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 .
Claims 1-20 are pending and 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. The earliest effective filing date to which the instant application is entitled is 09/24/2020.
Information Disclosure Statement
Receipt of information disclosure statements on 06/23/2023 and 10/04/2023 is acknowledged. The signed and initialed PTO-1449‘s have been mailed with this action.
Drawings
The drawings are objected to because:
With regard to Figure 12, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 781-788 are depicted therein. However, the sequences listed in Figure 12 are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 16, the drawings filed 03/23/2023 indicate that SEQ ID NOs 789 and 790 are depicted therein. However, the sequences listed in Figure 16 are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figures 18 and 21, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 791-794 are depicted therein. However, the sequences listed in Figures 18 and 21 are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 24, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 795-800 are depicted therein. However, the sequences listed in Figure 24 are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 26A, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 801-804 are depicted therein. However, the sequences listed in Figure 26A are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 27, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 805-810 are depicted therein. However, the sequences listed in Figure 27 are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 29D, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 811-817 are depicted therein. However, the sequences listed in Figure 29D are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 33, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 818 and 819 are depicted therein. However, the sequences listed in Figure 33 are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 39A, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 820 and 821 are depicted therein. However, the sequences listed in Figure 39A are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 44G, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 822 and 823 are depicted therein. However, the sequences listed in Figure 44G are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 45G, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 824 and 825 are depicted therein. However, the sequences listed in Figure 45G are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figures 48A-48C, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 826-828 are depicted therein. However, the sequences listed in Figures 48A-48C are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 51F, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 791 and 829-844 are depicted therein. However, the sequences listed in Figure 51F are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 51G, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 845-867 are depicted therein. However, the sequences listed in Figure 51G are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 53C, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 868-874 are depicted therein. However, the sequences listed in Figure 53C are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 53D, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 875-877 are depicted therein. However, the sequences listed in Figure 53D are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 53E, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 875-878 are depicted therein. However, the sequences listed in Figure 53E are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figures 54 and 59G, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 879-884 are depicted therein. However, the sequences listed in Figures 54 and 59G are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 60A, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 885-888 are depicted therein. However, the sequences listed in Figure 60A are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 62B, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 889-891 are depicted therein. However, the sequences listed in Figure 62B are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figures 70A-70I, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 892-893 and 3148 are depicted therein. However, the sequences listed in Figure 70A-70I are not consistent with the associated SEQ ID NOs in the sequence listing. Furthermore, there is no SEQ ID NO: 3148 in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 71A, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 897-898 are depicted therein. However, the sequences listed in Figure 71A are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 102, the drawings filed 03/23/2023 indicate that SEQ ID NO: 195 is depicted therein. However, the sequence listed in Figure 102 is not consistent with the associated SEQ ID NO in the sequence listing. It would be remedial to update either the listed sequence or the listed sequence identifier such that the listed sequence is consistent with the listed sequence identifiers.
With regard to Figures 141 and 142, the sequences depicted therein are of insufficient quality to be clearly legible and/or interpretable. It would be remedial to increase the image quality such that it is clearly legible and/or interpretable.
With regard to Figure 145, the drawings filed 03/23/2023 indicate that SEQ ID NO: 2043 is depicted therein. However, there is no SEQ ID NO: 2043 in the sequence listing. It would be remedial to update either the listed sequence or the listed sequence identifier such that the listed sequence is consistent with the listed sequence identifiers.
With regard to Figure 147, the drawings filed 03/23/2023 indicate that SEQ ID NO: 2024 is depicted therein. However, the sequence listed in Figure 147 is not consistent with the associated SEQ ID NO in the sequence listing. It would be remedial to update either the listed sequence or the listed sequence identifier such that the listed sequence is consistent with the listed sequence identifiers.
With regard to Figure 157, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 2030-2033 are depicted therein. However, the sequences listed in Figure 157 are not consistent with the associated SEQ ID NOs in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 163, the drawings filed 03/23/2023 indicate that SEQ ID NOs: 2034-2044 are depicted therein. However, the sequences listed in Figure 163 are not consistent with the associated SEQ ID NOs in the sequence listing (such as SEQ ID NO: 2042). Furthermore, there are no SEQ ID NOs 2043 and 2044 in the sequence listing. It would be remedial to update either the listed sequences or the listed sequence identifiers such that the listed sequences are consistent with the listed sequence identifiers.
With regard to Figure 164, the drawings filed 03/23/2023 indicate that SEQ ID NO: 2045 is depicted therein. However, there is no SEQ ID NO: 2045 in the sequence listing. It would be remedial to update either the listed sequence or the listed sequence identifier such that the listed sequence is consistent with the listed sequence identifiers.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings. As set forth above regarding the instant drawings, the Examiner notes that several SEQ ID NOs of the sequence listing are not consistent with the sequences listed in the drawings (see above). Accordingly, it is unclear what SEQ ID NOs are being listed in the drawings, as there are no appropriate sequence identifiers, as indicated above. Additionally, Figures 101, 163, and 164 include sequences that are not identified by an associated sequence identifier.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see paragraph [0236]; page 967, reference 9; page 968, reference 28). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The disclosure is further objected to because it references colors in the brief description of the drawings (starting at paragraph [0048]) that are not present in the black-and-white drawings of record, thereby complicating interpretation of said figures. Should Applicant deem these colors necessary to the interpretation of the figures, a petition must be filed under 37 CFR 1.84(a)(2).
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Claim Objections
Claim 1-20 are objected to because of the following informalities:
Claims 1-20 all recite “a pegRNA” or “the pegRNA,” which is an acronym for “prime editing guide RNA,” as set forth in paragraph [0003] of the instant specification. However, none of claims 1-20 recite that “pegRNA” is an acronymization of “prime editing guide RNA.” Before reciting an acronym, it is proper to recite the species that is being acronymized therein. It would be remedial to amend the instant claim set such that “prime editing guide RNA” is explicitly recited prior to the first recitation of its associated acronym (i.e. at instant claim 1).
Claim 1 recites that “the extension arm comprises a nucleic acid moiety attached thereto selected from the group consisting of a…G-quadraplex” (bolded emphasis added), which incorporates a typographical error. As recited at instant claim 5, the correct spelling is “G-quadruplex” (bolded emphasis added). It would be remedial to amend the instant claim to correct this typographical error as indicated.
With specific regard to claim 4, which recites “a Mpknot1 moiety” (bolded emphasis added), the article “a” is grammatically improper when preceding words articulated with an initial vowel sound. While “Mpknot1” is spelled such that it recites a consonant letter “M,” the pronunciation of the “M” in “Mpknot1” nonetheless begins with a vowel sound. It would be remedial to update the instant claim language to be grammatically proper.
Furthermore, claim 15 also recites “napDNAbp,” which is an acronym for “nucleic acid programmable DNA binding protein,” as set forth in paragraph [0003] of the instant specification. Before reciting an acronym, it is proper to recite the species that is being acronymized therein. It would be remedial to amend the instant claim set such that “nucleic acid programmable DNA binding protein” is explicitly recited prior to the first recitation of its associated acronym (i.e. at instant claim 15).
Finally, claim 18 recites “the nucleic acid extension arm [of the pegRNA of claim 1] is at least 5 nucleotides…or at least 50 nucleotides.” While not technically improper, this recitation is inconsistent with the length limitations recited at instant claims 13 and 19, both of which recite some number of “nucleotides in length.” It would be remedial to amend the instant claim set such that the language of instant claim 18 is internally consistent with the language recited throughout the rest of the claim set.
Appropriate correction is required.
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 1-20 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.
►Claims 1-20 are broadly drawn to a pegRNA for prime editing, said pegRNA comprising a guide RNA and at least one nucleic acid extension arm comprising a DNA synthesis template and a primer binding site, wherein said extension arm comprises an attached nucleic acid moiety of a toe-loop, hairpin, stem-loop, pseudoknot, aptamer, G-quadruplex, tRNA, riboswitch, or ribozyme, wherein the sequences are not further limited. Claims 4-9 are further limit these claimed nucleic acid moieties to a set of nucleotide sequences that must encode an Mpknot1 pseudoknot, a G-quadruplex, evopreq1, a tRNA moiety, an xrn1 moiety, and a grp1 intron P4P6 moiety. These claims encompass nucleotide sequences having at least 80% sequence identity to said nucleotide sequences. While claims 4-9 limit the claimed set of nucleotide sequences to having at least 80% sequence identity with any of the recited SEQ ID NOs, the remainder of the instant claim set necessarily encompasses sequences with less than 80% sequence identity, as said claims are drawn to any sequence corresponding to the claimed species. The rejected claims thus comprise a set of nucleotide sequences with a large number of variable residues, all variations of which must encode the recited nucleic acid moiety of the prime editing guide RNA (pegRNA) of the instant invention.
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of a complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, and any combination thereof. While the specification describes Mpknot-1 sequences and variants (Table 4), G quadruplex sequences (Table 5), and evopreq1 and similar/variant motifs (Table 6), these sequences are identical to those recited at instant claims 4-6, which are shown in the alignments below.
As shown in the alignments below, certain sequences (such as the Mpknot1 sequences) exhibit a high level of sequence identity, while the G-quadruplex and evopreq1 sequences exhibit more variable levels of sequence identity that are substantially lower. While the disclosed nucleotide sequences encode the instantly claimed Mpknot1, G-quadruplex, and evopreq1 moieties, it is not clear whether sequences encompassed by the recited limitation of 80% sequence identity to each sequence would necessarily encode the instantly claimed moieties as well, as no description is provided of sequences with at least 80% sequence identity
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to these sequences.
Thus, even if one accepts that the examples described in the specification meet the claim limitations of the rejected claims with regard to structure and function, the examples are only representative of the disclosed sequences set forth above, which include sequences with both greater than 80% sequence identity to each other (i.e. Mpknot1 sequences share greater than 90% identity; see alignments above) and sequences with less than 80% sequence identity to each other (i.e. G-quadruplex and evopreq1, both of which include sequences that share less than 60% identity; see alignments above). Accordingly, the results are not necessarily predictive of sequences with at least 80% identity to each other, as the disclosed sequences overall share either a high level of sequence identity or a low level of sequence identity, with no guidance from the instant specification as to the essentiality of any particular sequence or other general principles for designing functional nucleotide sequences sharing at least 80% sequence identity to the instantly claimed sequences. Thus, it is impossible for one to extrapolate from the few examples described herein those sequences that would necessarily meet the structural/functional characteristics of the rejected claims.
Regarding instant claims 7-9, the specification also describes a modified tRNA that is used by MMLV RT as a primer for reverse transcription (Table 7) and miscellaneous motifs xrn1 and grp1 intron P4P6 for use therein (Table 8). These disclosed sequences are identical to those recited at instant claims 7-9.
The instantly claimed modified tRNA sequence (SEQ ID NO: 222) has a length of 81 nucleotides, meaning a sequence with at least 80% identity thereto may vary from the instantly claimed sequence by as many as 16 nucleotides, while the instantly claimed miscellaneous motifs (SEQ ID NOs: 223 and 224) each have a length of 43 and 160 nucleotides, respectively, meaning sequences with at least 80% identity thereto may vary from the instantly claimed sequences by as many as 8 or 32 nucleotides, respectively. As set forth above regarding instant claims 4-6, the instant specification provides no guidance as to the essentiality of any particular sequence or other general principles for designing functional nucleotide sequences sharing at least 80% sequence identity to the instantly claimed sequences. Thus, it is impossible for one to extrapolate from the few examples described herein those sequences that would necessarily meet the structural/functional characteristics of the rejected claims.
The prior art does not appear to offset the deficiencies of the instant specification in that it does not describe a set of nucleotide sequences with less than or at least 80% sequence identity to the instantly claimed sequences that are capable of functioning in the instantly claimed system. As is known to those of ordinary skill in the art, the prior art teaches that sequence conservation is a hallmark indicator of functionality, and that as conservation decreases, functionality comes into question, as sequences subject to transient or lower constraints cannot be distinguished easily from neutrally evolving, non-functional sequences (Ponting, 2017: abstract). Thus, based on the disclosure, it is not clear to someone of ordinary skill in the art whether a sequence with less than or at least 80% sequence identity across the entirety of said sequence would necessarily meet the structural/functional characteristics of the rejected claims.
Therefore, the skilled artisan would have reasonably concluded applicants were not in possession of the claimed invention for claims 1-20.
►Claims 18 and 19 are further drawn to a set of nucleic acid sequences of variable length, said nucleic acid sequences corresponding to a nucleic acid extension arm and a DNA synthesis template.
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of a complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, and any combination thereof. With regard to the instantly claimed nucleic acid extension arm, the specification describes SEQ ID NOs: 197, 222, and 224, which are 60, 81, and 160 nucleotides in length, respectively. While these sequences meet the limitation of a nucleic acid extension arm that is at least 50 nucleotides (as recited at instant claim 18), the recitation of at least 50 nucleotides necessarily encompasses a nucleic acid extension arm with theoretically infinite length. No description is provided of such lengthy nucleic acid extension arms.
Similarly, with regard to the instantly claimed DNA synthesis template, the specification discloses synthesis templates up to 35 nucleotides in length (paragraph [0163]; Figure 105C). As set forth above, while these sequences meet the limitation of a DNA synthesis template that is at least 15 nucleotides in length (as recited at instant claim 19), the recitation of at least 15 nucleotides necessarily encompasses a DNA synthesis template with theoretically infinite length. No description is provided of such lengthy DNA synthesis templates.
Even if one accepts that the examples described in the specification meet the claim limitations of the rejected claims with regard to structure and function, the examples are only representative of nucleic acid extension arms and DNA synthesis templates that are much shorter than the theoretically infinite length encompassed by the instant claim language of “at least.” The results are not necessarily predictive of the very lengthy nucleic acid extension arms and DNA synthesis templates encompassed by the instant claim language of “at least.” Thus, it is impossible for one to extrapolate from the few examples described herein those very lengthy nucleic acid extension arms and DNA synthesis templates that would necessarily meet the structural/functional characteristics of the rejected claims.
The prior art does not appear to offset the deficiencies of the instant specification in that it does not describe a set of very lengthy nucleic acid extension arms and DNA synthesis templates that would necessarily meet the structural/functional characteristics of the rejected claims. As set forth above, the instant claim language necessarily encompasses nucleic acids with a theoretically infinite number of nucleotide residues. The prior art is silent as to the utility or practicality of working with very lengthy nucleic acids, as encompassed by the instant claim language.
Therefore, the skilled artisan would have reasonably concluded applicants were not in possession of the claimed invention for claims 18 and 19.
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 6 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 6 recites the limitation "the evopreq1" in line 1. There is insufficient antecedent basis for this limitation in the claim. It would be remedial to amend the instant claim set such that there is sufficient antecedent basis for the limitation “the evopreq1” in line 1 of claim 6.
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.
Claims 1-3 and 14-20 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by WO 2018/049168 A1 (hereinafter Smith; as cited in the IDS filed 06/23/2023), as evidenced by Jiang and Doudna, 2017 (hereinafter Jiang).
With regard to claim 1, which recites “a pegRNA for prime editing comprising a guide RNA and at least one nucleic acid extension arm comprising a DNA synthesis template and a primer binding site, wherein the extension arm comprises a nucleic acid moiety attached thereto selected from the group consisting of a toe-loop, hairpin, stem-loop, pseudoknot, aptamer, G-quadraplex [sic], tRNA, riboswitch, and ribozyme,” Smith discloses compositions and methods for high-efficiency genome editing, including the utility of retron-guide RNA cassettes (abstract;
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figure 1-shown below).
As shown in figure 1 above, the retron-guide RNA cassette of Smith comprises a guide RNA linked to an extension arm comprising: a DNA synthesis template that also serves as a self-primer for synthesis by a reverse transcriptase, thereby yielding donor DNA sequence for insertion into the genome (paragraphs [0021], [0024], [0122], and [0133]; figure 1); and inverted repeats (which read on the instantly claimed hairpin) (paragraphs [0006], [0007], and [0048]; figure 1). Accordingly, Smith anticipates each and every limitation of instant claim 1.
With regard to claims 2 and 3, which respectively recite “the nucleic acid moiety [of the pegRNA of claim 1] is attached to the 3’ end of the extension arm” and “the nucleic acid moiety [of the pegRNA of claim 1] is attached to the 5’ end of the extension arm,” as set forth above, Smith discloses retron-guide RNA cassettes that anticipate the pegRNA of instant claim 1. Smith further discloses that the inverted repeat sequences (i.e. the hairpins) taught therein may be located at the 5’ or 3’ end of the retron (paragraphs [0007], [0008], [0010], [0065], and [0122]), as instantly claimed. Accordingly, Smith anticipates each and every limitation of instant claims 2 and 3.
With regard to claim 14, which recites “the extension arm [of the pegRNA of claim 1] is positioned at the 3’ or 5’ end of the guide RNA, and wherein the nucleic acid extension arm is DNA or RNA,” as set forth above, Smith discloses retron-guide RNA cassettes that anticipate the pegRNA of instant claim 1. Smith further discloses that the gRNA coding region of the cassette may be located 3’ or 5’ of the retron (paragraph [0102]; claims 8 and 9) and that the retron taught therein encodes an RNA molecule that, when reverse transcribed, results in a multicopy single-stranded DNA molecule that comprises both RNA and DNA (paragraph [0009]; claims 4 and 5). Accordingly, Smith anticipates each and every limitation of instant claim 14.
With regard to claim 15, which recites “the pegRNA [of claim 1] is capable of binding to a napDNAbp and directing the napDNAbp to a target DNA sequence,” as set forth above, Smith discloses retron-guide RNA cassettes that anticipate the pegRNA of instant claim 1. Smith further discloses that the retron-guide RNA cassettes taught therein are compatible with Cas9 nucleases (which read on the instantly claimed napDNAbp), directing said Cas9 nuclease to make a double-strand DNA cut at a desired genomic location and facilitating insertion of a donor DNA sequence (paragraphs [0048], [0127], and [0136]). Accordingly, Smith anticipates each and every limitation of instant claim 15.
With regard to claim 16, which recites “the target DNA sequence [of the pegRNA of claim 15] comprises a target strand and a complementary non-target strand,” as set forth above, Smith discloses that the retron-guide RNA cassettes taught therein are compatible with Cas9 nucleases (which read on the instantly claimed napDNAbp), directing said Cas9 nuclease to make a double-strand DNA cut at a desired genomic location (which reads on the instantly claimed target DNA sequence) (paragraphs [0048], [0127], and [0136]). While Smith specifies that the crRNA of the retron-guide RNA cassette taught therein is complementary to a targeted genomic DNA sequence (paragraphs [0048], [0127], [0128], and [0136]), Smith does not specifically disclose that the target DNA sequence comprises a complementary non-target strand. However, the double-stranded nature of genomic DNA in which the target strand is complementary to the non-target strand is well-known to those of ordinary skill in the art and is considered to be an inherent characteristic of target DNA sequences. This is supported by the disclosure of Jiang, which teaches that the Cas9 enzyme (as disclosed in Smith) cleaves the DNA strand complementary to the guide RNA sequence (i.e. the target strand) with an HNH-like nuclease domain and the DNA strand opposite the complementary strand (i.e. the nontarget strand) with a RuvC-like nuclease domain (page 509, paragraph 4). Accordingly, in view of the inherent nature of a target DNA sequence comprising a target strand and a complementary nontarget strand, Smith anticipates each and every limitation of instant claim 16.
With regard to claim 17, which recites “the guide RNA [of the pegRNA of claim 16] hybridizes to the target strand to form an RNA-DNA hybrid and an R loop,” as set forth above, Smith anticipates each and every limitation of instant claim 16 (in view of the inherent nature of a target DNA sequence comprising a target strand and a complementary nontarget strand). While Smith does not explicitly disclose the formation of an RNA-DNA hybrid and an R loop, these are considered to be inherent properties of nucleases such as Cas9 interacting with targeted double-stranded DNA. This is supported by the disclosure of Jiang, which teaches that once Cas9 has found a target site with the appropriate PAM, local DNA melting is triggered at the PAM-adjacent nucleation site, followed by RNA strand invasion to form an RNA-DNA hybrid and a displaced DNA strand (the R-loop) from PAM-proximal to PAM-distal ends (page 516, paragraph 2: “TARGET SEARCH AND RECOGNITION”). Accordingly, in view of the inherent nature of formation of an RNA-DNA hybrid and an R-loop upon Cas9 contacting a targeted double-stranded DNA sequence, Smith anticipates each and every limitation of instant claim 17.
With regard to claim 18, which recites “the nucleic acid extension arm [of the pegRNA of claim 1] is at least 5 nucleotides…” Smith discloses that the retron-gRNA cassette taught therein is at least 5,000 nucleotides in length, of which 100 nucleotides account for the length of the gRNA molecule (paragraphs [0103] and [0132]). Given that the retron-gRNA cassette taught therein is at least 5,000 nucleotides in length, of which only 100 nucleotides correspond to the length of the gRNA molecule of said cassette, the retron (which reads on the instantly claimed nucleic acid extension arm) must be at least 5 nucleotides in length, as instantly claimed. Accordingly, Smith anticipates each and every limitation of instant claim 18.
With regard to claim 19, which recites “the DNA synthesis template [of the pegRNA of claim 1] is at least 3 nucleotides…in length,” as set forth above, Smith discloses retron-guide RNA cassettes that anticipate the pegRNA of instant claim 1. Smith further discloses that the retron-guide RNA cassettes taught therein are compatible with Cas9 nucleases, directing said Cas9 nuclease to make a double-strand DNA cut at a desired genomic location and facilitating insertion of a donor DNA sequence (paragraphs [0048], [0127], and [0136]). The donor DNA sequence taught therein is produced by reverse transcription of the DNA synthesis template of the disclosed retron-guide RNA cassette (paragraphs [0021], [0024], [0122], and [0133]; figure 1) and is disclosed to be at least 500 nucleotides in length (paragraph [0135]). nucleic acid extension arm) must be at least 5 nucleotides in length, as instantly claimed. Accordingly, Smith anticipates each and every limitation of instant claim 19.
With regard to claim 20, which recites “the DNA synthesis template [of the pegRNA of claim 1] encodes a desired edit,” as set forth above, Smith discloses that the retron-guide RNA cassettes taught therein are compatible with Cas9 nucleases, directing said Cas9 nuclease to make a double-strand DNA cut at a desired genomic location and facilitating insertion of a donor DNA sequence derived from reverse transcription of the template of the retron-guide RNA cassette (paragraphs [0021], [0024], [0048], [0122], [0127], [0133], and [0136]). Smith specifically discloses that the one or more donor DNA sequences taught therein are homologous to the corresponding one or more target loci and comprise sequence modifications compared to the one or more target nucleic acids, thereby incorporating a modified sequence into the targeted locus (paragraph [0024]). These sequence modifications may result in the insertion of one or more sequence encoding cellular localization tags, degrons, or synthetic response elements (paragraph [0031]). These sequence modifications are considered to read on the instantly claimed “desired edit.” Accordingly, Smith anticipates each and every limitation of instant claim 20.
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.
Claims 1-3 and 14-20 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2018/049168 A1 (hereinafter Smith; as cited in the IDS filed 06/23/2023) in view of Nahar et al., 2018 (hereinafter Nahar; as cited in the IDS filed 06/23/2023), as evidenced by Jiang and Doudna, 2017 (hereinafter Jiang).
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With regard to claim 1, which recites “a pegRNA for prime editing comprising a guide RNA and at least one nucleic acid extension arm comprising a DNA synthesis template and a primer binding site, wherein the extension arm comprises a nucleic acid moiety attached thereto selected from the group consisting of a toe-loop, hairpin, stem-loop, pseudoknot, aptamer, G-quadraplex [sic], tRNA, riboswitch, and ribozyme,” Smith discloses compositions and methods for high-efficiency genome editing, including the utility of retron-guide RNA cassettes (abstract; figure 1-shown below).
As shown in figure 1 above, the retron-guide RNA cassette of Smith comprises a guide RNA linked to an extension arm comprising: a DNA synthesis template that also serves as a self-primer for synthesis by a reverse transcriptase, thereby yielding donor DNA sequence for insertion into the genome (paragraphs [0021], [0024], [0122], and [0133]; figure 1); and inverted repeats (which read on the instantly claimed hairpin) (paragraphs [0006], [0007], and [0048]; figure 1). Accordingly, as set forth above, Smith anticipates each and every limitation of instant claim 1. However, the disclosure of Smith in view of Nahar also reads on each and every limitation of instant claim 1 in an embodiment in which the attached nucleic acid moiety is a G-quadruplex (not disclosed in Smith).
Nahar discloses that appending a naturally forming RNA G-quadruplex motif to the 3’ end of sgRNAs results in improved guide RNA stability and target cleavage efficiency in zebrafish embryos without inducing off-target activity (abstract; Figure 1). Given that Smith discloses a retron-guide RNA cassette for high-efficiency genome editing with nucleases such as Cas9 and that Nahar discloses that appending a naturally forming RNA G-quadruplex motif to the 3’ end of sgRNAs results in improved guide RNA stability and target cleavage efficiency, it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the claimed invention to further modify the retron-guide RNA cassette of Smith such that it comprises a G-quadruplex at the 3’ end of the guide RNA as in Nahar to predictably improve guide RNA stability and target cleavage efficiency. One would have been motivated to make such a modification in order to receive the expected benefit of improving guide RNA stability and target cleavage efficiency.
With regard to claims 2 and 3, which respectively recite “the nucleic acid moiety [of the pegRNA of claim 1] is attached to the 3’ end of the extension arm” and “the nucleic acid moiety [of the pegRNA of claim 1] is attached to the 5’ end of the extension arm,” as set forth above, Smith discloses retron-guide RNA cassettes that anticipate the pegRNA of instant claim 1. Smith further discloses that the inverted repeat sequences (i.e. the hairpins) taught therein may be located at the 5’ or 3’ end of the retron (paragraphs [0007], [0008], [0010], [0065], and [0122]), as instantly claimed. Accordingly, Smith and Nahar collectively disclose each and every limitation of instant claims 2 and 3.
With regard to claim 14, which recites “the extension arm [of the pegRNA of claim 1] is positioned at the 3’ or 5’ end of the guide RNA, and wherein the nucleic acid extension arm is DNA or RNA,” as set forth above, Smith discloses retron-guide RNA cassettes that anticipate the pegRNA of instant claim 1 while Nahar discloses that appending a naturally forming RNA G-quadruplex motif to the 3’ end of sgRNAs results in improved guide RNA stability and target cleavage efficiency in zebrafish embryos without inducing off-target activity (abstract; Figure 1). Smith further discloses that the retron taught therein encodes an RNA molecule that, when reverse transcribed, results in a multicopy single-stranded DNA molecule that comprises both RNA and DNA (paragraph [0009]; claims 4 and 5). Accordingly, Smith and Nahar collectively disclose each and every limitation of instant claim 14.
With regard to claim 15, which recites “the pegRNA [of claim 1] is capable of binding to a napDNAbp and directing the napDNAbp to a target DNA sequence,” as set forth above, Smith discloses retron-guide RNA cassettes that anticipate the pegRNA of instant claim 1. Smith further discloses that the retron-guide RNA cassettes taught therein are compatible with Cas9 nucleases (which read on the instantly claimed napDNAbp), directing said Cas9 nuclease to make a double-strand DNA cut at a desired genomic location and facilitating insertion of a donor DNA sequence (paragraphs [0048], [0127], and [0136]). Accordingly, Smith and Nahar collectively disclose each and every limitation of instant claim 15.
With regard to claim 16, which recites “the target DNA sequence [of the pegRNA of claim 15] comprises a target strand and a complementary non-target strand,” as set forth above, Smith discloses that the retron-guide RNA cassettes taught therein are compatible with Cas9 nucleases (which read on the instantly claimed napDNAbp), directing said Cas9 nuclease to make a double-strand DNA cut at a desired g