CTNF 17/742,503 CTNF 71972 DETAILED ACTION Notice of Pre-AIA or AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Applicants’ filed a Preliminary Amendment on October 24, 2022, in which claims 1-28 were canceled and new claims 29-54 were added. Thus, claims 29-54 are pending in this application, and are under examination. Information Disclosure Statement The Information Disclosure Statements filed October 24, 2022 (2); October 4, 2023; November 1, 2023; June 7, 2024; October 3, 2024; and November 14, 2024 have been considered. 06-49-06 AIA The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered. Nucleotide and/or Amino Acid Sequence Disclosures REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES Items 1) and 2) provide general guidance related to requirements for sequence disclosures. 37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," 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 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted: In accordance with 37 CFR 1.821(c)(1) 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") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying: the name of the ASCII text file; ii) the date of creation; and iii) the size of the ASCII text file in bytes; In accordance with 37 CFR 1.821(c)(1) 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 of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying: the name of the ASCII text file; the date of creation; and the size of the ASCII text file in bytes; In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended). When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824. If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical. If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical. Specific deficiencies and the required response to this Office Action are as follows: Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. Figure 13C does not include sequence identifiers. Required response – Applicant must provide: Replacement and annotated 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 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 07-29 AIA The disclosure is objected to because of the following informalities: All genus and species names in the specification should be italicized. The specification filed January 16, 2024 does not have page numbers. Paragraph [1249] recites that Cas-associated transposase systems are shown in Table 26 below. However, Table 27 is shown below. Further, Table 26 is shown prior to Example 11 on page 400 and lists NGS primer sequences, rather than sequences of the Cas-associated transposase systems. The use of the terms TALEN® at paragraphs [0245], [0246], [0714] , [0718], [0812], [0821], [0847], and [0867]; PIGGYBAC® at paragraph s[0820], [0821], and [1194]; MIRNEASY® at paragraphs [1175] and [1231]; NEBNEXT® at paragraphs [1175] and [1231]; NEXTSEQ® at paragraphs [1176], [1187], and [1232]; GENEIOUS PRIME® at paragraphs [1176] and [1232]; DNEASY® at paragraphs [1177], [1185], [1233], and [1243]; HOTSTART® at paragraphs [1177], [1185], [1187], [1233], [1241], and [1243]; GIBSON ASSEMBLY® at paragraphs [1178] and [1234]; QX200® at paragraphs [1180], [1236], and [1242]; QUANTASOFT® at paragraphs [1180] and [1236]; QIAPREP® at paragraphs [1181] and [1237]; STREP-TACTIN® at paragraphs [1182] and [1238]; AKTA PURE® at paragraphs [1182] and [1238] ; SUPERDEX® at paragraphs [1182] and [1238]; HISCRIBE® at paragraphs [1183] and [1239]; AMPURE® at paragraphs [1183] and [1239]; MISEQ® at paragraphs [1186], [1234], and [1242]; QIAQUICK® at paragraphs [1187] and [1243]; HITRAP® at paragraph [1238]; PUREEXPRESS® at paragraph [1251]; LIPOFECTAMINE® at paragraph [1261]; and QUICK EXTRACT® at paragraph 1261]; which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term. Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks . Appropriate correction is required. 07-30-03-h AIA Claim Interpretation 07-30-03 AIA The following is a quotation of 35 U.S.C. 112(f): (f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph: An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. 07-30-05 The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked. As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph: (A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function; (B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and (C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function. Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function. Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function. Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. 07-30-06 This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitations are: “[a] delivery system configured to deliver one or more components of an engineered nucleic acid targeting system” (claims 29-54). Because this claim limitation is being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it is being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. If applicant does not intend to have this limitation interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. Claim Rejections - 35 USC § 112 07-30-01 AIA The following is a quotation of the first paragraph of 35 U.S.C. 112(a): (a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention. The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112: The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention. 07-31-01 Claims 29-54 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 claims contain 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 applications subject to pre-AIA 35 U.S.C. 112, the inventors, at the time the application was filed, had possession of the claimed invention. The claims comprise limitations that invoke 35 U.S.C. 112(f), but the specification does not link structure to function. Thus, the specification does not disclose adequate structure to perform the claimed functions. 07-30-02 AIA 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. 07-34-01 Claims 29-54 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. 07-34-23 Claim limitation “[a] delivery system configured to deliver one or more components of an engineered nucleic acid targeting system” invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. Therefore, the claims are indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. Applicant may: (a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph; (b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or (c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)). If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either: (a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or (b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181. At claim 37, lines 1-2, it is not clear how the one or more vectors “comprise one or more viral vectors.” It is suggested that the claim be changed to “wherein the one or more vectors are one or more viral vectors.” Claim 38 depends from claim 37, and is therefore included in this rejection. At claim 38, lines 1-2, it is not clear how the one or more viral vectors “comprise retroviral, lentiviral, adenoviral, adeno-associated, or herpes simplex viral vectors.” It is suggested that the claim be changed to “wherein the one or more viral vectors are retroviral, lentiviral, adenoviral, adeno-associated, or herpes simplex viral vectors.” Claim 51 recites that the proteins are selected from Table 28 or Table 29, or are encoded by polynucleotides selected from Table 26 or Table 27. However, incorporation by reference to a specific figure or table “is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.” Ex parte Fressola , 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993). Here, the proteins and polynucleotides can be listed using the respective sequence identifiers. In addition, Table 26 lists NGS primers, not proteins or polynucleotides encoding TnsB, TnsC, or TniQ. Claim 53 depends from claim 51, and is therefore included in this rejection. Claim 53 recites that the Cas12k is encoded by a polynucleotide selected from Table 26 or Table 27. However, incorporation by reference to a specific figure or table “is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.” Ex parte Fressola , 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993). Here, the polynucleotides encoding the Cas12k can be listed using the respective sequence identifiers or by listing the organisms from which the Cas12k is obtained. In addition, Table 26 lists NGS primers, not polynucleotides encoding Cas12k. Claim 54 recites that the guide molecule comprises a polynucleotide sequence selected from Table 26. However, incorporation by reference to a specific figure or table “is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.” Ex parte Fressola , 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993). Here, the guide molecules can be listed using the respective sequence identifiers. Double Patenting 08-33 AIA 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 1384344www.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 29-54 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 11,384,344. Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘344 patent claims an engineered nucleic acid targeting system and the instant application claims a delivery system for an engineered nucleic acid targeting system. Regarding claim 29, the ‘344 patent claims an engineered nucleic acid targeting system for insertion of donor polynucleotides, the system comprising one or more CRISPR-associated Tn7 transposase or Tn7-like transposase proteins that form a transposase; a catalytically inactive Type V Cas protein capable of forming a complex with the transposase; a guide molecule capable of forming a complex with the Type V Cas protein and directing sequence-specific binding of a guide-Cas protein complex to a target sequence of a target polynucleotide; and a donor construct, comprising a heterologous donor polynucleotide sequence flanked by a first and second binding sequence capable of complexing the donor construct with the one or more Tn7 or Tn7-like transposase proteins. The ‘344 patent claims that the Cas protein lacks nuclease activity. Regarding claims 30-36, the ‘344 patent claims an engineered system comprising one or more polynucleotides encoding components (a), (b) and/or (c) of claim 1, or a vector comprising the one or more polynucleotides. Regarding claim 39, the ‘344 patent claims the one or more CRISPR-associated transposase proteins comprises TnsB and TnsC, or TniA and TniB. Regarding claim 46, the ‘344 patent claims that the one or more CRISPR-associated transposase proteins comprises: TnsA, TnsB, TnsC, and TniQ; TnsA, TnsB, and TnsC; TnsB, TnsC, and TniQ; TnsA, TnsB, and TniQ; TnsE; TniA, TniB, and TniQ; TnsB, TnsC, and TnsD; TnpA; or any combination thereof. Regarding claim 48, the ‘344 patent claims that the one or more CRISPR-associated transposase proteins comprises TnsB, TnsC, and TniQ. Regarding claim 51, the ‘344 patent claims that the TnsB, TnsC, and TniQ is selected from SEQ ID NOs: 829, 831, 833, 837, 839, 841, 845, 847, 849, 853, 855, 857, 861, 863, 865, 869, 871, 873, 877, 879, 881, 885, 887, 889, 893, 895, 897, 901, 903, 905, 909, 910, and 911, or are encoded by polynucleotides selected from SEQ ID NOs: 828, 830, 832, 836, 838, 840, 844, 846, 848, 852, 854, 856, 860, 862, 864, 868, 870, 872, 876, 878, 880, 884, 886, 888, 892, 894, 896, 900, 902, 904, 917, and 918. Regarding claim 52, the ‘344 patent claims that the Cas protein is Cas12k. Regarding claim 53, the ‘344 patent claims that the Cas12k is encoded by a polynucleotide selected from SEQ ID NOs: 834, 842, 850, 858, 866, 874, 882, 890, 898, 906, 967, 976, 985, 994, 1003, 1012, 1021, 1030, 1039, 1048, 1057, 1066, 1075, 1084, 1093, 1102, 1111, 1120, 1129, 1138, 1147, 1156, 1165, 1174, 1183, 1192, 1201, 1210, 1219, 1228, 1237, 1246, 1255, 1264, 1273, 1282, 1291, 1300, 1309, 1318, and 1327 or is a protein comprising SEQ ID NO: 835, 843, 851, 859, 867, 875, 883, 891, 899, 907, or 912, or obtained from an organism selected from Leptolyngbya frigida ULC18 , Phormidium tenue NIES 30, filamentous cyanobacterium CCT1 , Chamaesiphon minutus PCC 6605 , Geitlerinema sp PCC 7407 , Leptolyngbya ohadii, Aphanocapsa montana BDHKU210001, filamentous cyanobacterium CCP4 , Phormidesmis priestleyi , filamentous cyanobacterium CCP2 , Leptolyngbya ohadii, filamentous cyanobacterium CCP2 , Cyanothece sp PCC 7425, filamentous cyanobacterium CCP5 , Trichormus variabilis ATCC 29413 , Nostoc sp Peltigera membranacea cyanobiont 232 , Cyanothece sp PCC 8801 , Scytonema hofmanni PCC 7110 , Calothrix sp PCC 7103 , Nostoc sp NIES 2111 , Calothrix sp NIES 2100 , Scytonema sp HK 05 , Nostoc sp Peltigera malacea cyanobiont DB3992 , Nostoc sp NIES 4103 , Nostoc sp PCC 7107 , Nostoc piscinale CENA21 , Nostoc sp MBR 210 , Nostoc sp NIES 3756 , Trichormus variabilis ATCC 29413 , Anabaena sp 4 3 , Nostoc sp CENA543 , Nostoc sp HK 01 , Chlorogloea sp CCALA 695 , Anabaena cylindrica PCC 7122 , Aphanizomenon flos aquae, Calothrix sp PCC 6303 , Nodosilinea nodulosa, Aphanocapsa montana BDHKU210001 , Leptolyngbya sp, Leptolyngbya boryana IAM M 101 , Nostoc linckia zl, Fremyella diplosiphon NIES 3275 , Tolypothrix sp PCC 7601 , Anabaena sp WA102 , Cuspidothrix issatschenkoi CHARLIE 1 , Mastigocoleus testarum BC008 , Calothrix sp NIES 4101 , Calothrix parasitica NIES 267 , Pseudanabaena frigida, Hassallia byssoidea VB512170 , Anabaena sp WA113 , Chlorogloea sp CCALA 695 , Tolypothrix tenuis PCC 7101 , Trichormus variabilis NIES 23 , Nostoc sp PCC 7120 , Nostoc carneum NIES 2107 , Scytonema hofmanni UTEX B 1581 , Nostoc punctiforme PCC 73102, filamentous cyanobacterium CCP3 , Alkalinema sp CACIAM 70d, Microcoleus sp PCC 7113 , Crinalium epipsammum PCC 9333 , Cyanobacterium aponinum IPPAS B 1201 , Geminocystis sp NIES 3708 , Geminocystis sp NIES 3709 , Cyanobacterium sp HL 69 , Cyanobacterium sp IPPAS B 1200 , Geminocystis sp NIES 3709 , Myxosarcina sp GI1 , Xenococcus sp PCC 7305 , Gloeocapsa sp PCC 73106 , Cyanothece sp PCC 8802 , Cyanothece sp CCY0110 , Cyanothece sp PCC 8801 , Spirulina major, Halothece sp PCC 7418 , Nostoc flagelliforme CCNUN1 , Tolypothrix sp PCC 7601 , Tolypothrix tenuis PCC 7101 , Nostoc cycadae WK 1 , Nostoc cycadae, Nostocaceae Nostoc sp KVJ20, and Scytonema sp NIES 4073. Regarding claim 54, the ‘344 patent claims that the guide molecule comprises a guide sequences selected from SEQ. ID NOs: 804, 807, 810, 813, 816, 819, 821, and 824. Regarding claims 37-38, while the ‘344 patent does claim the use of vectors to deliver the claimed polynucleotides, the ‘344 patent does not explicitly claim that the vectors are viral vectors selected from retroviral, lentiviral, adenoviral, adeno-associated, or herpes simplex viral vectors. However, it would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention that the well-known viral vectors, including, for example, lentiviral and adeno-associated viral vectors could be used to deliver the claimed polynucleotides. One of ordinary skill in the art would have been motivated to use such vectors in order to provide the transposases to the cell, which will, in turn, provide for delivery and integration of a donor polynucleotide. Regarding claims 40-45, 47, and 49-50, while the ‘344 patent does not explicitly claim the vector location or number for the location of the transposases, it would have been obvious to one with ordinary skill in the art before the effective filing date of the claims invention to determine the number of vectors used to deliver the transposases to a cell in order to optimize the expression of the transposases. One of ordinary skill in the art would have been motivated to do so in order to provide the transposases to the cell, which will, in turn, provide for delivery and integration of a donor polynucleotide. Claims 29-36 and 39-54 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 7, 9, 11, 16, 21, 28, 38, 45-46, and 52-53 of copending Application No. 17/928,355 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘355 application claims an engineered targeting system for insertion of a polynucleotide and the instant application claims a delivery system for an engineered targeting system for insertion of a polynucleotide. Regarding claim 29, the ‘355 application claims a system comprising transposase proteins, a Cas protein, a guide molecule and a donor polynucleotide. The ‘355 application claims that the Cas protein can be Cas12k, which is a Type V Cas protein. The ‘355 application claims that the transposases can be Tm7 or Tn-7 like transposases. The ‘355 application claims that the Cas protein can have an activation mutation and can be a dead (inactive) Cas protein. Regarding claims 30-35, 40-45, 47, and 49-50, the ‘355 application claims vectors that comprise one or more of the claimed polynucleotides. Regarding claim 36, the ‘355 application claims a eukaryotic cell. Regarding claim 39, the ‘355 application claims the one or more CRISPR-associated transposase proteins comprises TnsB and TnsC, or TniA and TniB. Regarding claim 46, the ‘355 application claims that the one or more CRISPR-associated transposase proteins comprises: TnsA, TnsB, TnsC, and TniQ; TnsA, TnsB, and TnsC; TnsB, TnsC, and TniQ; TnsA, TnsB, and TniQ; TnsE; TniA, TniB, and TniQ; TnsB, TnsC, and TnsD; TnpA; or any combination thereof. Regarding claim 48, the ‘355 application claims that the one or more CRISPR-associated transposase proteins comprises TnsB, TnsC, and TniQ. Regarding claim 51, the ‘355 application claims that the TnsB, TnsC, and TniQ is selected from SEQ ID NOs: 829, 831, 833, 837, 839, 841, 845, 847, 849, 853, 855, 857, 861, 863, 865, 869, 871, 873, 877, 879, 881, 885, 887, 889, 893, 895, 897, 901, 903, 905, 909, 910, and 911, or are encoded by polynucleotides selected from SEQ ID NOs: 828, 830, 832, 836, 838, 840, 844, 846, 848, 852, 854, 856, 860, 862, 864, 868, 870, 872, 876, 878, 880, 884, 886, 888, 892, 894, 896, 900, 902, 904, 917, and 918. Regarding claim 52, the ‘355 application claims that the Cas protein can be Cas12k, which is a Type V Cas protein. Regarding claim 53, the ‘355 application claims sequences of the Cas12k protein or polynucleotide encoding the Cas12k. Regarding claim 54, the ‘355 application claims sequences of the guide molecules. Therefore, the claims are not deemed to be patentably distinct. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented. Claims 29-36 and 39-52 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5, 7-10, 13-16, and 26-30 of copending Application No. 18/270,854 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘854 application claims an engineered targeting system for insertion of a polynucleotide and the instant application claims a delivery system for an engineered targeting system for insertion of a polynucleotide. Regarding claim 29, the ‘854 application claims a system comprising transposase proteins, a Cas protein, a guide molecule and a donor polynucleotide. The ‘854 application claims that the Cas protein can be Cas12k, which is a Type V Cas protein. The ‘854 application claims that the transposases can be Tm7 or Tn-7 like transposases. The ‘854 application claims that the Cas protein can have an activation mutation and can be a dead (inactive) Cas protein. Regarding claims 30-35, 40-45, 47, and 49-50, the ‘854 application claims vectors that comprise one or more of the claimed polynucleotides. Regarding claim 36, the ‘854 application claims a eukaryotic cell. Regarding claims 39, 46, and 48, the ‘854 application claims that the transposase proteins can be TnsB, TnsC, TniA, TniB, or TnpA Regarding claim 51, the ‘355 application claims that the TnsB, TnsC, and TniQ is selected from sequences in Tables 1-6. Regarding claim 52, the ‘854 application claims that the Cas protein can be Cas12k, which is a Type V Cas protein. Therefore, the claims are not deemed to be patentably distinct. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented. Conclusion 07-96 AIA The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Peters et al. (15 Genes and Development 737-747 (2001), and cited in the Information Disclosure Statement filed October 24, 2022) disclose that Tn7 transposons recognize target structures using the DNA-binding protein TnsE, which interacts directly at target DNA molecules (abstract and paragraph bridging pages 743 and 744). Scott et al. (U.S. Patent No. 12,054,754) 17disclose CRISPR-associated transposon systems and methods of nucleic acid manipulation. However, the ‘754 patent does not disclose that the transposon is a T7 or T7-like transposon. Nor does the ‘754 patent disclose that the CRISPR protein is a Type V (Cas12 or Cas12k) CRISPR protein. Any inquiry concerning this communication or earlier communications from the examiner should be directed to NANCY J LEITH whose telephone number is (313)446-4874. The examiner can normally be reached Monday - Thursday 8:00 AM - 6:30 PM. 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, NEIL HAMMELL can be reached at (571) 270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. NANCY J. LEITH Primary Examiner Art Unit 1636 /NANCY J LEITH/Primary Examiner, Art Unit 1636 Application/Control Number: 17/742,503 Page 2 Art Unit: 1636 Application/Control Number: 17/742,503 Page 3 Art Unit: 1636 Application/Control Number: 17/742,503 Page 4 Art Unit: 1636 Application/Control Number: 17/742,503 Page 5 Art Unit: 1636 Application/Control Number: 17/742,503 Page 6 Art Unit: 1636 Application/Control Number: 17/742,503 Page 7 Art Unit: 1636 Application/Control Number: 17/742,503 Page 8 Art Unit: 1636 Application/Control Number: 17/742,503 Page 9 Art Unit: 1636 Application/Control Number: 17/742,503 Page 10 Art Unit: 1636 Application/Control Number: 17/742,503 Page 11 Art Unit: 1636 Application/Control Number: 17/742,503 Page 12 Art Unit: 1636 Application/Control Number: 17/742,503 Page 13 Art Unit: 1636 Application/Control Number: 17/742,503 Page 14 Art Unit: 1636 Application/Control Number: 17/742,503 Page 15 Art Unit: 1636 Application/Control Number: 17/742,503 Page 16 Art Unit: 1636 Application/Control Number: 17/742,503 Page 17 Art Unit: 1636 Application/Control Number: 17/742,503 Page 18 Art Unit: 1636 Application/Control Number: 17/742,503 Page 19 Art Unit: 1636
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