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 .
Applicants Reply, filed on 07/07/2026 is hereby acknowledged.
Claims 5 and 20-28 are pending and examined herein on the merits.
Claim Rejections - 35 USC § 112
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.
Claims 5 and 20-28 remain rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claims contain 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 at the time the application was filed, had possession of the claimed invention.
The claims are drawn to a very large genus of molecules comprising any hybrid nucleic acid sequence and any Cpf1 polypeptide wherein these elements are associated in any functional way wherein the hybrid nucleic acid is DNA and RNA wherein the DNA is a repair template nucleic acid sequence wherein the hybrid nucleic acid is in the form of a non-vector connected single-stranded or double stranded nucleic acid.
The claims are further drawn to plants, plant cells, derivatives or progeny thereof, wherein the plants are from a substantially large list of different species such as in claim 23. All claims require the genus of molecules instantly claimed. The claims encompass a near limitless and certainly numbering in the billions of embodiments wherein literally ANY DNA target sequence, and literally ANY second DNA target sequence is encompassed. In addition to combinations of any target sequences across multiple species, the claims also encompass at least thousands of Cpf1 polypeptides from thousands of species. When considering that the polypeptide is of unspecified length and function, this becomes millions of different polypeptides. It is noted that the instant claims are product claims and as such require adequate written description in the specification over their entire breadth.
In contrast, the specification does not reduce to practice any such molecules with Cpf1 as instantly claimed, nor does the specification describe an adequate number of CPF1 nucleic acids or describe any consensus sequences or motifs that must be retained to be considered a CPF1 for use with the instant invention. The specification does provide some specific examples of target DNA, but does not describe any other DNA targets for use with the instant invention.
The Federal Circuit has clarified the application of the written description requirement. The court stated that a written description of an invention “requires a precise definition, such as by structure, formula, [or] chemical name, of the claimed subject matter sufficient to distinguish it from other materials.” University of California v. Eli Lilly and Co., 119 F.3d 1559, 1568; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997). The court also concluded that “naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not a description of that material.” Id. Further, the court held that to adequately describe a claimed genus, Patent Owner must describe a representative number of the species of the claimed genus, and that one of skill in the art should be able to “visualize or recognize the identity of the members of the genus.” Id. This applies to Cpf1 molecules in particular.
Finally, the court held:
A description of a genus of cDNAs may be achieved by means of a recitation of a representative number of cDNAs, defined by nucleotide sequence, falling within the scope of the genus or a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus. Id.
See also MPEP section 2163, page 174 of chapter 2100 of the August 2005 version, column 1, bottom paragraph, where it is taught that
[T]he claimed invention as a whole may not be adequately described where an invention is described solely in terms of a method of its making coupled with its function and there is no described or art-recognized correlation or relationship between the structure of the invention and its function. A biomolecule sequence described only by a functional characteristic, without any known or disclosed correlation between that function and the structure of the sequence, normally is not a sufficient identifying characteristic for written description purposes, even when accompanied by a method of obtaining the claimed sequence.
See also Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ 2d 1016 at 1021, (Fed. Cir. 1991) where it is taught that a gene (is not reduced to practice until the inventor can define it by "its physical or chemical properties" (e.g. a DNA sequence).
Given the claim breadth and lack of guidance as discussed above, the specification fails to provide an adequate written description of the genus of sequences as broadly claimed. Given the lack of written description of the claimed genus of sequences, any method of using them, such as transforming plant cells and plants therewith, and the resultant products including the claimed transformed plant cells and plants containing the genus of sequences, would also be inadequately described. Accordingly, one skilled in the art would not have recognized Applicant to have been in possession of the claimed invention at the time of filing. See the Written Description Requirement guidelines published in Federal Register/ Vol. 66, No. 4/ Friday January 5, 2001/ Notices: pp. 1099-1111.
Response to Arguments
Applicant's arguments filed 07/07/2026 have been fully considered but they are not persuasive.
Applicants urge that the claims have been amended to limit the sequences to plants and to nucleic acids of interest located in loci associated with a number of processes.
This is not persuasive because the claims are drawn to products that must be described by structure, and the scope of the claims is still nearly limitless in at least regard to the sequence of interest, but additionally still incorporates numerous Cpf1 encoding nucleic acids from numerous species with no limitations with regard to sequence.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 5 and 20-28 remain rejected under 35 U.S.C. 103 as being unpatentable over Cong et al (US Patent 8932814 published 01/13/2015) in view of Kennedy et al (USPGPUB 20170058298, effectively filed on 08/31/2015), and in view of Zetsche et al (2015 Cell 163:759-771).
The claims are drawn to a hybrid nucleic acid sequence comprising at least one RNA nucleic acid sequence, at least one DNA nucleic acid sequence, and a CRISPR nucleic acid sequence wherein the sequence is Cpf1, comprising at least one RNA nucleic acid sequence, wherein the CRISPR nucleic acid sequence comprises a first sequence portion that is complementary to a first DNA target sequence, and a second sequence portion wherein the second sequence portion is configured to interact with a CRISPR polypeptide, a repair template nucleic acid comprising a DNA nucleic acid sequence wherein the repair template comprises a portion complementary to a second DNA target sequence wherein the repair template nucleic acid is configured to mediate targeted homology directed repair and plants and plant cells comprising same.
Cong et al teach a method of altering gene expression comprising introducing into a eukaryotic cell containing and expressing a DNA molecule having a target sequence and encoding a gene product an engineered, synthetic CRISPR-CRISPR associated system comprising a first regulatory element operable in a eukaryotic cell operably linked to at least one nucleotide sequence encoding a CRISPR-Cas system guide RNA that hybridizes with the target sequence wherein a homologous recombination template is inserted and two sites are altered meeting the limitation of a second target site where the recombination template is inserted (see claims 1-3) and wherein the guide RNA is an RNA, the system and therefore the hybrid nucleic acid sequence (see claim 25), wherein the Cas polypeptide is from Streptococcus pyogenes (see claim 27), wherein the nucleic acid is attached to the 5’ or 3’ end of the CRISPR encoding nucleic acid (see figures, particularly 43 A-D) and a linker sequence (see paragraph discussing CRISPR as a fusion protein complete with selective markers so that the modification is selected as required by the instant claims) wherein the target sequence is an agronomic trait (see paragraph that begins “With recent advances in crop genomics..”) wherein the traits are incorporated by reference wherein the trait is modified in micro-algae which is included in the instant specification as meeting the definition of a plant or plant cell (see Example 15).
Cong et al do not explicitly state wherein RNA elements are attached to DNA elements nor do Cong et al teach the specified plant species other than micro algae or Cpf1.
Kennedy et al teach tethering the guide-RNAS to the translated Cas9 protein for increased efficiency in bringing the repair template in proximity to the target site using hybrid molecules (see 4th paragraph and 6th paragraph under background of invention and Figures 4-6, for example) for use in a plant cell (see first paragraph under “Genome Editing”)..
Zetsche et al teach using the Cpf1 as a nuclease, that it might be preferred to other CRISPR nucleases, and as indicated in the instant specification is interchangeable with other CRISPR nucleases.
Given the state of the art, the disclosures by Cong et al, Kennedy et al, and Zetsche et al it would have been obvious to modify the system taught by Cong et al as was known in practice in mammalian systems in view of Kennedy et al to utilize RNA-DNA hybrid molecules for use in plants and use Cpf1 as taught and suggested by Zetsche et al. Due to the generic nature of the claimed molecules in that any Cpf1 and any target sequence is envisioned, the plant species specified in claims 24 and 28 would have been obvious design choices for one of skill in the art
No claims are allowed.
Response to Arguments
Applicant's arguments filed 07/07/2026 have been fully considered but they are not persuasive.
Applicants urge that the tethering system that is instantly claimed differs from the tethering system disclosed by Cong et al and is patentably distinct from the disclosed system in that the disclosed system is silent on the repair template being tethered to the RNA component, and further urge that Cong et al teaches their system for use with Cas9 not Cpf1.
This is not persuasive because Cong et al are not being cited to teach each and every element of the instant claims wherein it would qualify as anticipatory art applicable under 35 USC 102. Rather, the instant rejection is a combination of references.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
In the instant case, Cong et al establishes that tethering systems for Crispr systems were known and taught in the prior art. Kennedy et al establishes numerous options for said tethering systems and Zetsche both teach and suggest using Cpf1 instead of Cas9 which provided the motivation for altering the system taught by Cong et al for use with Cpf1 as in the instant invention.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRENT T PAGE whose telephone number is (571)272-5914. The examiner can normally be reached M-F 7-4 EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached at 5712707058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BRENT T PAGE/Primary Examiner, Art Unit 1663
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