DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-2, 8-10, 21-24, 27-28, and 44-45 (a variant polypeptide) in the reply filed on 02/19/2026 is acknowledged.
Upon further consideration, the Examiner has determined that claims 13-14, 19-20, 32, 36, and 40, drawn to a gene editing system comprising the variant polypeptide of claim 1, should be grouped with the invention of Group I, directed to the variant polypeptide. Accordingly, claims 1-2, 8-10, 13-14, 19-24, 27-28, 32, 36, 40, and 44-45 will be examined herein as Group I.
Claim 49 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Status of Claims
Claims 27 and 36 have been cancelled and claims 50-51 are newly added.
Claims 1-2, 8-10, 13-14, 19-24, 28, 32, 40, 44-45, and 50-51 are currently under consideration.
Priority
Acknowledgment is made of applicant’s claim for benefit under 35 U.S.C. 119(e) of Provisional application No. 63/391,682, filed on 07/22/2022. The present application and all claims are being examined with an effective filing date of 07/22/2022. In future actions, the effective filing date may change due to amendments or further review of priority documents.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 02/19/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claim Objections
Claims 1, 14, 22, 24, 28, and 32 are objected to because the recitation of a percent “identity” to a sequence (e.g., “98% identity to SEQ ID NO: 3”) does not specify that the identity refers to sequence identity, and thus could be interpreted as referring to, for example, functional identity rather than sequence comparison. It is suggested that the claims be amended to recite “sequence identity” when referring to percent identity to a sequence.
Appropriate correction is required.
Claim 19 is objected to because of the following informalities:
Claim 19 recites “wherein N is any nucleotide, Y is C or T, and R is A or G”, even though there are no occurrences “Y” in any of the recited PAM sequences. Accordingly, the definition of “Y” appears to be unused, is therefore superfluous and may cause unnecessary confusion. It is suggested that the claim be amended to remove the phrase “Y is C or T”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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.
Claim 1 (and claims 2, 8-10, 13-14, 19-24, 28, 32, 40, 44-45, and 50-51 dependent therefrom) is 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.
Claim 1 is indefinite and unclear due to the recitation of “a variant polypeptide having at least 98% identity to SEQ ID NO: 3 and comprising a substitution at each of positions: P14, D32, I61, E311, T338, and E736”, because it does not specify the sequence to which the recited residue positions correspond. Because the claim is directed to a variant polypeptide, it is unclear whether the recited positions refer to the numbering of SEQ ID NO: 3 or to the numbering of the variant polypeptide itself. Variants having less than 100% sequence identity to SEQ ID NO: 3 may differ in length or alignment relative to the reference sequence, and therefore the positions of residues within the variant polypeptide may not correspond to the same residue numbers in SEQ ID NO: 3. It is suggested that the claim be amended to clarify the reference sequence for the recited residue positions, for example by reciting that the substitutions occur at positions relative to SEQ ID NO: 3.
Appropriate response and amendment is requested.
Claim Rejections - 35 USC § 112(a)
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.
Claims 1-2, 10, 13-14, 19-24, 28, 32, 40, 44-45, and 50-51 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 claim(s) contains 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 inventor(s), at the time the application was filed, had possession of the claimed invention.
It is noted that MPEP 2111.01 states that ''[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow. Claim 1 has been broadly interpreted as encompassing a genus of variant polypeptides having at least 98% identity to SEQ ID NO:3 and comprising any substitution at each of positions P14, D32, I61, E311, T338, and E736 relative to SEQ ID NO:3. Claim 2 has been broadly interpreted as encompassing the genus of variant polypeptides of claim 1 wherein at least one of the substitutions recited at positions P14, D32, I61, E311, T338, or E736 is the specific substitution recited in claim 2, while the remaining positions may comprise any substitution. Claim 10 has been broadly interpreted as encompassing the genus of variant polypeptides of claim 1 that further exhibit functional characteristics including increased binary complex formation with an RNA guide, increased stability, or increased nuclease activity relative to a parent polypeptide. Claim 13 has been broadly interpreted as encompassing a genus of gene editing systems comprising the genus of variant polypeptides recited in claim 1 together with any RNA guide or nucleic acid encoding the RNA guide. Claim 14 has been broadly interpreted as encompassing the genus of gene editing systems of claim 13 wherein the RNA guide comprises a genus of direct repeat sequences having at least 90% identity to any of SEQ ID NOs: 4–15 and/or a genus of spacer sequences having a length of about 15–35 nucleotides or targeting a sequence adjacent to a PAM sequence. Claims 19-20 has been broadly interpreted as encompassing the genus of gene editing systems of claim 14 wherein the PAM sequence comprising the recited nucleotide motifs. Claim 21 has been broadly interpreted as encompassing the genus of variant polypeptides of claim 1 that further comprise additional components including a nuclear localization signal (NLS) and/or peptide tags, fluorescent proteins, base-editing domains, DNA methylation domains, histone modification domains, localization factors, transcription modification factors, light-gated control factors, chemically inducible factors, or chromatin visualization factors. Claims 22–24 and 28 have been broadly interpreted as encompassing the genus of variant polypeptides of claim 21 further comprising various NLS configurations and linker sequences. Claim 32 has been broadly interpreted as encompassing the genus of gene editing systems of claim 13 wherein the first nucleic acid comprises a nucleic acid sequence of Tables 9–11 or a nucleic acid sequence having at least 70% identity thereto, or wherein the first nucleic acid is mRNA, or wherein the second nucleic acid is included in any vector. Claim 40 has been broadly interpreted as encompassing the genus of gene editing systems of claim 32 wherein the vector comprises both the first nucleic acid encoding the variant polypeptide and the second nucleic acid encoding the RNA guide or is selected from a retroviral vector, lentiviral vector, phage vector, adenoviral vector, adeno-associated vector, or herpes simplex vector. Claims 44–45 have been broadly interpreted as encompassing the genus of variant polypeptides of claim 1 present within delivery systems or cells. Claims 50–51 have been broadly interpreted as encompassing the genus of variant polypeptides of claim 1 further comprising substitutions at catalytic residues including D328 and E530 and/or D684, D646, or D621.
MPEP 2163 I. states that to “satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention.
MPEP 2163. II.A.3.(a) states that “Possession may be shown in many ways. For example, possession may be shown by describing an actual reduction to practice of the claimed invention. Possession may also be shown by a clear depiction of the invention in detailed drawings or in structural chemical formulas which permit a person skilled in the art to clearly recognize that inventor had possession of the claimed invention. An adequate written description of the invention may be shown by any description of sufficient, relevant, identifying characteristics so long as a person skilled in the art would recognize that the inventor had possession of the claimed invention.
According to MPEP 2163.II.A.3.(a).ii), “Satisfactory disclosure of a ‘representative number' depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. Genome editing systems involving engineered nucleases and base editors constitute an unpredictable biological art in which small sequence changes may substantially alter structure or function.
In the instant case, the claimed variant polypeptides are defined relative to SEQ ID NO:3, which is 745 amino acids in length, and require at least 98% sequence identity thereto. A sequence identity of 98% permits approximately 15 amino acid substitutions relative to SEQ ID NO:3. Because claim 1 requires substitutions at six specific positions (P14, D32, I61, E311, T338, and E736), the claims still permit approximately nine additional substitutions at any other position within the sequence. Furthermore, the claims do not limit the identity of the substitutions at the six recited positions. Each position therefore potentially encompasses 19 alternative amino acids, resulting in approximately 19⁶ possible substitution combinations (over 47 million possible variants) at the six recited positions alone, even before considering additional substitutions permitted elsewhere by the 98% identity limitation.
While the specification discloses a number of variant polypeptides, including those listed in Table 8, the disclosed variants repeatedly employ specific substitutions, particularly P14R, D32R, I61R, E311R, and frequently T338G and E736G, often in combination with a limited set of additional substitutions such as D590G, D145G, E154G, D55G, K35G, K221G, D567G, or L38G. The specification therefore describes specific substitution patterns, rather than the full genus of variant polypeptides encompassing any substitution at the recited positions as required by the claims. The specification does not identify structural features, conserved residue classes, or substitution rules that would allow a person of ordinary skill in the art to determine which substitutions at these positions would yield the claimed variant polypeptides or retain the recited functional properties. Accordingly, although the specification describes certain species, it fails to describe structural features common to the members of the claimed genus that would allow a skilled artisan to recognize which sequences fall within the full scope of the claimed invention.
In addition to the deficiencies discussed above with respect to the claimed variant polypeptide, claim 32 recites that the first nucleic acid comprises a nucleic acid sequence of Table 9, Table 10, or Table 11, or a sequence having at least 70% identity thereto. The specification discloses only a limited number of specific nucleic acid sequences in Tables 9–11, including sequences encoding the variant polypeptide and sequences corresponding to NLS and linker elements. However, the claimed genus encompasses nucleic acid sequences sharing as little as 70% sequence identity with the disclosed sequences. For example, Table 9 discloses only two nucleic acid sequences encoding the variant polypeptide (e.g., SEQ ID NOs: 54 and 55), each approximately 2,235 nucleotides in length. Table 10 discloses only a small number of short nucleic acid sequences corresponding to NLS and linker elements (e.g., SEQ ID NOs: 56–57 and 59), and Table 11 discloses a limited number of variant nuclease sequences incorporating NLS and linker sequences (e.g., SEQ ID NOs: 64–75).
A nucleic acid sequence sharing 70% identity with the disclosed sequences may differ by hundreds of nucleotides across sequences of this length. Such a large degree of permitted variation encompasses an enormous number of possible sequences. The specification does not provide sufficient representative species or structural features common to the members of this genus that would allow a person of ordinary skill in the art to recognize which sequences within this vast range would encode the claimed variant polypeptides or otherwise maintain the properties attributed to the disclosed sequences. Accordingly, the specification does not reasonably convey possession of the full scope of nucleic acid sequences defined by ≥70% sequence identity to the sequences of Tables 9–11.
Given this lack of description of the representative species encompassed by the genus of the claims, the specification fails to sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that applicants were in possession of the full scope of the claimed invention.
Accordingly, claims 1-2, 10, 13-14, 19-24, 28, 32, 40, 44-45, and 50-51 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.
Claims 1-2, 10, 13-14, 19-24, 28, 32, 40, 44-45, and 50-51 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for variant polypeptides comprising the specifically disclosed substitutions in the SEQ ID NO: 3 nuclease scaffold (e.g., P14R, D32R, I61R, E311R, T338G, and E736G as exemplified by SEQ ID NO:53), does not reasonably provide enablement for the full scope of the claimed genus of variant polypeptides having at least 98% identity to SEQ ID NO:3 and comprising any substitutions at positions P14, D32, I61, E311, T338, and E736. Additionally, the specification while being enabling for gene editing systems comprising nucleic acids encoding variant polypeptides, comprising the specific nucleic acid sequences provided in Tables 9-11, does not reasonably provide enablement for the full scope of the claimed genus of nucleic acids encoding variant polypeptides comprising nucleic acid sequences having at least 70% identity to the sequences in Tables 9-11. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
The specification fails to enable the claim (or the full scope of the claim) if a person of ordinary skill in the art would be faced with an undue burden of experimentation when trying to implement the invention based on the disclosure. In re Wands (858 F.2d 731 at 737, 8 USPQ2d 1400 at 1404 (Fed. Cir. 1988)) sets forth a non-exclusive list of factors by which this burden of experimentation may be judged to be due or undue; factors that are germane to the instant case include the breadth of the claims, nature of the invention, the amount of direction provided by the inventor, the existence of working examples, the state of the prior art, and quantity of experimentation required.
Breadth of the Claims and Nature of the Invention
As indicated above, claim 1 encompasses a genus of variant polypeptides having at least 98% sequence identity to SEQ ID NO:3, which encodes a 745 amino acid CRISPR nuclease; and claim 32 encompasses a genus of gene editing systems wherein the first nucleic acid comprises a nucleic acid sequence having at least 70% identity to the sequences provided in Tables 9-11, which encodes variant polypeptides over 2000 nucleotides in length and NLS and linker components. With respect to SEQ ID NO: 3, a 98% sequence identity limitation permits approximately 15 amino acid substitutions relative to SEQ ID NO:3. Because the claims require substitutions at six specific positions (P14, D32, I61, E311, T338, and E736) while not limiting the identity of the substituted residues, each position potentially encompasses 19 alternative amino acids, resulting in approximately 19⁶ possible substitution combinations (over 47 million variants) at these six positions alone. In addition, the 98% identity limitation permits additional substitutions elsewhere within the polypeptide sequence beyond the six required substitutions.
With respect to the sequences provided in Tables 9-11, a 70% sequence identity limitation permits differences of approximately 600 nucleotides relative to a 2000 nucleotide sequence. Such variation represents an extremely large number of possible nucleotide substitutions, insertions, or deletions that could substantially alter the encoded polypeptide sequence and resulting functional properties. Accordingly, claim 32 encompasses a vast genus of nucleic acid sequences encoding potentially numerous undisclosed variant polypeptides.
State of the Prior Art and Level of Predictability
While CRISPR-based gene editing systems are known in the art, engineering functional CRISPR nucleases through amino acid substitutions constitutes an unpredictable biological art. Even a single amino acid substitution in a large nuclease enzyme may significantly alter protein folding, guide RNA binding, nuclease activity, target recognition, etc. Because the claimed variants permit numerous substitutions distributed throughout a large enzyme, it would not be predictable which substitutions would preserve the functional characteristics recited in the claims. The unpredictability of protein engineering in complex biological systems weighs against enablement across the full scope of the claimed genus.
Similarly, the relationship between nucleic acid sequence variation and the resulting activity of encoded CRISPR nucleases is not fully predictable in the art. Because claim 32 permits nucleic acid sequences having as little as 70% identity to the disclosed sequences of Tables 9–11, the claim encompasses sequences that may encode substantially altered polypeptides with unpredictable structural and functional properties. Given the complexity of CRISPR nuclease systems and guide RNA interactions, it would not have been predictable which of the numerous possible nucleic acid variants would encode functional nucleases capable of the activities recited in the claims.
Amount of Direction and Presence of Working Examples
The specification provides examples describing the construction and testing of certain SEQ ID NO: 3 variant polypeptides and reports experimental evaluation of indel activity for 175 specific variants. These examples demonstrate functional activity for a limited set of substitution combinations primarily involving specific substitutions such as P14R, D32R, I61R, E311R, T338G, and E736G and related variants. However, the examples are confined to these particular substitution patterns and do not provide guidance for designing or predicting functionality across the extremely broad range of substitutions permitted by the claims. The specification also includes Table 2, which lists potential amino acid substitutions at each position of SEQ ID NO: 3 and suggests that substitutions may include residues such as R, G, A, K, Q, N and H. However, there is no experimental validation for these substitutions across the numerous positions of the protein and does not provide guidance regarding which substitutions or combinations of substitutions preserve nuclease activity or the other functional characteristics recited. Accordingly, despite the inclusion of this table, the specification does not provide sufficient direction that would enable a person of ordinary skill in the art to determine which amino acid substitutions at the recited positions, or elsewhere within the sequence, would retain nuclease activity or other claimed functional characteristics without undue experimentation, and therefore does not provide sufficient direction for practicing the full scope of the claimed genus.
In addition, while the specification provides several nucleic acid sequences in Tables 9–11, these represent only a limited number of specific examples relative to the extremely broad genus encompassed by claim 32, which permits sequences having as little as 70% identity to the disclosed sequences. The specification does not provide sufficient guidance or representative examples describing which nucleotide substitutions, deletions, or insertions across these large sequences would preserve the functional properties required of the claimed gene editing systems. Thus, the disclosure does not provide sufficient direction to enable a person of ordinary skill in the art to practice the full scope of claim 32.
Undue Experimentation
Absent additional guidance, a person of ordinary skill in the art would be required to engage in extensive experimentation to identify operable variants within the claimed genus. Such experimentation would include generating numerous candidate variants meeting the sequence identity threshold, introducing substitutions at the specified residues, expressing the resulting proteins, and experimentally evaluating nuclease activity, RNA guide binding, and other functional properties. Given the breadth of the claims relative to the limited number of disclosed variants, the unpredictability of protein engineering, and the large number of potential substitution combinations, practicing the full scope of the claimed invention would require undue experimentation.
The breadth of claim 32 further increases the experimentation required because a person of ordinary skill in the art would need to generate and test numerous nucleic acid variants having up to approximately 30% sequence divergence from the disclosed sequences. Determining which of these variants encode functional polypeptides capable of performing the claimed gene editing activities would require extensive screening and experimental validation.
Thus, claims 1-2, 10, 13-14, 19-24, 28, 32, 40, 44-45, and 50-51 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, for lack of enablement.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-2, 8-9, 13, 32, and 40 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 4-5, 7, 11-13 and 30 of copending Application No. 18442529 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘539 claims recite a gene editing system comprising a nuclease, comprising the amino acid set forth in SEQ ID NO: 4, which has 99.2% sequence identity to instant SEQ ID NO: 3, 100% sequence identity to instant SEQ ID NO: 53, and comprises the following substitutions: P14R, D32R, I61R, E311R, T338G, and E736G; and one or more guide RNAs.
Claim 4 of application ‘539 recites “the gene editing system of claim 1, wherein in Type V CRISPR nuclease is a nuclease comprising the amino acid sequence of any one of SEQ ID NO: 4-6”.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claim is in condition for allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NAGHMEH NINA MOAZZAMI whose telephone number is (703)756-4770. The examiner can normally be reached Monday-Friday, 9:00-5:00.
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/NAGHMEH NINA MOAZZAMI/Examiner, Art Unit 1652
/RICHARD G HUTSON/Primary Examiner, Art Unit 1652