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 1-5, in the reply filed on 8/1/2025 is acknowledged.
Claims 6-21 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected groups, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 8/1/2025.
Applicants elected SEQ ID NO: 1 for claim 4 and SEQ ID NO: 65 for claim 5.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: For example, Figure 3B uses reference numbers 1-48 for “sgRNA handle”. These reference numbers are not recited in the specification. Similar issues arise for most figures, such as at least Figure 3E, 5-7, 14, 15. Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) 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. 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.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on page 21. 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.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). For example, see at least Figures 3, 5, 6, 7, 14, 15 which lack SEQ IDs for the handle sequences and promoters tested. The numbers identified as Promoter#, Handle# do not match the SEQ ID numbers.
Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Claim Interpretation
Claim 1 is directed to a nucleic acid molecule comprising an extra long sgRNA array (ELSA) wherein the ELSA comprises nucleotide sequences encoding two or more sgRNA and a maximum shared repeat length of 20 nucleotides. The nucleotide sequences that encode the two or more sgRNA are not required to be contiguous, thus claimed ELSA also embraces non-contiguous nucleotide sequences.
The nucleic acid molecule of claim 1-3 is broadly interpreted to embrace DNA and RNA molecules. Claims 4 and 5 recite DNA sequences and thus implicitly result in the nucleic acid molecule to be in DNA form.
The claims recites the term “sgRNA” which is conventionally understood to mean a single guide RNA, generally for use in a CRISPR-based system. However, other definitions for this term were known in the art. For example, In “The Complete Guide to Understanding CRISPR sgRNA” from Synthego (Commercial CRISPR reagent vendor), it states “The term “sgRNA” has been previously used elsewhere to refer to different types of CRISPR RNAs, including synthetic guide RNA and short guide RNA. In this guide, we have used the conventional definitions to avoid confusion: gRNA is the term that describes all CRISPR guide RNA formats, and sgRNA refers to the simpler alternative that combines both the crRNA and tracrRNA elements into a single guide RNA molecule.” (page 3, last para; see Guide in PTO-892). In the instant case, the claimed “nucleotide sequence” that encode the sgRNAs do not comprise or encode the sgRNA handle sequence, instead only ‘operable linkage’ is sufficient. The specification does not provide a specific definition for the term “sgRNA handle sequence” but states “Generally, an sgRNA is made up of two parts: a crispr RNA (crRNA), a 17-20 nucleotide sequence complementary to the target DNA, and a tracr RNA, (herein referred to as an sgRNA handle), which serves as a binding scaffold for the Cas nuclease.” (page 27). However the claim recites an sgRNA and a separate sgRNA handle sequence. Therefore, in the instant case the ‘sgRNA’ encoded by the nucleotide sequence are not required to be limited to the conventional sgRNA which comprises the combined crRNA and tracrRNA but embrace sequences that comprise only a short or synthetic gRNA such as crRNAs only. Thus, sgRNA is broadly interpreted to embrace crRNA, short gRNA, synthetic gRNA or single guide RNA with crRNA and tracrRNA combined. Furthermore, based on the guidance in the specification noted above, sgRNA handle sequences are interpreted to include structures that “serves as a binding scaffold for the Cas nuclease”.
The claims also recites that the nucleotide sequences that encode the sgRNA are under the control of a “sgRNA promoter”. No definition is provided for this term. When describing sgRNA promoters, the specification states that “The invention is based, in part, on the development of promoter sequences for expression of sgRNAs of the invention.” (page 29). Thus, the term “sgRNA promoter” is broadly interpreted as any promoter capable of allowing expression of a nucleotide sequence, such as ones encoding a sgRNA.
Furthermore, the sgRNA promoter in claim 1 that controls the nucleotide sequences encoding sgRNAs is not required to be comprised by these nucleotide sequences. Since the ELSA of claim 1 only comprises the nucleotide sequences encoding sgRNAs, the sgRNA promoter is not required to be structurally part of the ELSA in at least claims 1-3, 5. Additionally, a single sgRNA promoter could control the expression of multiple nucleotide sequences encoding sgRNAs for at least claims 1-3, 5. Of note, Claim 4 requires the ELSA to comprise two sgRNA promoters.
Similarly, the sgRNA handle sequence of claim 1 that is ‘operable linked’ to the nucleotide sequences encoding sgRNAs are not comprised by these nucleotide sequences. Since the ELSA of claim 1 only comprises the nucleotide sequences encoding sgRNAs, the sgRNA handle sequences are not required to be structurally part of the ELSA of at least claims 1-4. Of note, Claim 5 requires the ELSA to comprise two sequences selected from the recited alternatives and these sequences are of sgRNA handle sequences disclosed in the specification.
Finally, regarding the phrase “a maximum shared repeat length”. This is not a phrase in the art and no definition is provided for this phrase. On page 30, the specification provides the following guidance “In various embodiments, the ELSA are designed to have a maximum shared repeat length of less than 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, or less than 7 consecutive nucleotides. For example, for an ELSA with a maximum shared repeat length of 20, no nucleotide sequence greater than 20 nucleotides long is repeated throughout the full length of the ELSA sequence”. Thus, it is understood that “a maximum shared repeat length” is a property of a nucleotide sequence, wherein such a nucleotide sequence does not comprise repeat subsequences with length greater than the maximum allowed (shared repeat length). In the instant claim, due to the use of the open transitional phrase ‘ELSA comprises’, the claimed ELSA is not limited to require the property of “a maximum shared repeat length of 20 nucleotides or less” throughout the more than one nucleotide sequences it comprises. ELSA is broadly interpreted to require at least one nucleotide sequence encoding a sgRNA with the property of a maximum shared repeat length of 20 or less. A narrower interpretation wherein the claimed ELSA has the recited maximum shared repeat length over the entire sequence i.e. “ELSA with a maximum shared repeat length” throughout the more than one nucleotide sequences it comprises is also used for art rejection below.
Claim 3 requires the ELSA of claim 1 to comprise nucleotide sequences “for expression of at least 5 sgRNAs”. Claim 3 does not limit the “nucleotide sequences encoding two or more sgRNA” of claim 1, thus claim 3 is broadly interpreted to recite additional nucleotide sequences that allow for expression of at least 5 sgRNAs.
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.
Claims 1-5 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites nucleic acid molecules that embrace both RNA and DNA molecules. The sgRNA of claim 1 is broadly interpreted to embrace crRNAs (see Claim interpretation above). The claim requires the sequences encoding the sgRNA and the sgRNA handle to be ‘operable linked’. An ‘operable linkage’ between crRNAs (=embraced by claimed sgRNA) and tracrRNA (=claimed sgRNA handle sequence) is known for RNA molecules (for example: these sequences operably link to target Cas enzyme to a target sequence). However, it is unclear how these sequences are ‘operably linked’ when these sequences are DNA molecules, such as in claim 4 and 5. In other words, the operational relationship between sgRNA and the sgRNA handle sequences is unclear in situations these sequences are DNA sequences. Furthermore, the structure that allows for such an operational relationship is unclear. This is especially essential for claims 4 and 5 that implicitly limit the nucleic acid molecule of claim 1 to DNA molecule (see Claim interpretation above).
Claim 2-5 is/are rejected due their dependence on claim 1 because they do not clarify the 112b issue noted with claim 1.
Claim 4 recites the limitation "sgRNA promoter sequences" in line 2. There is insufficient antecedent basis for this limitation in the claim. Claim 4 depends from claim 1 that recites sgRNA promoter. It is unclear if the sgRNA promoter sequences of claim 4 that are required to be comprised in the ELSA of claim 1 are the same as or different from the sgRNA promoters of claim 1 that are not required to be comprised in ELSA but are required to control the expression of the nucleotide sequences encoding the sgRNAs. For the purpose of compact prosecution, the claim(s) 4 is/are interpreted as “wherein the comprise sequences selected from the group consisting of SEQ ID NO:1-64”.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 3 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Subject Matter Eligibility Guidance: A three-part inquiry has been established to determine subject matter eligibility under 35 U.S.C. 101 for process claims that involve laws of nature. See Subject Matter Eligibility Guidance. This inquiry comprises answering: 1) Is the claimed invention directed to one of the four statutory patent-eligible subject matter categories: process, machine, manufacture, or composition of matter? 2A) Does the claim recite or involve one or more judicial exceptions? Judicial exceptions include abstract ideas, laws of nature/natural principles, natural phenomena, and natural products. 2B) Does the claim as a whole recite something significantly more than the judicial exception(s)?
Claim Interpretation: With respect to claims 1-3, a detailed claim interpretation is provided above. Briefly, applicant' s invention is interpreted as comprising nucleotide sequences that encode two or more sgRNAs for claim 1 and at least 5 sgRNAs for claim 3, wherein at least one of the nucleotide sequences has a specific property of “a maximum shared repeat length of 20 nucleotides or less” which is interpreted based on the description provided on page 30 of the specification. Claim 2 recites “a maximum shared repeat length of 12 nucleotides or less”.
The sgRNAs of the claims that are encoded by the nucleotide sequences are broadly interpreted to embrace crRNA, short gRNA, synthetic gRNA or single guide RNA with crRNA and tracrRNA combined.
For the purpose of the U.S.C. 101 analysis, claims 1-3 embrace nucleic acid molecules that comprise an array of nucleotide sequences that encode at least 2-5 crRNAs wherein each nucleotide sequence does not comprise repeat subsequences with length greater than the maximum allowed (shared repeat length) or wherein all the nucleotide sequences together do not comprise repeat subsequences with length greater than the maximum allowed. Although claim 1 does recite sgRNA promoters and sgRNA handle sequences, the claimed nucleic acid product is not required to comprise the sgRNA promoters and sgRNA handle sequences.
Analysis in View of Claim Interpretation and Subject Matter Eligibility Guidance
1) Statutory Subject Matter: Claims 1-3 are directed to A nucleic acid molecule, which is a product. Therefore, claims 1-3 are directed to statutory subject matter.
2A) Judicial Exception:
(i) Does the claim recite a judicial exception? Claims 1-3 recite a judicial exception because the claims are directed to a nature-based product of an array of nucleotide sequences encoding crRNA. Such sequence arrays are found naturally in bacterial genomes. Wright et al (Cell 164, January 14, 2016) provide a review of bacterial CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) adaptive immune systems (Abstract). They teach that “CRISPR-Cas systems are generally defined by a genomic locus called the CRISPR array, a series of ~20–50 base-pair (bp) direct repeats separated by unique ‘‘spacers’’ of similar length and preceded by an AT-rich ‘‘leader’’ sequence” (Introduction, para 2). Thus, the naturally occurring CRISPR arrays in bacterial genomes comprise nucleotide sequences that each encode a crRNA (spacer + direct repeat) (see Figure 1). Further, bacterial genomes transcribe these DNA arrays into RNA array such that an RNA array of nucleotide sequences encoding crRNA is also naturally occurring. The multiple spacer sequences in any CRISPR array are unique such that the maximum shared repeat length between the spacers is less than 12 nucleotides. The direct repeat sequences comprised in CRISPR arrays comprise some repeat subsequence however the length of the repeated subsequence is less than 12 nucleotides in some bacteria. For example see Figure S3 in Jinek et al (Science, Vol. 337, 2012, 816-821) that shows the sequence for direct repeat in crRNA of S.pyogenes (shown in red highlight) that does comprise a repeating motif of “GUUUU” but this is smaller than 12 nucleotides. Lin et al (Molecular Therapy Vol. 26 No 11 November 2018) shows the sequence for the 19nt direct repeat in crRNA of F. novicida (shown in green and yellow highlight in Figure 1) that does not comprise a repeating motif. Thus, F. novicida CRISPR array comprises unique spacers and less than 20nt direct repeat resulting in an array that has less than 20 maximum shared repeat length over its entire length.
Thus, the claimed array of nucleotide sequences encoding crRNA are naturally-occurring sine they embrace naturally occurring bacterial CRISPR arrays. The recited property of claimed nucleotide sequences i.e. wherein each nucleotide sequence does not comprise repeat subsequences with length greater than 12 or 20 nucleotides or wherein all the nucleotide sequences together do not comprise repeat subsequences with length greater than the 20 nucleotides is also found in some natural CRISPR arrays.
(ii) Does the claim recite additional elements that integrate the judicial exception into a practical application? Claims 1-3 do not recite additional elements that integrate the judicial exception into a practical application. The additional elements recited in the claims, but not structurally part of the claimed product, are sgRNA promoters that control the expression of the array of nucleotide sequences encoding the crRNA and sgRNA handle sequences that operationally link with the nucleotide sequences encoding the crRNA. Both promoters and handle sequences (=tracr sequences, serves as a binding scaffold for the Cas nuclease) are also naturally occurring in bacterial genomes. See Figure S1 in Jinek that shows the S.pyogenes CRISPR array with the tracr sequence (in red) and promoter (black arrows). Even inclusion of these additional elements in the structure of the claimed nucleic acid would not be distinguishable from a natural CRISPR array. Thus, the additional elements do not integrate the judicial exception into a practical application.
2B) Significantly More: The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional elements are naturally occurring in CRISPR arrays. An inventive concept "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself." Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016).
Summary
On balance the relevant factors weigh against eligibility and claims do not qualify as eligible subject matter under 35 U.S.C. § 101.
Claim Rejections - 35 USC § 112
Claims 4, 5 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
Members of a Markush group share a "single structural similarity" when they belong to the same recognized physical or chemical class or to the same art-recognized class. A recognized physical class, a recognized chemical class, or an art-recognized class is a class wherein there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention. In other words, each member could be substituted one for the other, with the expectation that the same intended result would be achieved.
The Markush grouping of SEQ ID NOs: 1-64 in Claim 4 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: The recited SEQ ID NOs: 1-64 do not belong to an art-recognized class (physical, chemical or otherwise) because these sequences were not known in the art and thus there was no expectation regarding the function of these sequences. Furthermore, although the specification classifies these sequences as promoter, a substantial structural similarity is lacking across these sequences. A comparison of SEQ ID NO: 1 with some of the other sequences such as SEQ ID NOs: 2-5 and 26, 29 and 65 results in only about 22-47% query match. See exemplar sequence alignment below between SEQ ID No: 1 and
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191
757
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SEQ ID NO: 64.
There is no disclosed structure across each of these claimed sequences that the common use of “promoter” is expected to flow from. Considering that these sequences are substantially different from each other, no common sequence could be identified that could be considered the source of a common function. Finally, although the specification does not clearly identify which of these claimed sequences are related to the sequences tested in the examples, at least Figure 2A shows that the variants tested were not equivalent.
The Markush grouping of SEQ ID NOs: 65-118 in claim 5 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: The recited SEQ ID NOs: 65-118 do not belong an art-recognized class (physical, chemical or otherwise) because only SEQ ID NO: 65 was known in the art as a Cas9 sgRNA handle sequence. See for example SEQ 159 in Zhang et al (US 2016/0340660 A1, Nov. 24, 2016; Sequence alignment in PTO-892 with additional references also using SEQ 65). The remainder of the claimed sequences (SEQ ID NO: 66-118) were not known in the art and thus there was no expectation regarding the function of these sequences. Furthermore, although the specification classifies these sequences as sgRNA handle sequences, a substantial structural similarity is lacking across these sequences. A comparison of SEQ ID NO: 65 with some of the other sequences such as SEQ ID NOs: 66, 67, 99, 117 and 118 results in only about 48-75% query match. See exemplar sequence alignment below between SEQ ID No: 66 and SEQ ID NO: 118 which shows only 32.1% query match.
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196
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There is no disclosed structure across each of these claimed sequences that the common use of “sgRNA handle” is expected to flow from. Considering that these sequences are substantially different from each other, no common sequence could be identified that could be considered the source of a common function. Finally, although the specification does not clearly identify which of these claimed sequences are related to the sequences tested in the examples, at least Figure 3B shows that the variants tested were not equivalent.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
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.
Claim(s) 1-3 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tsai et al (WO 2015/099850 A1, July 2, 2015).
Regarding claims 1 and 2 , Tsai discloses a DNA molecule (=claimed nucleic acid) comprising a plurality of nucleotide sequences encoding guide RNAs (=claimed nucleotide sequences encoding two or more sgRNA sequences, =claimed ELSA) (page 2, paras 3, 4; page 4, last para, Figure 1).
Tsai discloses the DNA molecule is operably linked to a promoter (=claimed each sgRNA encoding nucleotide sequence is under the control of a sgRNA promoter).
Tsai discloses the DNA molecule wherein the sgRNA can be either a single guide RNA comprising a fused tracrRNA and crRNA or can be just a crRNA with the tracr RNA expressed from the same or different DNA molecule, wherein tracrRNA serves the purpose of operationally linking the crRNA to the Cas enzyme (=claimed operably linked sgRNA handle sequence; see interpretation presented in 112b rejection above) (page 2, paras 3, 4; page 4, last para, Figure 1).
Tsai discloses sgRNA sequences with the combined tracrRNA and crRNA sequences of various lengths for use in their DNA molecule. SEQ ID NO:5 is a sgRNA with 17-20nt spacer and 12nt repeat sequence (page 8). Use of sgRNA-encoding sequence complementary to SEQ ID NO:5 in Tsai’s DNA molecule inherently results in “the plurality of sequences encoding guide RNAs” (i.e. ELSA) to have a maximum shared repeat length of 12nt over the entire length of the “the plurality of sequences encoding guide RNAs” (i.e. ELSA) (as required by claim 1 and 2; see both the broad and the narrow interpretation presented in claim interpretation above for maximum shared repeat length).
Regarding claim 3, Tsai discloses DNA molecule with five sgRNA (page 3, line 11).
Therefore, Tsai anticipates the claimed invention.
Claim(s) 1-3 is/are rejected under 35 U.S.C. 102(a)(1) as anticipated by Abuddayeh et al (Science, Vol. 353, Issue 6299, 2016) as evidenced by Stuber et al (PNAS, Vol. 78, No.167-171, Jan 1981)
Regarding claim 1 and 2, Abuddayeh discloses a plasmid (=claimed nucleic acid) comprising the natural L. Shahii CRISPR array wherein the wildtype spacer sequences are replaced with unique synthetic spacer sequences and thus Abuddayeh’ plasmid comprises nucleotide sequences that encode a plurality of crRNAs (=claimed nucleotide sequences encoding two or more sgRNA sequences, =claimed ELSA; see interpretation presented in claim interpretation above for sgRNA) (SUPPLEMENTARY MATERIALS AND METHODS: Cloning of C2c2 locus and screening libraries for MS2 activity Screen).
Abuddayeh’s plasmid pACYC184 comprises promoters for the expression of the introduced sequence, as evidenced by Stuber Figure 3 that shows the promoters in pACYC184. Thus Abuddayeh nucleotide sequences encoding crRNA are operably linked to a promoter (=claimed each sgRNA encoding nucleotide sequence is under the control of a sgRNA promoter’; see interpretation presented in claim interpretation above for sgRNA promoters). This is also evident from the fact that the crRNA is expressed and functional (Figure 1B, 1E).
Abuddayeh’s nucleotide sequences encodes crRNA which comprise a spacer sequence followed by the wild type direct repeats because only wild type spacers in the L. shahii CRISPR array were replaced with the unique synthetic spacer sequences (SUPPLEMENTARY MATERIALS AND METHODS: Cloning of C2c2 locus and screening libraries for MS2 activity Screen). The direct repeats serves the purpose of operationally linking the crRNA to the Cas enzyme (=claimed operably linked sgRNA handle sequence wherein the handle sequence “serves as a binding scaffold for the Cas nuclease”; see claim interpretation presented above; see Figures 7, S16 and S17 in Abuddayeh).
Regarding the maximum shared repeat length, Abuddayeh nucleotide sequences encoding crRNA each are sequences with less than 12nt maximum shared repeat length because each nucleotide sequence encoding a crRNA comprises a 28nt spacer with less than 12nt maximum shared repeat length and a 24nt direct repeat with less than 12nt maximum shared repeat length (see Figure S16 for the sequence of L. shahii crRNA spacer and direct repeat). Therefore, Abuddayeh discloses nucleotide sequences encoding crRNA wherein each nucleotide sequence has a maximum shared repeat length of 12nt (see the broad interpretation presented in claim interpretation above for maximum shared repeat length).
Regarding claim 3, Abuddayeh discloses plasmid with 3473 unique spacers i.e. greater than five sgRNA (page aaf5573-1, col. 3, para 3).
Therefore, Abuddayeh anticipates the claimed invention.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1-3 is/are rejected under 35 U.S.C. 103 as being unpatentable over Abuddayeh et al (Science, Vol. 353, Issue 6299, 2016) as evidenced by Stuber et al (PNAS, Vol. 78, No.167-171, Jan 1981).
The following rejection uses the narrower interpretation presented in claim interpretation above for maximum shared repeat length.
Regarding claim 1 and 2, Abuddayeh teaches a plasmid (=claimed nucleic acid) comprising the natural L. Shahii CRISPR array wherein the wildtype spacer sequences are replaced with unique synthetic spacer sequences and thus Abuddayeh’ plasmid comprises nucleotide sequences that encode a plurality of crRNAs (=claimed nucleotide sequences encoding two or more sgRNA sequences, =claimed ELSA; see interpretation presented in claim interpretation above for sgRNA) (SUPPLEMENTARY MATERIALS AND METHODS: Cloning of C2c2 locus and screening libraries for MS2 activity Screen).
Abuddayeh’s plasmid pACYC184 comprises promoters for the expression of the introduced sequence, as evidenced by Stuber Figure 3 that shows the promoters in pACYC184. Thus Abuddayeh nucleotide sequences encoding crRNA are operably linked to a promoter (=claimed each sgRNA encoding nucleotide sequence is under the control of a sgRNA promoter’; see interpretation presented in claim interpretation above for sgRNA promoters). This is also evident from the fact that the crRNA is expressed and functional (Figure 1B, 1E).
Abuddayeh’s nucleotide sequences encoding crRNA comprise a spacer sequence followed by the wild type direct repeats because only wild type spacers in the L. shahii CRISPR array were replaced with the unique synthetic spacer sequences (SUPPLEMENTARY MATERIALS AND METHODS: Cloning of C2c2 locus and screening libraries for MS2 activity Screen). The direct repeats serves the purpose of operationally linking the crRNA to the Cas enzyme (=claimed operably linked sgRNA handle sequence wherein the handle sequence “serves as a binding scaffold for the Cas nuclease”; see claim interpretation presented above; see Figures 7, S16 and S17 in Abuddayeh).
Regarding claim 3, Abuddayeh discloses plasmid with 3473 unique spacers i.e. greater than five sgRNA (page aaf5573-1, col. 3, para 3
Regarding the maximum shared repeat length wherein the nucleotide sequences encoding a plurality of crRNA together have a maximum shared repeat length of less than 20 or 12, Abuddayeh teaches nucleotide sequences encoding crRNA with a 28nt spacer and a 24nt direct repeat (see Figure S16 for the sequence of L. shahii crRNA spacer and direct repeat). Abuddayeh also teaches different spacer sequences as well as different direct repeat sequences (Figure S16-S18; Table S1).
Although, Abbudayyeh does not explicitly teach a nucleotide sequences encoding crRNA with different direct repeat sequences such that the nucleotide sequences encoding a plurality of crRNA together have a maximum shared repeat length of less than 20 or 12, Abudayyeh teaches several direct repeat sequences with mutations, especially insertion and substitution mutations, with different levels of cleavage activity which when incorporated in their nucleic acid molecule would result in fewer than 12 repeated nucleotides (Figure S17). They suggest that these results have implications for applications that require guide engineering for modulation of activity (page 11f5573-6, para 1) thus motivating an ordinary artisan to pick and choose different direct repeat sequences to achieve different levels of cleavage activity at the different sgRNA target sites. Therefore, it would be obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify Abudayyeh’s nucleotide sequences encoding crRNA to comprise distinct direct repeat sequences based on the desired cleavage activity at the crRNA target site. An ordinary artisan would reasonably expect such a substitution of direct repeats in a crRNA array would result in crRNAs wherein the direct repeats would perform the function as taught by Abudayyeh.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in
the art at the effective time of filing of the invention, especially in the absence of evidence to the
contrary.
Conclusion
No claim is allowed.
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/MATASHA DHAR/Examiner, Art Unit 1632