DETAILED CORRESPONDENCE
Application Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. Applicants’ amendment to the claims filed on 07/31/2026 in response to the Restriction Requirement mailed on 06/10/2026 is acknowledged. This listing of claims replaces all prior listings of claims in the application.
3. Claims 59, 67-73, 75-77, and 112-113 are pending.
Election/Restrictions
4. Applicant’s election of Group I, claims 59, 67-73, 75-77, and 113, and the species SEQ ID NOs: 30, 111, 31, 32, 33, 123 and 124 in the reply filed on 07/31/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
5. Claim 112 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 07/31/2026.
Claims 59, 67-73, 75-77, and 113 are pending and will be examined to the extent that they read on the elected species SEQ ID NOs: 30, 111, 31, 32, 33, 123 and 124.
Priority
6. Acknowledgement is made of applicants’ claimed domestic priority to U.S. Provisional Application No. 63/313122, filed on 02/23/2022.
Information Disclosure Statement
7. The IDS filed on 07/31/2026 has been considered by the examiner and a copy of the Form PTO/SB/08 is attached to the office action.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specification
8. The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. In the instant case, paragraph 0166 contains an embedded hyperlink.
Claim Rejections - 35 USC § 112(b)
9. The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
10. Claims 59, 67-73, 75-77 and 113 are 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claims 59, 67-73, 75-77 and 113, the recitations of “a sequence having at least 80% sequence identity to SEQ ID NO…” is indefinite because it is unclear if the 80% sequence identity is over the entire SEQ ID NO or to fragments of said sequence. If applicants intend for the % identity to be over the entire SEQ ID NO, it is suggested that the claims be amended to recite “a sequence having at least 80% sequence identity to the amino acid sequence of SEQ ID NO…” or “a sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO…”. It is suggested that applicants clarify the meaning of the claims. In the interest of compact prosecution, the claims will be interpreted broadly to encompass fragments of the claimed sequences.
Further regarding claim 73, the term "about" in claim 73 is a relative term which renders the claim indefinite. The term "about" is a term of degree and the examiner has reviewed the specification and can find no examples or teachings that can be used for ascertaining the variance intended by the recited term of degree. Moreover, there is nothing in the specification or prior art of record to indicate that one of ordinary skill in the art could have ascertain the scope of the recited degree. It is suggested that applicant clarify the meaning of the claims. See Supplementary Examination Guidelines for Determining Compliance with 35 U.S.C. §112 and for Treatment of Related Issues in Patent Applications, 76 FR 7162 (Feb. 9, 2011), page 7165.
Claim Rejections - 35 USC § 102
11. The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
12. Claim(s) 59, 67-70, 73, 75-77, and 113 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhang et al. (US Patent Application Publication 2020/0190487 A1; examiner cited).
13. With respect to claim 59, Zhang et al. teach a system for transposing a cargo nucleotide sequence into a target nucleic acid site in a target nucleic acid comprising [see Abstract], a Cas effector complex configured to hybridize to the target nucleic acid site and comprising a class 2, type V Cas effector (interpreted as reading on SEQ ID NO: 30 given the breadth of the claim reading on fragments), an engineered guide polynucleotide (interpreted as reading on SEQ ID NO: 111 given the breadth of the claim reading on fragments), a Tn7 type transposase complex configured to bind the Cas effector complex and comprising TnsB, TnsC, and TniQ components (interpreted reading on SEQ ID NOs: 31-33 given the breadth of the claim reading on fragments), a double stranded nucleic acid configured to interact with the Tn7 type transposase complex comprising a left-hand recombinase sequence, the cargo nucleotide and a right hand recombinase sequence (interpreted as reading on SEQ ID NOs: 123 and 124 given the breadth of the claim reading on fragments) [see Abstract; Figure 18; paragraphs 0008-0013; 0179-0181].
With respect to claim 67, Zhang et al. teach the system wherein the class 2, type V Cas effector is a Cas12k effector [see paragraph 0011].
With respect to claim 68, Zhang et al. teach the system wherein the target nucleic acid comprises a PAM sequence compatible with the Cas effector complex [see paragraph 0012].
With respect to claim 69, Zhang et al. teach the system wherein the PAM sequence is located 5’ of the target nucleic acid site [see paragraph 0012].
With respect to claim 70, Zhang et al. teach the system wherein the PAM sequence comprises 5’-nGTn [see paragraph 0012].
With respect to claim 73, Zhang et al. teach the system wherein the class 2, type V Cas effector and the Tn7 type transposase complex are encoded by polynucleotide sequences comprising fewer than about 10 kilobases [see paragraphs 0008-0010].
With respect to claim 75, Zhang et al. teach the system wherein the Cas effector complex binds non-covalently to the Tn7 type transposase complex [see paragraphs 0008-0009; 0476].
With respect to claim 76, Zhang et al. teach the system wherein the Cas effector complex is covalently linked to the Tn7 type transposase complex [see paragraphs 0008-0009; 0476].
With respect to claim 77, Zhang et al. teach the system wherein the Cas effector complex is fused to the Tn7 type transposase complex [see paragraphs 0008-0009; 0476].
With respect to claim 113, Zhang et al. teach a cell comprising the system [see paragraphs 0015-0016].
Claim Rejections - 35 USC § 103
14. The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
15. Claim(s) 71-72 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (US Patent Application Publication 2020/0190487 A1; examiner cited) in view of Serganov et al. (The EMBO Journal, 2003; cited on IDS filed on 07/31/2026).
16. The relevant teachings of Zhang et al. as applied to claims 59, 67-70, 73, 75-77, and 113 are set forth in the 102(a)(1) above.
With respect to claims 71-72, Zhang et al. teach that localization tags such as to ribosomes [see paragraph 0369].
However, Zhang et al. does not teach the systems of claims 71 and 72, wherein the Cas effector complex comprises a small prokaryotic ribosomal protein subunit S15 wherein the small ribosomal protein subunit S15 comprises a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 494-659.
Serganov et al. teach that the small ribosomal protein subunit S15 is a key component in the assemble of the small ribosomal subunit and forms one of the bridges between the two subunits in 70S ribosomes in prokaryotes [see Abstract; p. 1898, column 2].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Zhang et al. and Serganov et al. to include the small ribosomal protein subunit S15 in the systems of Zhang et al. because Zhang et al. teach Cas effector systems for transposing a cargo nucleotide sequence into a target site and localization of the system to the ribosome. Serganov et al. teach that the small ribosomal protein subunit S15 is a key component in the assemble of the small ribosomal subunit and forms one of the bridges between the two subunits in 70S ribosomes in prokaryotes. One of ordinary skill in the art would have had a reasonable expectation of success and a reasonable level of predictability to combine the teachings of Zhang et al. and Serganov et al. because Serganov et al. acknowledges that the small ribosomal protein subunit S15 is a key component in the assemble of the small ribosomal subunit and forms one of the bridges between the two subunits in 70S ribosomes in prokaryotes. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Double Patenting
17. 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.
18. Claims 59, 67-73, 75-77 and 113 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 142-157 and 159-161 of copending Application No. 18/481769. Although the claims at issue are not identical, they are not patentably distinct from each other because claims 142-157 and 159-161 of the ‘769 application are drawn to systems 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: said Class II, type V Cas effector comprises a polypeptide having at least 95% sequenc identity to SEQ ID NO: 30 or 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.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
19. Claims 59, 67-73, 75-77 and 113 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 82, 90-92, 94-96, 99-101, 139-142, and 148-150 of copending Application No. 18/840729. 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, 139-142, and 148-150 of the ‘729 application are drawn to systems for transposing a cargo nucleotide sequence to a target nucleic acid site comprising: 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).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
20. Claims 59, 67-73, 75-77 and 113 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6, 8-9, 13-14, 17, 20, 23, 25, and 27-33 of copending application no. 18/840719. Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-6, 8-9, 13-14, 17, 20, 23, 25, and 27-33 of the ‘719 application are drawn to 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 comprising a class 2, type V Cas effector, a small prokaryotic ribosomal protein subunit S15, and an engineered guide polynucleotide configured to hybridize to the target nucleic acid site; b) a Tn7 type transposase complex configured to bind the Cas effector complex and comprising a TnsB, TnsC, and TniQ component; c) a double-stranded nucleic acid configured to interact with the Tn7 type transposase complex and comprising the cargo nucleotide sequence; and d) a functional domain comprising a DNA Binding domain (DBD) or a chromatin modulating domain (CMD).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
21. Claims 59, 67-73, 75-77 and 113 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4, 8-9, 13-14, 17, 20-27 and 89 of copending application no. 18/840844. Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-4, 8-9, 13-14, 17, 20-27 and 89 of the ‘844 application are drawn to 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 comprising a class 2, type V Cas effector, a small prokaryotic ribosomal protein subunit S15, and an engineered guide polynucleotide configured to hybridize to the target nucleic acid site; b) a Tn7 type transposase complex configured to bind the Cas effector complex and comprising a TnsB, TnsC, and TniQ component; and c) a double-stranded nucleic acid configured to interact with the Tn7 type transposase complex and comprising the cargo nucleotide sequence, wherein the cargo nucleotide sequence is flanked by a left-hand transposase recognition sequence and a right- hand transposase recognition sequence recognized by the Tn7 type transposase complex, wherein the left-hand recombinase sequence comprises a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 9, 11, 36-38, 76, and 78, and wherein the right- hand recombinase sequence comprises a sequence having at least 80% identity to any one of SEQ ID NOs: 8, 10, 39-44, 77, 79, and 93.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
22. Claims 59, 67-73, 75-77 and 113 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13, 29, 52, 75-77, and 86 of copending application no. 19/163801. Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-13, 29, 52, 75-77, and 86 of the ‘801 application are drawn to a ystem for transposing a cargo nucleotide sequence into a target nucleic acid site in a target nucleic acid comprising: a. a Cas effector complex that hybridizes to the target nucleic acid site and comprising: i) a class 2, type V Cas effector comprising a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1, 81, 82, 83, and 85; and ii) an engineered guide polynucleotide having at least 80% identity to any one of SEQ ID NOs: 5, 6, 45-63, 68-75, 96-103, 123-140, and 754-944; b. a Tn7 type transposase complex that binds the Cas effector complex and comprises a TnsB, TnsC, and TniQ component, the TnsB, TnsC, or TniQ component comprising a sequence having at least 80% identity to any one of SEQ ID NOs: 2-4, and an accessory protein comprising a sequence having at least 70% sequence identity to any one of SEQ ID NOs: 228-230 and 235-249; and c. a double-stranded nuclcic acid that interacts with the Tn7 type transposase complex and comprising in 5' to 3' order: i) a left-hand transposase recognition sequence comprising a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 9, 11, 36, 37, and 38; ii) the cargo nucleotide sequence; and ii) a right-hand transposase recognition sequence comprising a sequence having at least 80% identity to any one of SEQ ID NOs: 8, 39-44, and 93.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
23. Status of the claims:
Claims 59, 67-73, 75-77, and 112-113 are pending.
Claim 112 stands withdrawn pursuant to 37 CFR 1.142(b).
Claims 59, 67-73, 75-77 and 113 are rejected.
No claims are in condition for an allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PAUL J HOLLAND whose telephone number is (571)270-3537. The examiner can normally be reached Monday to Friday from 8AM to 5PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath Rao can be reached at 571-272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PAUL J HOLLAND/Primary Examiner, Art Unit 1656
