DETAILED ACTION
Status of the Application
Claims 1-15 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s election without traverse of Group 36, claims 9-11, drawn in part to a protein that comprises SEQ ID NO: 9, as submitted in a communication filed on 12/31/2025 is acknowledged.
Claims 1-8, 12-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/31/2025.
Claims 9-11 are at issue and will be examined only to the extent they encompass the elected invention.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. See page 6, line 14; page 9, line 15; page 10, line 35; page 33, line 10; page 36, line 2; and page 39, line 21. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code. See MPEP § 608.01.
The specification is objected for not complying with sequence rules. While Figure 4 display nucleotide sequences, neither the drawings nor the Brief Description of the Drawings indicate the corresponding sequence identifiers. Applicant is required to insert the corresponding sequence identifiers in the Brief Description of the Drawings or amend the drawings to include the sequence identifiers in front of each sequence. See particularly 37 CFR 1.821(d). Appropriate correction is required.
Priority
Acknowledgment is made of a claim for foreign priority under 35 U.S.C. 119(a)-(d) to EUROPEAN PATENT OFFICE (EPO) 21000063.4 filed on 03/02/2021. Receipt is acknowledged of papers submitted under 35 U.S.C. 119(a)-(d), which papers have been placed of record in the file.
This is the US national application which entered the national stage from PCT/EP2022/055257 filed on 03/02/2022
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 8/30/2023 is acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Drawings
The drawings submitted on 8/30/2023 have been reviewed and are accepted by the Examiner for examination purposes.
Claim Objections
Claims 9-11 are objected to due to their dependency on a claim directed to a non-elected invention (i.e., claim 1). For examination purposes, the claims will be interpreted as reciting the limitations of claim 1 whenever possible. Appropriate correction is required.
Claim Rejections – Improper Markush Grouping
Claims 10-11 are rejected on the basis that they contain 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 § 706.03(y).
Claims 10-11 are directed to a composition comprising a protein, a composition comprising a nucleic acid molecule, a composition comprising a host cell, a composition comprising a plant, a composition comprising a seed, a composition comprising a part of a cell, or a composition comprising part of an animal.
The Markush grouping of compositions in claims 10-11 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 compositions do not share a single structural similarity by virtue of comprising compounds having different structural and functional characteristics. A protein comprises amino acids, a nucleic acid comprises nucleotide bases, a plant and an animal are multicellular organisms, a cell is the basic structural and functional unit of an organism, and a seed is a plant structure that comprises a plant embryo. Furthermore, a protein, a nucleic acid, a plant, an animal, a cell and a seed have different functions and do not belong to a same recognized class. A protein can have enzymatic activity, a nucleic acid encodes a protein, a plant can be used to produce a fruit, a cell can be used to produce a protein, a seed can be used to produce a plant, and an animal can be used as a transgenic model. 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 § 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 9-11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature without significantly more. The claims recite in part a protein that comprises SEQ ID NO: 9, which is a naturally occurring product, a composition that comprises the polypeptide of SEQ ID NO: 9, a pharmaceutical composition that comprises the protein of SEQ ID NO: 9, and a diagnostic composition comprising the protein of SEQ ID NO: 9, which are not different from a generic aqueous composition comprising the protein of SEQ ID NO: 9, which is a naturally-occurring product. This judicial exception is not integrated into a practical application because the protein of SEQ ID NO: 9 is a naturally occurring protein called BMC09 as described in the specification which teaches that the proteins labeled BMC01-BMC15 polypeptides were isolated from environmental samples (paragraph [0026] of the specification), including bacterial metagenome samples (paragraph [0038] in the published application), the intracellular contents of the bacterial organism that endogenously produces the polypeptide of SEQ ID NO: 9 is a naturally-occurring composition that comprises the polypeptide of SEQ ID NO: 9, and a pharmaceutical/diagnostic composition as claimed merely places the product of nature into a generic environment and does not add a meaningful limitation. Furthermore, to the extent that the terms “pharmaceutical” and “diagnostic” convey additional limitations to a generic composition comprising the polypeptide of SEQ ID NO: 9 in that the composition is not toxic or detrimental to an animal or a human being, a composition comprising water and the polypeptide of SEQ ID NO: 9 would be considered non-toxic or detrimental to an animal or a human being and can be used in a diagnostic assay. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because a protein that comprises SEQ ID NO: 9 and a composition that comprises the polypeptide of SEQ ID NO: 9 are naturally occurring products and a composition that comprises water and the polypeptide of SEQ ID NO: 9, which is a composition that can be considered a pharmaceutical composition, or a diagnostic composition, does not add a meaningful limitation to the protein of SEQ ID NO: 9 since the presence of water simply provides an inert medium for the naturally occurring product and does not have any effect on the functional properties of the protein of SEQ ID NO: 9. As such, the claims encompass subject matter which is not patent-eligible.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
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 9-11 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 pre-AIA the applicant regards as the invention.
Claims 9-10 (claim 11 dependent thereon) are indefinite due to the recitation in claim 1 of “(c) …the amino acid sequence of which is at least 70% identical to the amino acid sequence of (a), preferably at least 80% identical, more preferably at least 90% identical, and most preferred at least 95% identical; (d) a nucleic acid molecule comprising …which is at least 70% identical to the nucleotide sequence of (b), preferably at least 80% identical, more preferably at least 90% identical, and most preferred at least 95% identical..” for the following reasons. It is unclear whether the limitations followed after the terms “preferably”, “more preferably”, and “most preferred” are part of the claimed invention. For examination purposes, no patentable weight will be given to the limitations that follow after the terms “preferably”, “more preferably”, and “most preferred”. Correction is required.
When amending the claims, applicant is advised to carefully review all examined claims and make the necessary changes to ensure proper antecedent basis and dependency.
Claim Rejections - 35 USC § 112(d) or Fourth Paragraph (pre-AIA )
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 9-11 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claims 9-11 are directed in part to a protein and a composition that comprises a protein, and depend from claim 1, which is directed to a different product, namely a nucleic acid molecule. Therefore, claims 9-11 fail to further limit the subject matter of the claim from which they depend because limitations associated with a protein and a composition comprising a protein cannot further limit a nucleic acid. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements. Correction is required.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
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 9-11 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
As stated in MPEP 2111.01, during examination, the claims must be interpreted as broadly as their terms reasonably allow. Claims 9-11 are directed in part to a genus of RNA-guided DNA endonucleases which are variants of the polypeptide of SEQ ID NO: 9 that have at least 70% sequence identity to the polypeptide of SEQ ID NO: 9, a genus of RNA-guided DNA endonucleases which are variants of the polypeptide of SEQ ID NO: 9 encoded by a polynucleotide having at least 70% sequence identity to the polynucleotide of SEQ ID NO: 24, and compositions comprising said RNA-guided DNA endonucleases. The polynucleotide of SEQ ID NO: 24 encodes the polypeptide of SEQ ID NO: 9. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation.
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “A written description of an invention involving a chemical genus, like a description of a chemical species, ‘requires a precise definition, such as by structure, formula, [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials”. As indicated in MPEP § 2163, the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that a representative number of species means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
There is a significant amount of structural variability with respect to the members of the genus of proteins required by the claims. While the specification in the instant application discloses the structure of a limited number of RNA-guided DNA endonucleases, it provides no clue as to the structural elements required in any RNA-guided DNA endonuclease, nor does it teach which structural elements of the proteins disclosed, including the protein of SEQ ID NO: 9, are required in any RNA-guided DNA endonuclease as claimed. No disclosure of a structure/function correlation has been provided which would allow one of skill in the art to recognize which variants of the polypeptide of SEQ ID NO: 9 having the recited % sequence identity have RNA-guided DNA endonuclease activity.
The claims encompass a large genus of proteins which are substantially unrelated in structure. A polypeptide having at least 95% sequence identity with the polypeptide of SEQ ID NO: 9 allows for any combination of 64 amino acid modifications within SEQ ID NO: 9 (64 = 0.05x1274; SEQ ID NO: 9 has 1274 amino acids). A polynucleotide having at least 95% sequence identity with the polynucleotide of SEQ ID NO: 24 allows for any combination of 192 nucleotide modifications within SEQ ID NO: 24 (192 = 0.05x3825; SEQ ID NO: 24 has 3825 nucleotides). Since each one of the 192 nucleotide modifications can alter one codon, a polynucleotide having at least 95% sequence identity with the polynucleotide of SEQ ID NO: 24 can encode a variant of the polypeptide of SEQ ID NO: 9 having 192 amino acid modifications within SEQ ID NO: 9. The total number of variants of a polypeptide having a specific number of amino acid substitutions can be calculated from the formula N!x19A/(N-A)!/A!, where N is the length in amino acids of the reference polypeptide and A is the number of allowed substitutions. Thus, the total number of variants of the polypeptide of SEQ ID NO: 9 that have at least 95% sequence identity to the polypeptide of SEQ ID NO: 9 that result from amino acid substitutions is 1274!x1964/(1274-64)!/64! or 5.87x10190 variants, while the total number of variants of the polypeptide of SEQ ID NO: 9 encoded by polynucleotides that have at least 95% sequence identity to the polynucleotide of SEQ ID NO: 24 that result from amino acid substitutions is 1274!x19192/(1274-192)!/192! or 3.74x10478 variants.
A sufficient written description of a genus of polypeptides may be achieved by a recitation of a representative number of polypeptides defined by their amino acid sequence or a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus. However, in the instant case, the recited structural feature, e.g., 70% sequence identity to SEQ ID NO: 9, 70% sequence identity to SEQ ID NO: 24, is not representative of all the members of the genus of RNA-guided DNA endonucleases recited since there is no information as to which are the structural elements within the polypeptide of SEQ ID NO: 9 that are essential for the recited activity, which are the remaining structural elements required in the recited polypeptides in addition to those recited in the claims such that the desired RNA-guided DNA endonuclease activity is displayed, or a correlation between structure and function which would provide those unknown structural features. Furthermore, while one could argue that the few species disclosed are representative of the structure of all the members of the genus, it is noted that the art teaches several examples of how even highly structurally homologous polypeptides can have different enzymatic activities. For example, Witkowski et al. (Biochemistry 38:11643-11650, 1999) teach that one conservative amino acid substitution transforms a β-ketoacyl synthase into a malonyl decarboxylase and completely eliminates β-ketoacyl synthase activity. Tang et al. (Phil Trans R Soc B 368:20120318, 1-10, 2013) teach that two Dehalobacter reductive dehalogenases, CfrA and DcrA, having 95.2% sequence identity to teach other have exclusively different substrate (Abstract; page 7, left column, Discussion, CfrA and DcrA). Seffernick et al. (J. Bacteriol. 183(8):2405-2410, 2001) teach that two naturally occurring Pseudomonas enzymes having 98% amino acid sequence identity catalyze two different reactions: deamination and dehalogenation, therefore having different function. Therefore, since minor structural differences may result in changes affecting function, and no additional information correlating structure with the desired functional characteristics has been provided, one cannot reasonably conclude that the few species disclosed are representative of the structure of all the RNA-guided DNA endonucleases claimed.
Due to the fact that the specification only discloses a limited number of species of the genus of RNA-guided DNA endonucleases required by the claims, and the lack of description of any additional species by any relevant, identifying characteristics or properties, one of skill in the art would not recognize from the disclosure that Applicant was in possession of the claimed invention.
Claims 9-11 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the protein of SEQ ID NO: 9 and a composition comprising the protein of SEQ ID NO: 9, does not reasonably provide enablement for a protein which is a variant of the polypeptide of SEQ ID NO: 9, or a composition comprising said variant. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2nd 1400 (Fed. Cir. 1988)) as follows: 1) quantity of experimentation necessary, 2) the amount of direction or guidance presented, 3) the presence and absence of working examples, 4) the nature of the invention, 5) the state of prior art, 6) the relative skill of those in the art, 7) the predictability or unpredictability of the art, and 8) the breadth of the claims. The factors which have led the Examiner to conclude that the specification fails to teach how to make and/or use the claimed invention without undue experimentation, are addressed in detail below.
The breadth of the claims. Claims 9-11 broadly encompass RNA-guided DNA endonucleases which are variants of the polypeptide of SEQ ID NO: 9 that have at least 70% sequence identity to the polypeptide of SEQ ID NO: 9, RNA-guided DNA endonucleases which are variants of the polypeptide of SEQ ID NO: 9 encoded by a polynucleotide having at least 70% sequence identity to the polynucleotide of SEQ ID NO: 24, and compositions comprising said RNA-guided DNA endonucleases. The polynucleotide of SEQ ID NO: 24 encodes the polypeptide of SEQ ID NO: 9. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation.
The enablement provided is not commensurate in scope with the claims due to the lack of information regarding the structural elements within the polypeptide of SEQ ID NO: 9 which are required and those which can be modified to obtain the extremely large number of variants having RNA-guided DNA endonuclease activity required by the claims. In the instant case, the specification enables the protein of SEQ ID NO: 9 and a composition comprising said protein.
The amount of direction or guidance presented and the existence of working examples. The specification discloses the amino acid sequence of a limited number of RNA-guided DNA endonucleases, including the protein of SEQ ID NO: 9, as working examples. However, the specification fails to provide any clue as to the structural elements required in any RNA-guided DNA endonuclease, including which structural features within SEQ ID NO: 9 can be modified and which ones should be present for a variant having the recited % sequence identity to display the same RNA-guided DNA endonuclease activity as that of the polypeptide of SEQ ID NO: 9. No correlation between structure and function has been presented.
The state of prior art, the relative skill of those in the art, and the predictability or unpredictability of the art. The amino acid sequence of a polypeptide determines its structural and functional properties. While the art discloses a limited number of RNA-guided DNA endonucleases, neither the specification nor the art provide a correlation between structure and function such that one of skill in the art can envision the structure of any RNA-guided DNA endonuclease. In addition, the art does not provide any teaching or guidance as to which changes can be made to the protein of SEQ ID NO: 9 such that the resulting variant would display the desired functional characteristics, or the general tolerance of RNA-guided DNA endonucleases to structural modifications and the extent of such tolerance. The art clearly teaches that (i) there is a high level of unpredictability associated with accurate functional annotation of proteins based solely on structural homology, and (ii) modification of a protein’s amino acid sequence to obtain the desired activity without any guidance/knowledge as to which amino acids in a protein are tolerant of modification and which ones are conserved is highly unpredictable. For example, Singh et al. (Current Protein and Peptide Science 19(1):5-15, 2018) disclose different protein engineering approaches and state that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility and conformational changes (page 11, left column, last paragraph). Sadowski et al. (Current Opinion in Structural Biology 19:357-362, 2009) teach that much of the problem in assigning function from structure comes from functional convergence, where although a stable structure is required to perform many functions it is not always necessary to adopt a particular structure to carry out a particular function (page 357, right column, first full paragraph). Sadowski et al. further explain that the unexpected and significant difficulties of predicting function from structure show that the potential of structural models for providing novel functional annotations has not yet fully realized. Sadowski et al. also states that while a few successes have been achieved which required manual intervention, the ability to vary the requirements for specificity in prediction means that it is difficult to determine how useful the end result may be for the user (page 361, left column, first full paragraph). The teachings of Singh et al. and Sadowski et al. are further supported by the teachings of Witkowski et al., Tang et al. and Seffernick et al. already discussed above, where it is shown that even small amino acid changes result in unpredictable enzymatic activity changes.
The quantity of experimentation required to practice the claimed invention based on the teachings of the specification. While methods of generating or isolating variants of a polypeptide and enzymatic assays were known in the art at the time of the invention, it was not routine in the art to screen by a trial and error process for an essentially infinite number of proteins to find a RNA-guided DNA endonuclease. In the absence of (i) a rational and predictable scheme for selecting those proteins most likely to have the desired functional features, and/or (ii) a correlation between structure and RNA-guided DNA endonuclease activity, one of skill in the art would have to test an essentially infinite number of proteins to determine which ones have the desired functional characteristics.
Therefore, taking into consideration the extremely broad scope of the claim, the lack of guidance, the amount of information provided, the lack of knowledge about a correlation between structure and the desired function, and the high degree of unpredictability of the prior art in regard to structural changes and their effect on function, one of ordinary skill in the art would have to go through the burden of undue experimentation in order to practice the claimed invention. Thus, Applicant has not provided sufficient guidance to enable one of ordinary skill in the art to make and use the invention in a manner reasonably correlated with the scope of the claims.
Conclusion
No claim is in condition for allowance.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to DELIA M RAMIREZ, Ph.D., whose telephone number is (571) 272-0938. The examiner can normally be reached on Monday-Friday from 8:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert B. Mondesi, can be reached at (408) 918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/DELIA M RAMIREZ/Primary Examiner, Art Unit 1652
DR
January 22, 2026