleotide sequence into a target nucleic acid site in a target nucleic acid comprising: a) a Cas effector complex configured to hybridize to the target nucleic acid site and comprising: i) a class 2, type V Cas effector comprising a polypeptide having a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 22, 26, 30, 34, 55- 89, 104, and 147; and ii) an engineered guide polynucleotide comprising a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 90-93, 111-114, 117, 151, 156- 181, 201-206, 255, 262, 256, 209, 257, 263, 258, and 210;b) a Tn7 type transposase complex configured to bind the Cas effector complex and comprising TnsB, TnsC, and TniQ components, the TnsB, TnsC, or TniQ component comprising a sequence having at least 80% identity to any one of SEQ ID NOs: 23-25, 27-29, 31-33, 35-37, 101-103, 105-107, and 148-150; c) a double-stranded nucleic acid configured to interact with the Tn7 type transposase complex and comprising in 5' to 3' order :i) a left-hand recombinase sequence comprising a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 125, 127, 123, 129, 131, 133, 153,and 134;ii) the cargo nucleotide sequence; and iii) a right-hand recombinase sequence comprising a sequence having at least 80% identity to any one of SEQ ID NOs: 124, 126, 128, 130, 132, 154, and 155; and d) a functional domain comprising a DNA Binding domain (DBD) or a chromatin modulating domain (CMD).
Instant claims 142-147 recite an engineered nuclease system comprising: an endonuclease comprising a RuvC domain, wherein said endonuclease is a Class II, type V endonuclease having at least 95% identity to SEQ ID NO: 30, and an engineered guide ribonucleic acid (RNA), wherein said engineered guide RNA capable of forming a complex with said endonuclease and said engineered guide RNA comprises a spacer sequence capable of hybridizing to a target nucleic acid sequence, and instant claims 145,146,155 and 156 recite wherein said engineered guide RNA comprises a sequence having at least 80% or 90% sequence identity to SEQ ID NO: 111.
Instant claims 148-157 and 159-161 also recite a system for transposing a cargo nucleotide sequence to a target nucleic acid site comprising: a first double-stranded nucleic acid comprising said cargo nucleotide sequence capable of interacting with a Tn7 type transposase complex; a Cas effector complex comprising a class II, type V Cas effector and an engineered guide polynucleotide capable of hybridizing to said target nucleic acid site; and said Tn7 type transposase complex, wherein said Tn7 type transposase complex is capable of binding said Cas effector complex, wherein said Tn7 type transposase complex comprises a TnsB component, a TnsC component, and a TniQ component, wherein: (a) said Class II, type V Cas effector comprises a polypeptide having at least 95% sequence identity to SEQ ID NO: 30; or b) said TnsB component, said TnsC component, and said TniQ component each comprise a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 31-33. Claims 155-156 further recite the engineered guide polynucleotide comprising a sequence having at least 80% or 90% sequence identity to SEQ ID NO: 111. Claims 160-161 further recite at least 80% sequence identity to SEQ ID NOs: 123 and 124.
Therefore, the claims of ‘729 recite a system having the same components of the instant claims and recite the same sequences of the instant claims: SEQ ID NOs: 30, 111, 31-33,123 and 124 and therefore are not patentably distinct.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant requested that the provisional nonstatutory double patenting rejections be held in abeyance until at least one claim of the application is deemed allowable.
While the instant application is earlier filed (08/23/21) than the ‘729 application, the provisional nonstatutory double patenting rejection is not the only rejection remaining in the application, and therefore, the double patenting rejection is maintained until the provisional nonstatutory double patenting rejection is the only rejection remaining. See MPEP 804.
Conclusion
Claims 142-157 and 159-161 are rejected.
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 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 STEPHANIE L SULLIVAN whose telephone number is (703)756-4671. The examiner can normally be reached Monday-Friday, 7:30-3:30 EST.
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/STEPHANIE L SULLIVAN/Examiner, Art Unit 1635
/ABIGAIL VANHORN/Primary Examiner, Art Unit 1636
