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 .
Status of the Claims
The amendments and arguments filed 30May2024 are acknowledged and have been fully considered. Claims 18, 20, 22-36, 38-65, 67-86 are canceled. Claims 1-17, 19, 21, 37, 66, 87-89 are pending. Claims 1-17 and 87-89 are original. Claims 19, 21, 37, 66 are currently amended.
Claims 1-17, 19, 21, 37, 66, 87-89 are examined on the merits herein.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) [US provisional 62580394 filed 01November2017], 35 U.S.C. 365(c) [national stage entry of PCT/US2018/058529 filed 31October2018], and 35 U.S.C. 120 [continuation of Appl. No. 16755535, now US Pat. 11970719, filed 10April2020].
Please note that the claims require both a CasY15 protein (comprising a sequence with at least 90% sequence identity to SEQ ID NO: 57, see part (a) of claim 1) and an RNA molecule, i.e. a trancRNA/scoutRNA molecule (comprising a sequence with at least 98% sequence identity to SEQ ID NO: 273, see part (c) of claim 1). While CasY15 comprising SEQ ID NO: 57 is described within the priority provisional application, the trancRNA/scoutRNA molecule comprising SEQ ID NO: 273 is not. Therefore, the effective priority date of these claims is that of the nonprovisional international application PCT/US2018/058529 (which does describe the trancRNA/scoutRNA molecule comprising SEQ ID NO: 273 as well as its use with a CasY15 protein comprising SEQ ID NO: 57).
Claims 1-17, 19, 21, 37, 66, 87-89 have an effective filing date of 31October2018.
Comment on Claims Terms
For the sake of a clear record, the Office notes the following:
The claims of record in this application were filed after substantive examination of the claims of parent application 16755535. The claims here were thoughtfully drafted so that they align to the format of the allowed claims of 16755535 (now US Pat. No. 11970719). Therefore, certain objections or rejections within the file for 16755535 are not made here because Applicant has proactively ensured that they are not relevant here.
Further to the comment above, please note that the “RNA molecule” of these claims (see part (c) of claim 1) is a “trancRNA” molecule (also referred to as a “scoutRNA” molecule per ¶328 on page 116). The claims of parent application 16755535 (now US Pat. No. 11970719) refer to “trancRNA” and the art sometimes refer to these molecules as “scoutRNA”1.
Given the sequence/structural limitations of the “CasY” protein of these claims, the CasY protein here is interpreted to be a CasY15 protein (also referred to as a “Cas12d15” protein in the art, see e.g. US20240067954 which describe SEQ ID NO: 59 thereof as “dCas12d15”—please note that their SEQ ID NO: 59 has 99.8% sequence identity to this application’s SEQ ID NO: 572).
Please note that the sequence SEQ ID NO: 273 (recited at claim 1) is a 50 nucleotide-long subsequence within the sequence 70 nucleotide-long sequence SEQ ID NO: 275 (recited at claims 88-89).
Specification
The disclosure is objected to because of the following informalities: the reference to “Table 3” at ¶656 on page 195 and ¶691 on page 211 of the specification appears to be a typographical error. Should the references there be to Table 5 instead of Table 3? Please note that Table 3 regards CasY15 molecules whereas the cited sections of the specification and Table 5 regard CasY14 molecules.
Appropriate correction is required.
Claim Objections
Claim 37 is objected to because of the following informalities: claim 37 recites “a detector DNA that is single stranded”. The concept of a “detector DNA” is only mentioned once within the specification (see ¶180 on page 67) and lacks a well-understood meaning within the art. However, it is believed that the concept may be used within the claims in a manner that a person with ordinary skill in the art may understand it such as by not only explaining that it is single stranded, but also explaining that it is “labeled”. To ensure clarity of claim 37, and for consistency with the language of claim 66, please amend claim 37 as follows: “… a labeled detector DNA that is single stranded and….” Appropriate correction is required.
Claim Rejections - 35 USC § 112 - Indefiniteness
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 37 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.
The phrase “the Class 2 CRISPR/Cas effector protein” lacks antecedent basis in the claim. Perhaps Applicant intended to recite “the CasY protein”?
Claim Rejections - 35 USC § 112 – Written Description
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 1-17, 19, 21, 37, 66, 87-89 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.
All claims (via reference to claim 1) currently recite a CasY protein comprising an amino acid sequence with at least 90% sequence identity to SEQ ID NO: 57. The sequence SEQ ID NO: 57 is a CasY15 protein.
With this application (via priority provisional application 62580394), Applicant appears to be the first to describe a CasY15 protein structure/sequence. However, the only CasY15 amino acid sequence described is SEQ ID NO: 57—there is no information within the specification as to how one may modify SEQ ID NO: 57 and maintain CasY15 function. For context, SEQ ID NO: 57 is 1258 amino acids long. This means that a sequence having 90% sequence identity to SEQ ID NO: 57 has about 127 changes with respect to SEQ ID NO: 57 (.9 x 1258 = 1132.2 or about 1133 identical residues; 1258-1133 = 127).
Neither this specification nor the prior art describes even one amino acid change (the nature of the change as well as its location) within the CasY15 sequence SEQ ID NO: 57 that may be made without disrupting CasY15 functionality. It follows that as many as 127 changes are certainly not described.
Without more information, a skilled artisan at the time this application was filed would not reasonably recognize Applicant as having possession of the full metes and bounds of what is claimed (namely, the full metes and bounds of structures/sequences being claimed without impacting CasY15 function).
It would be remedial of this rejection to amend “90%” at claim 1 part (a) to “95%”.
Claim Rejections - 35 USC §§ 101 & 112 - Utility
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.
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.
Claim 21 is rejected under 35 U.S.C. 101 because the claimed invention is not supported by either a specific and substantial asserted utility or a well-established utility.
Claim 21 is directed toward a eukaryotic cell comprising at least one of the CasY protein from claim 1, the CasY guide RNA from claim 1, or the RNA molecule of claim 1.
While it is clear from the specification, and well-understood in the art, how a skilled artisan may use a eukaryotic cell comprising all three of the CasY protein, CasY guide RNA, and RNA molecule from claim 1; there is no clear specific and substantial use of a eukaryotic cell that only comprises a CasY protein, or of a eukaryotic cell that only comprises a CasY guide RNA, or of a eukaryotic cell that only comprises an [tranc/scout] RNA molecule. Based on the specification3 and art, it is believed that all three must be present for one such eukaryotic cell to have a specific and substantial use.
Absent evidence to the contrary, please amend claim 21 to something like: “… comprising
As summarized at MPEP § 2103 (I)(A): “the claimed invention as a whole must be useful. The purpose of [the Utility] requirement is to limit patent protection to inventions that possess a certain level of ‘real world’ value, as opposed to subject matter that represents nothing more than an idea or concept, or is simply a starting point for future investigation or research” (internal citations omitted). See MPEP §§ 2164.01(c) and 2107.01-.03, e.g., 2107.02(III)(A) (“… a specification which contains a disclosure of utility which corresponds in scope to the subject matter sought to be patented must be taken as sufficient to satisfy the utility requirement of § 101 for the entire claimed subject matter unless there is a reason for one skilled in the art to question the objective truth of the statement of utility or its scope.”).
Claim 21 is also rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph. Specifically, because the claimed invention is not supported by either a specific and substantial asserted utility or a well-established utility for the reasons set forth above, one skilled in the art clearly would not know how to use the claimed invention. [← This is part of “Form Paragraph” 7.05.04, See MPEP § 2107.02]
Conclusion
The following is an examiner’s statement in support of indicating allowable subject matter: these claims appear to be free from the prior art at least because, with this application (via priority provisional application 62580394), Applicant appears to be the first to describe a specific CasY15 protein structure/sequence (in particular, a CasY15 protein having at least 95% sequence identity to the sequence SEQ ID NO: 57). Furthermore, with PCT/US2018/058529, Applicant appears to be the first to describe using one such CasY15 protein with a/an [trancRNA/scoutRNA] RNA molecule comprising a nucleic acid sequence with at least 98% sequence identity to the sequence SEQ ID NO: 273 (please note that the sequence SEQ ID NO: 273 is a 50 nucleotide-long subsequence within the sequence SEQ ID NO: 275 recited at claims 88-89, which is 70 nucleotides long).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Rebecca STEPHENS whose telephone number is (571)272-0070. The examiner can normally be reached Monday through Friday 8:30-4:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad ABRAHAM can be reached at (571) 270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/REBECCA STEPHENS/Examiner, Art Unit 1663
/MATTHEW R KEOGH/Primary Examiner, Art Unit 1663
1 See, e.g., HARRINGTON et al. 2020 Mol. Cell 79:416-424 (of record IDS 07June2024).
2 Per Result 3 of the ABSS sequence search results file “20250530_131934_us-18-618-668a-57.rapbm”.
3 See the specification at Figures 26-27 and Tables 3-4, as well as discussions thereof.