DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim(s) 106-125 are pending.
Preliminary Amendments
Applicant’s preliminary amendment filed on 11/22/2023 is acknowledged. The claims were amended to cancel claims 1-105 and add claims 106-125. The specification was amended to add the statement of “incorporation by reference of sequence listing”, adjust line spacing, and amend to add a brief description of the following figures: 1A-F, 2A-B, 3A-B, 4A-B, 5A-B, 7A-B, 8A-B, and 9A-B. The sequence listing named “2023-11-21 Sequence_Listing_ST26 062709-502C01US” was submitted. The drawings were replaced.
Applicant’s preliminary amendment filed on 01/29/2024 is acknowledged. The specification has been amended to be compliant with 37 CFR 1.74 and 1.77(b)(9).
Applicant’s preliminary amendment filed on 01/20/2026 is acknowledged. The specification has been amended to reflect the replacement Sequence Listing. The drawings were amended to add SEQ ID NOs in Fig. 3B and 7A. The sequence listing has been amended to add SEQ ID NOs: 68-75.
Applicant’s preliminary amendment filed on 02/04/2026 is acknowledged. The specification was amended to add an incorporation by reference statement.
Election/Restrictions
Applicant’s election without traverse of Species of Cas9 in the reply filed on 05/13/2026 is acknowledged.
Claim(s) 124 and 125 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 05/13/2026.
Claim(s) 106-123 are under consideration.
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. 112(a) 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. 63/109,396, 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.
Claim 106 recites “SEQ ID NO: 53” which was not previously disclosed in the prior-filed application. Claim(s) 107-112 depend upon claim 106 and further limit SEQ ID NO:53 through amino acid substitutions. Said substitution are not adequately described in the prior-filed application. Claim(s) 113-119 depend upon claim 106 and are not adequately described in the prior-filed application.
Claim(s) 120-123 depend upon claim 106, i.e., a nucleic acid encoding the chimeric nuclease of claim 106 (claim 120), a pharmaceutical composition comprising the chimeric nuclease of claim 106 and a pharmaceutically acceptable excipient, diluent, or carrier (claim 121), A composition comprising the chimeric nuclease of claim 106 encapsulated in a lipid nanoparticle (claim 122), and A method of genetically engineering the genome of a cell, the method comprising administering the chimeric nuclease of claim 106 to the cell (claim 123). Since claim 106 comprises SEQ ID NO: 53, which was not adequately described in the prior-filed application, Applicant would not have been in possession of a nucleic acid encoding, a pharmaceutical composition, a composition, or a method of genetically engineering. Hence, claims 120-123 are not adequately described in the prior-filed application.
Accordingly, claim(s) 106-123 have an effective filing date of the CON of the 371 filed as PCT/IB2021/060236 on 11/04/2021.
Information Disclosure Statement
Receipt of the information disclosure statement(s) on 01/07/2025, 12/29/2025, and 01/26/2026 are acknowledged. The signed and initialed PTO-1449 form(s) has/have been mailed with this action.
Specification
The use of the term(s)
GENEWIZ [0074];
Nucleofector [0074]; and
MaxCyte [0076],
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.
Claim Objections
Claim(s) 106, 107, 109, 110, 112, and 115 are objected to because of the following informalities:
Claim 106 contains an extra space after “53” and before the period, “. . .NO: 53 .”. It would be remedial to remove this space.
Claim 107 contains an extra space after “53” and before the comma, “. . .NO: 53 ,”. It would be remedial to remove this space.
Claim 109 does not have a period at the end of the claim.
Claim 110 recites, “. . . and or . . .” in line 2. It would be remedial to amend this claim to recite “. . . and/or. . .”.
Claim 112 contains periods after “a” and “b”. It would be remedial to amend this claim to recite “a)” and “b)”.
Claim 115 recites, “The method of claim 106 . . .”. It would be remedial to amend this to recite, “The chimeric nuclease of claim 106. . . ”.
Claim 115 recites, “. . . Streptococcus pyogenes . . .”. It would be remedial to italicize the genus and species of the recited organism.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(d) – Improper Dependent
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.
Claim(s) 110-112 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(s) 110-112 fail to include all of the limitations of claim 109, from which they depend. The specified sequence of claim 109 is no longer present due to the addition of one or more mutations.
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.
Claim Rejections - 35 USC § 102
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 106, 109-111, 116-117, 119-120, and 123, are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wolfs et al (Biasing genome-editing events toward precise length deletions with an RNA-guided TevCas9 dual nuclease, PNAS, volume 113, issue 52, pages 14988 to 14993, published December 12th, 2016; IDS filed 01/07/2025 under NPL #8)
Regarding claim(s) 106, 109, 116, 117, 119, and 123, Wolfs et al discloses, “We created a dual nuclease that introduces two noncompatible DNA breaks at a target site such that the majority of the target site is deleted, preventing regeneration of the target site and continued cleavage. We fused the monomeric nuclease and linker domains from the I-TevI homing endonuclease to Cas9 (27, 28), creating an RNA-guidedTevCas9 dual nuclease that functions robustly in HEK293 cells at endogenous target sites.”, (see page 14988, column 2, lines 6-11).
Wherein the sequences of the I-TevI endonuclease and linker can be found in the supplemental information one page 1, is the first sequence, and is named “Tev169-Cas9” and is 100% identical to SEQ ID NO: 53 of the instant application, i.e., 1-92 of SEQ ID NO: 53 (of
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claim 1) and 93-169 of SEQ ID NO: 53 (of claim 109).
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Regarding claim(s) 110 and 111, Wolfs et al teaches the substitution of V117F, K135N, N140S, and the combination of the three (see pages 1 and 2 of Wolfs et al supplemental) see alignment below.
Regarding claim 120, Wolfs et al teaches, “TevCas9 or Cas9 variants with C-terminal 6× histidine tags and gRNA were cloned in pACYC–Duet1 expression plasmids under control ofseparate T7-regulated promoters, and expression was induced overnight at 16 °Cwith 1 mM isopropyl β-D-thiogalactopyranoside (IPTG).”, (see page 14992, column 2, protein purification).
Accordingly, claim(s) 106, 109-111, 116, 117, 119-120, and 123 are anticipated by Wolfs et al.
Claim(s) 106-107, 110, 111, and 113-123 is/are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Edgell et al (WO 2020/225719 A1, published November 12th, 2020, effective filing date of May 4th, 2020; IDS filed 01/07/2025 under Foreign Documents #7).
Regarding claim(s) 106, 107, 110, 111, 113, 114, 116, 121, and 122, Edgell et al discloses, “The instant invention is directed to a chimeric nuclease comprising a modified I-TevI nuclease domain, preferably deleting Met1 and having Lys26 (which is Lys27 in the untruncated version of I-TevI) and/or Cys39 (which is Cys40 in the untruncated version of I-TevI) modification, a linker, in particular SEQ ID NOS: 7-12 or fragments thereof and/or containing one or more of the following mutations Thr95 (as referenced to the full-length I-TevI), Val117, Lys135, Gln158 or Asn140, and a modified RNA-guided nuclease Staphylococcus aureus Cas9 that may be the wild-type or a modified version, preferably containing a Glu10 or an Ala557 mutation thereof wherein said I-TevI polypeptide comprises the entire amino acid sequence of SEQ ID NO: 6 or a fragment thereof, and guide RNA, in particular, SEQ ID NOS: 15, 16 or 21 or fragments thereof, that targets the Cas9 domain and a pharmaceutically-acceptable formulation comprising the chimeric nuclease, cationic and/or neutral lipid nanoparticles, optionally DNA-binding compounds, in particular GL67 (N4-cholesteryl-spermine) and a pharmaceutically acceptable carrier thereof.”, ([0017]).
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Wherein SEQ ID NO: 6 of Edgell et al is 100% identical to instant SEQ ID NO: 8.
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Wherein SEQ ID NO: 7 of Edgell et al contains the linker domain and the V117 substitution to F. See alignment below.
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SEQ ID NO: 13 of Edgell et al represents the saCas9 and is identical to instant SEQ ID NO: 15, see alignment below.
Regarding claim 115, Edgell et al discloses, “Modifications of the Cas9 Domain: Other versions of the Cas9 domain might contain the following: a). . . . d). A version of the previously described spCas9 EQR mutant comprising the mutations D1135E, R1335Q and T1337R combined with the D10E mutation (SEQ ID NO: 19); . . .”, ([0082]).
Regarding claim 117, Edgell et al discloses, “Another embodiment of the invention is directed to methods to delete defined lengths of a DNA molecule or to replace select sequences from a DNA molecule by delivering a chimeric nuclease in vivo to a whole organism or to isolated cells in culture ex vivo wherein said cells are mammalian cells . . .”, ([0020]).
Regarding claim 118, Edgell et al discloses, “In eukaryotic organisms, the nuclease (TevCas9) 25 is targeted to the nucleus 23 of the cell 20 through one or more nuclear-localization sequences (“NLS”). As depicted in FIG. 2E, through its nuclear localization sequence, TevCas9 25 can enter the nucleus 23 and when in the nucleus 23, the TevCas9 nuclease 25 binds to and cleaves 26 the target genomic DNA 24 sequence.”, ([0011]).
Regarding claim 119, Edgell et al discloses, “. . . V. Circular double-strand DNA comprising an I-TevI target site and Cas9 target site where the product cleaved from the double-strand DNA contains complimentary ends to those cleaved by TevCas9.”, ([0076]).
Regarding claim 120, Edgell et al discloses, “FIG. 4B are cells transfected with a plasmid DNA version of TevCas9 fused to a cleavable GFP tag imaged using phase contrast and GFP imaging on a Cytation5 (Biotek Instruments Inc, VT, USA) after 48 hours treatment. Genomic DNA is extracted from harvested cells and editing at the CFTR gene is detected by PCR amplification and a T7 Endonuclease I cleavage assay.”, ([0013]).
Regarding claim 123, Edgell et al discloses, “Methods to edit genes by administering a chimeric nuclease to a cell or organism without the use of a viral vector.”, (abstract).
Accordingly, claim(s) 106-107, 110, 111, and 113-123 are rejected as being anticipated by Edgell et al.
Claim(s) 106-107, 110, 111, and 113-123 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by 658 (US 11,814,658 B2; published 11/14/2023; effective filing date of 5/3/2019; IDS filed 12/29/2025 as #5).
Regarding claim(s) 106, 107, 110, 111, 113, 114, 116, 121, and 122, 658 discloses, “The instant invention is directed to a chimeric nuclease comprising a modified I-TevI nuclease domain, preferably deleting Met1 and having Lys26 (which is Lys27 in the untruncated version of I-TevI) and/or Cys39 (which is Cys40 in the untruncated version of I-TevI) modification, a linker, in particular SEQ ID NOS: 7-12 or fragments thereof and/or containing one or more of the following mutations Thr95 (as referenced to the full-length I-TevI), Val117, Lys135, Gln158 or Asn140, and a modified RNA-guided nuclease Staphylococcus aureus Cas9 that may be the wild-type or a modified version, preferably containing a Glu10 or an Ala557 mutation thereof wherein said I-TevI polypeptide comprises the entire amino acid sequence of SEQ ID NO: 6 or a fragment thereof, and guide RNA, in particular, SEQ ID NOS: 15, 16 or 21 or fragments thereof, that targets the Cas9 domain and a pharmaceutically-acceptable formulation comprising the chimeric nuclease, cationic and/or neutral lipid nanoparticles, optionally DNA-binding compounds, in particular GL67 (N4-cholesteryl-spermine) and a pharmaceutically acceptable carrier thereof.”, (see column 4, lines 16-35).
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Wherein SEQ ID NO: 6 of 658 is 100% identical to instant SEQ ID NO: 8.
Wherein SEQ ID NO: 7 of 658 contains the linker domain and the V117 substitution to F. See alignment below.
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Wherein SEQ ID NO: 13 of 658 represents the saCas9 and is identical to instant SEQ ID NO: 15, see alignment below.
Regarding claim 115, 658 discloses, “Modifications of the Cas9 Domain: Other versions of the Cas9 domain might contain the following: a). . . . d). A version of the previously described spCas9 EQR mutant comprising the mutations D1135E, R1335Q and T1337R combined with the D10E mutation (SEQ ID NO: 19); . . .”, (see column 19, lines 31-43).
Regarding claim 117, 658 discloses, “Another embodiment of the invention is directed to methods to delete defined lengths of a DNA molecule or to replace select sequences from a DNA molecule by delivering a chimeric nuclease in vivo to a whole organism or to isolated cells in culture ex vivo wherein said cells are mammalian cells . . .”, (see column 4, lines 43-48).
Regarding claim 118, 658 discloses, “In eukaryotic organisms, the nuclease (TevCas9) 25 is targeted to the nucleus 23 of the cell 20 through one or more nuclear-localization sequences (“NLS”). As depicted in FIG. 2E, through its nuclear localization sequence, TevCas9 25 can enter the nucleus 23 and when in the nucleus 23, the TevCas9 nuclease 25 binds to and cleaves 26 the target genomic DNA 24 sequence.”, (see Example 1, column 24, lines 50-55).
Regarding claim 119, 658 discloses, “. . . V. Circular double-strand DNA comprising an I-TevI target site and Cas9 target site where the product cleaved from the double-strand DNA contains complimentary ends to those cleaved by TevCas9.”, (column 18, lines 54-56).
Regarding claim 120, 658 discloses, “FIG. 4B are cells transfected with a plasmid DNA version of TevCas9 fused to a cleavable GFP tag imaged using phase contrast and GFP imaging on a Cytation5 (Biotek Instruments Inc, VT, USA) after 48 hours treatment. Genomic DNA is extracted from harvested cells and editing at the CFTR gene is detected by PCR amplification and a T7 Endonuclease I cleavage assay.”, (column 3, lines 50-55).
Regarding claim 123, 658 discloses, “Another embodiment of the invention is directed to methods to edit genes by administering a chimeric nuclease to a cell or organism without the use of a viral vector by using a controlled dose in vivo.”, (column 4, lines 39-42).
Accordingly, claim(s) 106-107, 110, 111, and 113-123 are rejected as being anticipated by 658.
Claim(s) 106-107, 110, 111, and 113-123 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by 467 (US 12,297,467 B2; published 05/13/2025; effective filing date of 5/3/2019; IDS filed 12/29/2025 as #6).
Regarding claim(s) 106, 107, 110, 111, 113, 114, 116, 121, and 122, 467 discloses, “The instant invention is directed to a chimeric nuclease comprising a modified I-TevI nuclease domain, preferably deleting Met1 and having Lys26 (which is Lys27 in the untruncated version of I-TevI) and/or Cys39 (which is Cys40 in the untruncated version of I-TevI) modification, a linker, in particular SEQ ID NOS: 7-12 or fragments thereof and/or containing one or more of the following mutations Thr95 (as referenced to the full-length I-TevI), Val117, Lys135, Gln158 or Asn140, and a modified RNA-guided nuclease Staphylococcus aureus Cas9 that may be the wild-type or a modified version, preferably containing a Glu10 or an Ala557 mutation thereof wherein said I-TevI polypeptide comprises the entire amino acid sequence of SEQ ID NO: 6 or a fragment thereof, and guide RNA, in particular, SEQ ID NOS: 15, 16 or 21 or fragments thereof, that targets the Cas9 domain and a pharmaceutically-acceptable formulation comprising the chimeric nuclease, cationic and/or neutral lipid nanoparticles, optionally DNA-binding compounds, in particular GL67 (N4-cholesteryl-spermine) and a pharmaceutically acceptable carrier thereof.”, (see column 4, lines 16-35).
Wherein SEQ ID NO: 6 of 467 is 100% identical to instant SEQ ID NO: 8.
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Wherein SEQ ID NO: 7 of 467 contains the linker domain and the V117 substitution to F. See alignment below.
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Wherein SEQ ID NO: 13 of 467 represents the saCas9 and is identical to instant SEQ ID NO: 15, see alignment below.
Regarding claim 115, 467 discloses, “Modifications of the Cas9 Domain: Other versions of the Cas9 domain might contain the following: a). . . . d). A version of the previously described spCas9 EQR mutant comprising the mutations D1135E, R1335Q and T1337R combined with the D10E mutation (SEQ ID NO: 19); . . .”, (see column 19, lines 31-43).
Regarding claim 117, 467 discloses, “Another embodiment of the invention is directed to methods to delete defined lengths of a DNA molecule or to replace select sequences from a DNA molecule by delivering a chimeric nuclease in vivo to a whole organism or to isolated cells in culture ex vivo wherein said cells are mammalian cells . . .”, (see column 4, lines 43-48).
Regarding claim 118, 467 discloses, “In eukaryotic organisms, the nuclease (TevCas9) 25 is targeted to the nucleus 23 of the cell 20 through one or more nuclear-localization sequences (“NLS”). As depicted in FIG. 2E, through its nuclear localization sequence, TevCas9 25 can enter the nucleus 23 and when in the nucleus 23, the TevCas9 nuclease 25 binds to and cleaves 26 the target genomic DNA 24 sequence.”, (see Example 1, column 24, lines 50-55).
Regarding claim 119, 467 discloses, “. . . V. Circular double-strand DNA comprising an I-TevI target site and Cas9 target site where the product cleaved from the double-strand DNA contains complimentary ends to those cleaved by TevCas9.”, (column 18, lines 54-56).
Regarding claim 120, 467 discloses, “FIG. 4B are cells transfected with a plasmid DNA version of TevCas9 fused to a cleavable GFP tag imaged using phase contrast and GFP imaging on a Cytation5 (Biotek Instruments Inc, VT, USA) after 48 hours treatment. Genomic DNA is extracted from harvested cells and editing at the CFTR gene is detected by PCR amplification and a T7 Endonuclease I cleavage assay.”, (column 3, lines 50-55).
Regarding claim 123, 467 discloses, “Methods to edit genes by administering a chimeric nuclease to a cell or organism without the use of a viral vector.”, (abstract).
Accordingly, claim(s) 106-107, 110, 111, and 113-123 are rejected as being anticipated by 467.
Claim(s) 106-107, 110, 111, and 113-123 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by 615 (US 12,312,615 B2; published 05/27/2025; effective filing date of 5/3/2019; IDS filed 12/29/2025 as #7).
Regarding claim(s) 106, 107, 110, 111, 113, 114, 116, 121, and 122, 615 discloses, “The instant invention is directed to a chimeric nuclease comprising a modified I-TevI nuclease domain, preferably deleting Met1 and having Lys26 (which is Lys27 in the untruncated version of I-TevI) and/or Cys39 (which is Cys40 in the untruncated version of I-TevI) modification, a linker, in particular SEQ ID NOS: 7-12 or fragments thereof and/or containing one or more of the following mutations Thr95 (as referenced to the full-length I-TevI), Val117, Lys135, Gln158 or Asn140, and a modified RNA-guided nuclease Staphylococcus aureus Cas9 that may be the wild-type or a modified version, preferably containing a Glu10 or an Ala557 mutation thereof wherein said I-TevI polypeptide comprises the entire amino acid sequence of SEQ ID NO: 6 or a fragment thereof, and guide RNA, in particular, SEQ ID NOS: 15, 16 or 21 or fragments thereof, that targets the Cas9 domain and a pharmaceutically-acceptable formulation comprising the chimeric nuclease, cationic and/or neutral lipid nanoparticles, optionally DNA-binding compounds, in particular GL67 (N4-cholesteryl-spermine) and a pharmaceutically acceptable carrier thereof.”, (see column 4, lines 16-35).
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Wherein SEQ ID NO: 6 of 615 is 100% identical to instant SEQ ID NO: 8.
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Wherein SEQ ID NO: 7 of 615 contains the linker domain and the V117 substitution to F. See alignment below.
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Wherein, SEQ ID NO: 13 of 615 represents the saCas9 and is identical to instant SEQ ID NO: 15, see alignment below.
Regarding claim 115, 615 discloses, “Modifications of the Cas9 Domain: Other versions of the Cas9 domain might contain the following: a). . . . d). A version of the previously described spCas9 EQR mutant comprising the mutations D1135E, R1335Q and T1337R combined with the D10E mutation (SEQ ID NO: 19); . . .”, (see column 19, lines 45-56).
Regarding claim 117, 615 discloses, “Another embodiment of the invention is directed to methods to delete defined lengths of a DNA molecule or to replace select sequences from a DNA molecule by delivering a chimeric nuclease in vivo to a whole organism or to isolated cells in culture ex vivo wherein said cells are mammalian cells . . .”, (see column 4, lines 43-48).
Regarding claim 118, 615 discloses, “In eukaryotic organisms, the nuclease (TevCas9) 25 is targeted to the nucleus 23 of the cell 20 through one or more nuclear-localization sequences (“NLS”). As depicted in FIG. 2E, through its nuclear localization sequence, TevCas9 25 can enter the nucleus 23 and when in the nucleus 23, the TevCas9 nuclease 25 binds to and cleaves 26 the target genomic DNA 24 sequence.”, (see Example 1, column 25, lines 1-5).
Regarding claim 119, 615 discloses, “. . . V. Circular double-strand DNA comprising an I-TevI target site and Cas9 target site where the product cleaved from the double-strand DNA contains complimentary ends to those cleaved by TevCas9.”, (column 18, lines 66-67 to column 19, 1-2).
Regarding claim 120, 615 discloses, “FIG. 4B are cells transfected with a plasmid DNA version of TevCas9 fused to a cleavable GFP tag imaged using phase contrast and GFP imaging on a Cytation5 (Biotek Instruments Inc, VT, USA) after 48 hours treatment. Genomic DNA is extracted from harvested cells and editing at the CFTR gene is detected by PCR amplification and a T7 Endonuclease I cleavage assay.”, (column 3, lines 50-55).
Regarding claim 123, 615 discloses, “. . . methods to edit genes by administering a chimeric nuclease to a cell or organism without the use of a viral vector.”, (abstract).
Accordingly, claim(s) 106-107, 110, 111, and 113-123 are rejected as being anticipated by 615.
Claim(s) 106-107, 110-111, and 113-123 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by 192 (US 12,460,192 B2; published 11/04/2025; effective filing date of 5/3/2019).
Regarding claim(s) 106, 107, 110, 111, 113, 114, 116, 121, and 122, 192 discloses, “The instant invention is directed to a chimeric nuclease comprising a modified I-TevI nuclease domain, preferably deleting Met1 and having Lys26 (which is Lys27 in the untruncated version of I-TevI) and/or Cys39 (which is Cys40 in the untruncated version of I-TevI) modification, a linker, in particular SEQ ID NOS: 7-12 or fragments thereof and/or containing one or more of the following mutations Thr95 (as referenced to the full-length I-TevI), Val117, Lys135, Gln158 or Asn140, and a modified RNA-guided nuclease Staphylococcus aureus Cas9 that may be the wild-type or a modified version, preferably containing a Glu10 or an Ala557 mutation thereof wherein said I-TevI polypeptide comprises the entire amino acid sequence of SEQ ID NO: 6 or a fragment thereof, and guide RNA, in particular, SEQ ID NOS: 15, 16 or 21 or fragments thereof, that targets the Cas9 domain and a pharmaceutically-acceptable formulation comprising the chimeric nuclease, cationic and/or neutral lipid nanoparticles, optionally DNA-binding compounds, in particular GL67 (N4-cholesteryl-spermine) and a pharmaceutically acceptable carrier thereof.”, (see column 4, lines 16-35).
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Wherein SEQ ID NO: 6 of 192 is 100% identical to instant SEQ ID NO: 8.
Wherein SEQ ID NO: 7 of 192 contains the linker domain and the V117 substitution to F. See alignment below.
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Wherein, SEQ ID NO: 13 of 192 represents the saCas9 and is identical to instant SEQ ID NO: 15, see alignment below.
Regarding claim 115, 192 discloses, “Modifications of the Cas9 Domain: Other versions of the Cas9 domain might contain the following: a). . . . d). A version of the previously described spCas9 EQR mutant comprising the mutations D1135E, R1335Q and T1337R combined with the D10E mutation (SEQ ID NO: 19); . . .”, (see column 19, lines 31-43).
Regarding claim 117, 192 discloses, “Another embodiment of the invention is directed to methods to delete defined lengths of a DNA molecule or to replace select sequences from a DNA molecule by delivering a chimeric nuclease in vivo to a whole organism or to isolated cells in culture ex vivo wherein said cells are mammalian cells . . .”, (see column 4, lines 43-48).
Regarding claim 118, 192 discloses, “In eukaryotic organisms, the nuclease (TevCas9) 25 is targeted to the nucleus 23 of the cell 20 through one or more nuclear-localization sequences (“NLS”). As depicted in FIG. 2E, through its nuclear localization sequence, TevCas9 25 can enter the nucleus 23 and when in the nucleus 23, the TevCas9 nuclease 25 binds to and cleaves 26 the target genomic DNA 24 sequence.”, (see Example 1, column 24, lines 49-54).
Regarding claim 119, 192 discloses, “. . . V. Circular double-strand DNA comprising an I-TevI target site and Cas9 target site where the product cleaved from the double-strand DNA contains complimentary ends to those cleaved by TevCas9.”, (column 18, lines 53-56 ).
Regarding claim 120, 192 discloses, “FIG. 4B are cells transfected with a plasmid DNA version of TevCas9 fused to a cleavable GFP tag imaged using phase contrast and GFP imaging on a Cytation5 (Biotek Instruments Inc, VT, USA) after 48 hours treatment. Genomic DNA is extracted from harvested cells and editing at the CFTR gene is detected by PCR amplification and a T7 Endonuclease I cleavage assay.”, (column 3, lines 50-55).
Regarding claim 123, 192 discloses, “. . . the instant invention is directed to a method of treating a lung-related disease in a patient in need thereof by administering a novel chimeric nuclease that modifies the DNA of lung epithelial cells wherein the chimeric nuclease replaces the CFTR delta F508 mutation from the CFTR gene in an effort to treat cystic fibrosis or cleaves an EGFR exon 19 deletion in an effort to treat non-small cell lung cancer.”, (column 4, lines 66-67 to column 4, lines 1-6).
Accordingly, claim(s) 106-107, 110-111, and 113-123 are rejected as being anticipated by 192.
Claim(s) 106-107, 110-111, and 113-123 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by 238 (US 2025/027238 A1; published 09/25/2025; effective filing date of 5/3/2019; IDS filed 12/29/2025 as PG pub #6).
Regarding claim(s) 106, 107, 110, 111, 113, 114, 116, 121, and 122, 238 discloses, “The instant invention is directed to a chimeric nuclease comprising a modified I-TevI nuclease domain, preferably deleting Met1 and having Lys26 (which is Lys27 in the untruncated version of I-TevI) and/or Cys39 (which is Cys40 in the untruncated version of I-TevI) modification, a linker, in particular SEQ ID NOS: 7-12 or fragments thereof and/or containing one or more of the following mutations Thr95 (as referenced to the full-length I-TevI), Val117, Lys135, Gln158 or Asn140, and a modified RNA-guided nuclease Staphylococcus aureus Cas9 that may be the wild-type or a modified version, preferably containing a Glu10 or an Ala557 mutation thereof wherein said I-TevI polypeptide comprises the entire amino acid sequence of SEQ ID NO: 6 or a fragment thereof, and guide RNA, in particular, SEQ ID NOS: 15, 16 or 21 or fragments thereof, that targets the Cas9 domain and a pharmaceutically-acceptable formulation comprising the chimeric nuclease, cationic and/or neutral lipid nanoparticles, optionally DNA-binding compounds, in particular GL67 (N4-cholesteryl-spermine) and a pharmaceutically acceptable carrier thereof.”, ([0018]).
Wherein, SEQ ID NO: 6 of 238 is 100% identical to instant SEQ ID NO: 8.
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Wherein SEQ ID NO: 7 of 238 contains the linker domain and the V117 substitution to F. See alignment below.
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Wherein SEQ ID NO: 13 of 238 represents the saCas9 and is identical to instant SEQ ID NO: 15, see alignment below.
Regarding claim 115, 238 discloses, “Modifications of the Cas9 Domain: Other versions of the Cas9 domain might contain the following: a). . . . d). A version of the previously described spCas9 EQR mutant comprising the mutations D1135E, R1335Q and T1337R combined with the D10E mutation (SEQ ID NO: 19); . . .”, ([0120]).
Regarding claim 117, 238 discloses, “Another embodiment of the invention is directed to methods to delete defined lengths of a DNA molecule or to replace select sequences from a DNA molecule by delivering a chimeric nuclease in vivo to a whole organism or to isolated cells in culture ex vivo wherein said cells are mammalian cells . . .”, ([0021]).
Regarding claim 238, discloses, “In eukaryotic organisms, the nuclease (TevCas9) 25 is targeted to the nucleus 23 of the cell 20 through one or more nuclear-localization sequences (“NLS”). As depicted in FIG. 2E, through its nuclear localization sequence, TevCas9 25 can enter the nucleus 23 and when in the nucleus 23, the TevCas9 nuclease 25 binds to and cleaves 26 the target genomic DNA 24 sequence.”, (see Example 1, [0147]).
Regarding claim 119, 238 discloses, “. . . V. Circular double-strand DNA comprising an I-TevI target site and Cas9 target site where the product cleaved from the double-strand DNA contains complimentary ends to those cleaved by TevCas9.”, ([0109]).
Regarding claim 120, 238 discloses, “FIG. 4B are cells transfected with a plasmid DNA version of TevCas9 fused to a cleavable GFP tag imaged using phase contrast and GFP imaging on a Cytation5 (Biotek Instruments Inc, VT, USA) after 48 hours treatment. Genomic DNA is extracted from harvested cells and editing at the CFTR gene is detected by PCR amplification and a T7 Endonuclease I cleavage assay.”, ([0014]).
Regarding claim 123, 238 discloses, “. . . the instant invention is directed to a method of treating a lung-related disease in a patient in need thereof by administering a novel chimeric nuclease that modifies the DNA of lung epithelial cells wherein the chimeric nuclease replaces the CFTR delta F508 mutation from the CFTR gene in an effort to treat cystic fibrosis or cleaves an EGFR exon 19 deletion in an effort to treat non-small cell lung cancer.”, ([0025]).
Accordingly, claim(s) 106-107, 110-111, and 113-123 are rejected as being anticipated by 238.
Claim(s) 106-107, 110-111, and 113-123 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by 248 (US 2026/0098248 A1; published 04/09/2026; effective filing date of 5/3/2019).
Regarding claim(s) 106, 107, 110, 111, 113, 114, 116, 121, and 122, 248 discloses, “The instant invention is directed to a chimeric nuclease comprising a modified I-TevI nuclease domain, preferably deleting Met1 and having Lys26 (which is Lys27 in the untruncated version of I-TevI) and/or Cys39 (which is Cys40 in the untruncated version of I-TevI) modification, a linker, in particular SEQ ID NOS: 7-12 or fragments thereof and/or containing one or more of the following mutations Thr95 (as referenced to the full-length I-TevI), Val117, Lys135, Gln158 or Asn140, and a modified RNA-guided nuclease Staphylococcus aureus Cas9 that may be the wild-type or a modified version, preferably containing a Glu10 or an Ala557 mutation thereof wherein said I-TevI polypeptide comprises the entire amino acid sequence of SEQ ID NO: 6 or a fragment thereof, and guide RNA, in particular, SEQ ID NOS: 15, 16 or 21 or fragments thereof, that targets the Cas9 domain and a pharmaceutically-acceptable formulation comprising the chimeric nuclease, cationic and/or neutral lipid nanoparticles, optionally DNA-binding compounds, in particular GL67 (N4-cholesteryl-spermine) and a pharmaceutically acceptable carrier thereof.”, ([0018]).
Wherein SEQ ID NO: 6 of 248 is 100% identical to instant SEQ ID NO: 8.
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Wherein SEQ ID NO: 7 of 248 contains the linker domain and the V117 substitution to F. See alignment below.
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Wherein, SEQ ID NO: 13 of 248 represents the saCas9 and is identical to instant SEQ ID NO: 15, see alignment below.
Regarding claim 115, 248 discloses, “Modifications of the Cas9 Domain: Other versions of the Cas9 domain might contain the following: a). . . . d). A version of the previously described spCas9 EQR mutant comprising the mutations D1135E, R1335Q and T1337R combined with the D10E mutation (SEQ ID NO: 19); . . .”, ([0162]).
Regarding claim 117, 248 discloses, “Another embodiment of the invention is directed to methods to delete defined lengths of a DNA molecule or to replace select sequences from a DNA molecule by delivering a chimeric nuclease in vivo to a whole organism or to isolated cells in culture ex vivo wherein said cells are mammalian cells . . .”, ([0021]).
Regarding claim 248, discloses, “In eukaryotic organisms, the nuclease (TevCas9) 25 is targeted to the nucleus 23 of the cell 20 through one or more nuclear-localization sequences (“NLS”). As depicted in FIG. 2E, through its nuclear localization sequence, TevCas9 25 can enter the nucleus 23 and when in the nucleus 23, the TevCas9 nuclease 25 binds to and cleaves 26 the target genomic DNA 24 sequence.”, (see Example 1, [0191]).
Regarding claim 119, 248 discloses, “. . . V. Circular double-strand DNA comprising an I-TevI target site and Cas9 target site where the product cleaved from the double-strand DNA contains complimentary ends to those cleaved by TevCas9.”, ([0151]).
Regarding claim 120, 248 discloses, “FIG. 4B are cells transfected with a plasmid DNA version of TevCas9 fused to a cleavable GFP tag imaged using phase contrast and GFP imaging on a Cytation5 (Biotek Instruments Inc, VT, USA) after 48 hours treatment. Genomic DNA is extracted from harvested cells and editing at the CFTR gene is detected by PCR amplification and a T7 Endonuclease I cleavage assay.”, ([0014]).
Regarding claim 123, 248 discloses, “. . . the instant invention is directed to a method of treating a lung-related disease in a patient in need thereof by administering a novel chimeric nuclease that modifies the DNA of lung epithelial cells wherein the chimeric nuclease replaces the CFTR delta F508 mutation from the CFTR gene in an effort to treat cystic fibrosis or cleaves an EGFR exon 19 deletion in an effort to treat non-small cell lung cancer.”, ([0025]).
Accordingly, claim(s) 106-107, 110-111, and 113-123 are rejected as being anticipated by 248.
Claim(s) 106-123 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by 427 (US 2024/0360427 A1; published 10/31/2024; effective filing date of 03/26/2021; IDS filed 12/29/2025 PG Pub #5).
Regarding claim(s) 106-116, 118, 121 and 122, 427 discloses, “In an aspect, the present disclosure provides a composition comprising: a chimeric nuclease, wherein the chimeric nuclease comprises an I-TEVI nuclease domain, an RNA-guided nuclease Cas domain, and a guide RNA, wherein the guide RNA comprises a nucleic acid sequence that targets an oncogenic mutation that is not a deletion in exon 19 of EGFR.”, ([0005]).
More specifically, 427 discloses, “. . .In some embodiments, the composition further comprises a linker that is operably linked to the I-TEVI nuclease domain and the RNA-guided nuclease Cas domain. In some embodiments, the linker comprises an amino acid sequence as set forth in SEQ ID NO: 701, 702, 703, or 704. In some embodiments, the linker comprises a mutation corresponding to any one of positions T95, 5101, A119, K120, K135, P126, D127, N140, T147, Q158, A161, V117, 5165, or a combination thereof. In some embodiments, the linker comprises a mutation selected from a mutation corresponding to any one of T95S, S101Y, A119D, K120N, K135N, K135R, P126S, D127K, N140S, T1471, Q158R, A161V, V117F, S165G, or a combination thereof. . . . In some embodiments, the RNA-guided nuclease Cas domain is a RNA-guided nuclease Cas9 domain. In some embodiments, the RNA-guided nuclease Cas9 domain is any one of an RNA-guided nuclease Staphylococcus aureus Cas9 domain, an RNA-guided nuclease Streptococcus pyogenes Cas9 domain,. . . In some embodiments, the RNA-guided nuclease Staphylococcus aureus Cas9 domain comprises an amino acid sequence as set forth in SEQ ID NO: 710. In some embodiments, the RNA-guided nuclease Staphylococcus aureus Cas9 domain comprises a mutation corresponding to any one of positions D10, H557, N580, H840, . . . In some embodiments, the RNA-guided nuclease Staphylococcus aureus Cas9 domain comprises a mutation selected from a mutation corresponding to any one of D10A, D10E, H557A, N580A, H840A, . . . In some embodiments, the RNA-guided nuclease Streptococcus pyogenes Cas9 domain comprises an amino acid sequence as set forth in SEQ ID NO: 711. In some embodiments, the RNA-guided nuclease Streptococcus pyogenes Cas9 domain comprises a mutation corresponding to any one of positions D10, S29, F32, D39, R40, . . . In some embodiments, the RNA-guided nuclease Streptococcus pyogenes Cas9 domain comprises a mutation selected from a mutation corresponding to any one of D10E, D10A, S29T, F32M, D39N, R40K, . . . In some embodiments, the I-TEVI nuclease domain comprises a mutation at any one of positions corresponding to T11, V16, N14, E25, K26, R27, E36, K37, G38, C39, S41, L45, F49, I60, and E81, or a combination thereof. In some embodiments, the I-TEVI nuclease domain comprises a mutation selected from any one of corresponding to T11V, V161, N14G, E25D, K26R, R27A, E36S, K37N, G38N, C39V, S41H, L45F, F49Y, 160V, E811, or a combination thereof. In some embodiments, the I-TEVI nuclease domain comprises a mutation corresponding to a K26R mutation. In some embodiments, the I-TEVI nuclease domain comprises an amino acid sequence as set forth in SEQ ID NO: 700. . . . In some embodiments, the chimeric nuclease further comprises a nuclear localization signal. . . In some embodiments, the composition further comprises a pharmaceutically acceptable excipient, diluent or carrier. In some embodiments, the composition is encapsulated in a lipid nanoparticle. . .”, (see [0006]).
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Wherein SEQ ID NO: 701 of 427 is 100% identical to amino acids 93-169 of instant SEQ ID NO: 53 (regarding claim 109), see alignment below.
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Wherein SEQ ID NO: 710 of 427 is 100% identical to instant SEQ ID NO: 15 (regarding claim 113), see alignment below.
Wherein SEQ ID NO: 700 of 427 is 100% identical to instant SEQ ID NO: 8.
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Regarding claim 119, 427 discloses, “In certain embodiments, the donor DNA comprises circular double-strand DNA comprising an I-TevI target site and Cas target site where the product cleaved from the double-strand DNA contains complimentary ends to those cleaved by the chimeric nuclease.”, (see [0174]).
Regarding claim(s) 117, 120 and 123, 427 discloses, “The present disclosure describes methods of using the described nucleases to genetically engineer a cell population in order to target, contact, edit, silence, disrupt, restore, insert, modify, delete, or replace a nucleotides sequence at a genomic location. The disclosure describes forming a chimeric nuclease guide RNA complexes and administering the chimeric nuclease guide RNA complexes to cells. Alternatively, a nucleic acid or plurality of nucleic acids encoding the guide RNA and/or the chimeric nuclease can be transferred into the cell using a method selected from electroporation, . . .”, (see [0099]). Wherein cell is defined as, “As used herein, a “cell” can generally refer to a biological cell. . . Some non-limiting examples include: a prokaryotic cell, eukaryotic cell, a bacterial cell, an archaeal cell, a cell of a single-cell eukaryotic organism, a protozoa cell, a cell from a plant, an animal cell, a cell from an invertebrate animal (e.g. fruit fly, cnidarian, echinoderm, nematode, etc.), a cell from a vertebrate animal (e.g., fish, amphibian, reptile, bird, mammal), a cell from a mammal (e.g., a pig, a cow, a goat, a sheep, a rodent, a rat, a mouse, a non-human primate, a human, etc.), et cetera. Sometimes a cell may not originate from a natural organism (e.g., a cell can be synthetically made, sometimes termed an artificial cell). In certain embodiments cells refers to human cells.”, (see [0077]).
Accordingly, claim(s) 106-123 are rejected as being anticipated by 427.
The applied reference(s) (i.e., WO 2020/225719 A1, 11,814658 B2; 12,297,467 B2; 12,312,615 B2; 12,460,192 B2; US20240360427A1; US20250297238A1; and US20260098248A1) have a common inventor, inventors, and applicant, with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 107, 108, and 112 are rejected under 35 U.S.C. 103 as being unpatentable over Wolfs et al (Biasing genome-editing events toward precise length deletions with an RNA-guided TevCas9 dual nuclease, PNAS, volume 113, issue 52, pages 14988 to 14993, published December 12th, 2016; IDS filed 01/07/2025 NPL #8) as applied to claims 106, 109-111, 116, 117, 119-120, and 123 above, and further in view of Roy et al (Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preferences, Nucleic Acids Research, Vol 44, Issue 15, Pages 7350-7359, Published July 7th, 2016; IDS 01/07/2025 NPL #7).
Wolfs et al does not teach one or more modifications corresponding to K26 of the I-TevI nuclease domain, one or more amino acid substitutions selected from the group consisting of T11V, V16I, N14G, E25D, K26R, E36S, K37N, G38N, C39V, S41H, L45F, F49Y, I60V, and E81I, and a chimeric nuclease with both the I-TevI nuclease domain and I-TevI linker containing modifications.
Regarding claim(s) 107, 108, and 112, Roy et al teaches K26R, Q158R, and T95S substitutions which encompass modifications on both the nuclease domain and the linker domain (see page 7354, column 1, paragraph 1).
Roy et al teaches “The krel data support the conclusion that the combination of the K26R/T95S/Q158R substitutions broaden the cleavage range of the I-TevI nuclease domain.”, (see page 7355, column 1, paragraph 2).
Therefore, it would have been obvious to one of skill in the art before the effective filing date of the claimed invention to substitute K26, T95, and Q158 of the I-TevI domain, as taught by Wolfs et al, with argining at position 26, serine at position 95, and arginine at position 158 of the I-TevI nuclease domain as taught by Roy et al. One of skill in the art could have substituted the known elements (i.e., K26R, T95S, and Q158R of the I-TevI nuclease domain and linker domain, as taught by Roy et al) for their original sequence, as taught by Wolfs et al to yield the predictable result of broadening the cleavage range of the I-TevI nuclease domain (with the combination of the linker domain) as taught by Roy et al.
Accordingly, claim(s) 107, 108, and 112 are rejected as being unpatentable over Wolfs et al in view of Roy et al.
Claim(s) 113-115, 118, and 121-122 are rejected under 35 U.S.C. 103 as being unpatentable over Wolfs et al (Biasing genome-editing events toward precise length deletions with an RNA-guided TevCas9 dual nuclease, PNAS, volume 113, issue 52, pages 14988 to 14993, published December 12th, 2016; IDS filed 01/07/2025 NPL #8) as applied to claims 106, 109-111, 116, 117, 119-120, and 123 above, and further in view of Ran et al (In vivo genome editing using Staphylococcus aureus Cas9, Nature, Volume 520, pages 186-191, Published April 1st, 2015) as evidenced by Addgene saCas9 (Addgene pX601 sequencing result, pages 1-20; Accessed May 30, 2026) and Addgene dead saCas9 (Addgene pX603 sequencing result, pages 1-18; Accessed May 30, 2026).
Wolfs et al does not teach a Cas9 domain comprising at least 90-100% sequence identity to SEQ ID NO: 15 (i.e., Staphylococcus aureus cas9), that the saCas9 has inactivating mutations (e.g., D10E, H557A, etc.), a dspCas9 (e.g., D10A, H840A) that the chimeric nuclease contains an NLS, a pharmaceutically acceptable composition, or the chimeric nuclease encapsulated in a lipid nanoparticle.
Regarding claim(s) 113, 114, and 118, Ran et al teaches “[T]he size of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for basic research and therapeutic applications that use the highly versatile adeno-associated virus (AAV) delivery vehicle. Here, we characterize six smaller Cas9 orthologues and show that Cas9 from Staphylococcusaureus (SaCas9) can edit the genome with efficiencies similar to those of SpCas9, while being more than 1 kilo base shorter.”, (see abstract).
saCas9 and catalytically inactive saCas9 (D10A and N580A), each with an NLS, were deposited to Addgene as disclosed by Ran et al, “All reagents described in this manuscript have been deposited with Addgene (plasmid IDs 61591, 61592 and 61593).”, (see page 191, under author information).
These sequences are evidenced by Addgene saCas9 (page 1-20) and Addgene dead saCas9 (page 1-18).
Regarding claim 115, Ran et al discloses “To fully characterize the Sa Cas9 PAM and the seed region within its guide sequence, we performed chromatin immunoprecipitation (ChIP) using catalytically mutant forms of SaCas9 (dSaCas9, D10A and N580A mutations, based on homology to SpCas9) or SpCas9 (dSpCas9, D10A and H840A mutations) and their corresponding sgRNAs. We targeted two loci in the human EMX1 gene with composite NGGRRT PAMs, which allow targeting by both dCas9s.”, (see page 187, column 2, paragraph 2).
Regarding claim(s) 121-122, Ran et al discloses transfection of 293T cells with Lipofectamine 2000 (Life technologies) (see page 192, paragraph 2 under Cell culture and transfection).
Therefore, it would have been obvious to one of skill in the art before the effective filing date of the claimed invention to substitute the D10 and H840 spCas9 of Wolfs et al with alanine at position 10 and 840 as taught by Ran et al. One of skill in the art could have substituted the known elements (i.e., D10A and H840A of the spCas9 as taught Ran et al) for their original sequence, as taught by Wolfs et al to yield the predictable result of targeting a genomic loci without cleaving said loci, as taught by Ran et al. It also would have been obvious to one of ordinary skill in the art before the effect filing date to substitute the spCas9 of Wolfs et al with the saCas9 of Ran et al. One of skill in the art could have substituted the known element (i.e., an saCas9) for the original spCas9 of Wolfs et al to yield the predictable result of using a Cas9 with efficiencies similar to those of SpCas9, while being more than 1 kilo base shorter. Lastly, it would have been obvious to one of ordinary skill in the art before the effective filing date to substitute the spCas9 of Wolfs et al with a dsaCas9 (i.e., D10A and N580A) as taught by Ran et al. One of skill in the art could have substituted the known element (i.e., a dsaCas9 of Ran et al) for the original spCas9 of Wolfs et al to yield the predictable result of using a Cas9 with efficiencies similar to those of SpCas9, while being more than 1 kilo base shorter, and being able to target a genomic loci without cleaving said loci, as taught by Ran et al.
Accordingly, claim(s) 113-115, 118, and 121-122 are unpatentable over Wolfs et al in view of Ran et al as evidenced by Addgene saCas9 and Addgene dead saCas9.
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.
Claim(s) 106, 113-114, and 116 rejected on the ground of nonstatutory double patenting as being unpatentable over claim 4 and 12 of U.S. Patent No. 11814658 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because claim 4 of 658 recites, “The nuclease domain of “A nuclease comprising a modified Staphylococcus aureus Cas9 comprising the sequence of SEQ ID NO: 14.”, wherein the I-TevI nuclease domain comprises the amino acid sequence set forth in SEQ ID NO: 6.”. Claim 12 of 658 recites, “The chimeric nuclease of “A chimeric nuclease comprising an I-TevI nuclease domain, a linker, a Staphylococcus aureus Cas9, and a guide RNA, wherein the Staphylococcus aureus Cas9 comprises the sequence of SEQ ID NO: 14”, wherein the I-TevI nuclease domain comprises the amino acid sequence set forth in SEQ ID NO: 6.”
SEQ ID NO: 6 is identical to instant SEQ ID NO: 8.
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SEQ ID NO: 14 is 99.9% identical to SEQ ID NO: 15 and contains a D10E substitution (see alignment below).
Claim(s) 106, 113, and 116 rejected on the ground of nonstatutory double patenting as being unpatentable over claim 4 and 12 of U.S. Patent No. 12297467 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because 467 claim recites, “The nuclease of “A nuclease comprising a modified Staphylococcus aureus Cas9, wherein said modified Staphylococcus aureus Cas9 comprises an aspartic acid to glutamic acid substitution at an amino acid corresponding to position 10 of SEQ ID NO: 13, and wherein the amino acid sequence of the Staphylococcus aureus Cas9 has at least 99% sequence identity to SEQ ID NO: 13”, further comprising an I-Tevl nuclease domain”, wherein the I-Tevl nuclease domain comprises the amino acid sequence set forth in SEQ ID NO: 6.” Claim 12 of 467 recites, “The chimeric nuclease of “A chimeric nuclease comprising an I-Tevl nuclease domain, a linker, a Staphylococcus aureus Cas9, and a guide RNA, wherein the Staphylococcus aureus Cas9 comprises an aspartic acid to glutamic acid substitution at an amino acid corresponding to position 10 of SEQ ID NO: 13, and wherein the amino acid sequence of the Staphylococcus aureus Cas9 has at least 99% sequence identity to SEQ ID NO: 13”, wherein the I-Tevl nuclease domain comprises the amino acid sequence set forth in SEQ ID NO: 6.”.
Wherein SEQ ID NO: 6 of 467 is identical to instant SEQ ID NO: 8 (see alignment above in the 102(a)(2) rejection).
Wherein SEQ ID NO: 13 of 467 is 100% identical to instant SEQ ID NO: 15 (see alignment above in the 102(a)(2) rejection).
Claim(s) 106, 113, 114, 116, 117, and 123 rejected on the ground of nonstatutory double patenting as being unpatentable over claim 9 of U.S. Patent No. 12312615 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because claim 9 of 615, despite being a methods claim, require the composition that is present in the claim. Claim 9 of 615 recites, “The method of “A method to edit genomic DNA of a mammalian cell comprising the step of administering a chimeric nuclease, the chimeric nuclease comprising a modified Enterobacteria Phage T4 (I-TevI) nuclease domain, a linker, an RNA-guided nuclease Staphylococcus aureus Cas9 and a guide RNA to the cell, thereby editing the genomic DNA of the cell, wherein the RNA-guided nuclease Staphylococcus aureus Cas9 comprises the sequence of SEQ ID NO: 13 with an aspartic acid to glutamic acid substitution at an amino acid corresponding to position 10 of SEQ ID NO: 13, wherein the I-Tevl nuclease domain comprises the amino acid sequence set forth in SEQ ID NO: 6.”
Wherein SEQ ID NO: 13 is identical to instant SEQ ID NO: 15 (see 102(a)(2) rejection above). Wherein SEQ ID NO: 6 is identical to instant SEQ ID NO: 8 (see 102(a)(2) rejection above).
Claims 106, 113-114, 123 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 18 of U.S. Patent No. 12460192 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because claim 18 of 192, despite being a methods claim, require the composition that is present in the claim. Claim 18 recites, “The method of “The method of “A method for editing DNA of a cell, comprising: contacting the cell with a nuclease comprising a Cas9 sequence that is at least 99% identical to SEQ ID NO: 13 and comprises a glutamate at an amino acid corresponding to position 10 of SEQ ID NO: 13, wherein the nuclease edits the DNA of the cell”, wherein the nuclease is a chimeric nuclease that further comprises an I-TevI sequence coupled with the Cas9 sequence”, wherein the I-TevI sequence comprises the amino acid sequence of SEQ ID NO: 6, or a sequence thereof comprising 1, 2 or 3 mutations each selected from the group consisting of: an amino acid substitution, deletion, and insertion.”
Wherein SEQ ID NO: 13 is identical to instant SEQ ID NO: 15 (see 102(a)(2) rejection above). Wherein SEQ ID NO: 6 is identical to instant SEQ ID NO: 8 (see 102(a)(2) rejection above).
Claims 106, 113-114, 123 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 18 of copending Application No. 19/355,897(reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because claim 18 of 897, despite being a methods claim, require the composition that is present in the claim. Claim 18 recites, “The method of “The method of “A method for editing DNA of a cell, comprising: contacting the cell with a nuclease comprising a Cas9 sequence that is at least 99% identical to SEQ ID NO: 13 and comprises a glutamate at an amino acid corresponding to position 10 of SEQ ID NO: 13, wherein the nuclease edits the DNA of the cell”, wherein the nuclease is a chimeric nuclease that further comprises an I-TevI sequence coupled with the Cas9 sequence”, wherein the I-TevI sequence comprises the amino acid sequence of SEQ ID NO: 6, or a sequence thereof comprising 1, 2 or 3 mutations each selected from the group consisting of: an amino acid substitution, deletion, and insertion.”
Wherein SEQ ID NO: 13 is identical to instant SEQ ID NO: 15 (see 248 102(a)(2) rejection above). Wherein SEQ ID NO: 6 is identical to instant SEQ ID NO: 8 (see 248 102(a)(2) rejection above).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 106, 113-114, 123 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 18 of copending Application No. 19/184,659 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because claim 18 of 659, despite being a methods claim, require the chimeric nuclease that is present in the claim. Claim 18 recites, “The method of “The method of “A method for editing DNA of a cell, comprising: contacting the cell with a nuclease comprising a Cas9 sequence that is at least 99% identical to SEQ ID NO: 13 and comprises a glutamate at an amino acid corresponding to position 10 of SEQ ID NO: 13, wherein the nuclease edits the DNA of the cell”, wherein the nuclease is a chimeric nuclease that further comprises an I-TevI sequence coupled with the Cas9 sequence”, wherein the I-TevI sequence comprises the amino acid sequence of SEQ ID NO: 6, or a sequence thereof comprising 1, 2 or 3 mutations each selected from the group consisting of: an amino acid substitution, deletion, and insertion.”
Wherein SEQ ID NO: 13 is identical to instant SEQ ID NO: 15 (see 238 102(a)(2) rejection above). Wherein SEQ ID NO: 6 is identical to instant SEQ ID NO: 8 (see 238 102(a)(2) rejection above).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 106, 107, 110, and 116 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 159 of copending Application No. 18/473, 042 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other. Despite claim 159 reciting a “composition” the composition requires the chimeric nuclease. Claim 159 of 042 recites, “ The composition of “A composition, comprising: a chimeric nuclease, wherein the chimeric nuclease comprises:(a) an I-TEVI nuclease domain, wherein the I-TEVI nuclease domain comprises a mutation at any one of positions corresponding to T11, V16, N14, E25, K26, R27,E36, K37, G38, C39, S41, L45, F49, 160, and E81 of SEQ ID NO: 700, or a combination thereof; (b) an RNA-guided nuclease Cas domain; and (c) a guide RNA, wherein the guide RNA comprises a nucleic acid sequence that targets an oncogenic mutation, wherein the oncogenic mutation is (i) an insertion of one or more nucleotides;(ii) a substitution or deletion of 10 or less nucleotides; or (iii) a single nucleotide polymorphism” wherein the I-TEVI nuclease domain comprises an amino acid sequence that is at least 85%, 90%, 95%, 97%, 98%, or 99% identical to SEQ ID NO: 700.”
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Wherein SEQ ID NO: 700 is 100% identical to instant SEQ ID NO: 8 (see alignment below).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims allowed.
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/L.M.T./Examiner, Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637
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