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 .
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Detail Action
Claims 178-192 are pending for examination.
Applicants’ election of group I (claims 178-190) directed to a method for modulating transcription of a gene comprising a hexanucleotide repeat sequence GGGGCC, the method comprising contacting a cell comprising the gene with an agent having a first terminus, a second terminus, and an oligomeric backbone, wherein:(a) the first terminus comprises a DNA-binding moiety capable of noncovalently binding to the hexanucleotide repeat sequence GGGGCC;(b) the second terminus comprises a
protein-binding moiety capable of binding to a regulatory molecule that modulates the expression of the gene comprising the hexanucleotide repeat sequence GGGGCC; and(c) the oligomeric backbone comprises a linker between the first terminus and the second terminus and species selection of linear polyamides (e.g., claim 179) for searching. Regarding the "second terminus protein binding moiety," and species selection selects bromodomain inhibitors (e.g., claim 182) capable of binding CREB binding protein (CBP) regulatory molecules (e.g., claim 181) on 7/1/2026 without traverse is acknowledged. Claims of groups II ( claims 191-192) are withdrawn. Restriction requirement of 4/2/26 made final.
Claims 178-190 will be examined.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 11/18/2024 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the examiner has considered the IDS statement.
Claim Rejections: 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 180, 186 and 190 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 180 is rejected being indefinite because it recites the limitation “hexanucleotide repeat comprises at least 20 repeats, at least 50 repeats, at least 100 repeats, at least 200 repeats, at least 500 repeats, or at least 1000 repeats” indefiniteness arises because claim includes a broad range and a narrow range within the same claim (e.g., least 20 repeats, --- or at least 1000 repeats,"). A claim with both a broad and a narrow range (e.g. least 20 repeats, --- or at least 1000 repeats) can be indefinite because it's unclear if the narrow part is required or just exemplary.
Claim 186 is rejected being indefinite because it recites the limitation “less than about 50 Angstroms” indefiniteness arises because It is unclear whether it is less than less than 50 Angstroms or about 50 Angstroms.
Claim 190 is rejected being indefinite because it recites the limitation “method comprises a 20%, 50%, 80%, 90%, 95%, or 99% decrease in expression of C90RF72” indefiniteness arises because claim includes a broad range and a narrow range within the same claim (e.g., 20%, 50%, --- or 99%,"). A claim with both a broad and a narrow range (e.g20%, 50%, --- or 99%,").) can be indefinite because it's unclear if the narrow part is required or just exemplary.
Claim Rejections, 35 U.S.C 112(a) 1st Paragraph
The following is a quotation of the first paragraph of 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 178-190 are rejected under 35 U.S.C. 112(a), first paragraph, as containing 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(s), at the time the application was filed, had possession of the claimed invention.
It is noted that MPEP 2111.01 states that "[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow." In this case, in light of the specification, the examiner has broadly interpreted the method for modulating transcription of a gene comprising a hexanucleotide repeat sequence GGGGCC, the method comprising contacting a cell comprising the gene with an agent having a first terminus, a second terminus, and an oligomeric backbone, wherein:(a) the first terminus comprises a DNA-binding moiety capable of noncovalently binding to the hexanucleotide repeat sequence GGGGCC;(b) the second terminus comprises a protein-binding moiety capable of binding to a regulatory molecule that modulates the expression of the gene comprising the hexanucleotide repeat sequence GGGGCC; and(c) the oligomeric backbone comprises a linker between the first terminus and the second terminus in claim 1” to encompass any transcription of a gene comprising only 6 nucleotide is defined ( GGGCC) a hexanucleotide repeat sequence GGGGCC, the method comprising contacting a cell comprising the gene having any structure with an agent having any structure having a first terminus, a second terminus, and an oligomeric backbone having any structure , wherein:(a) the first terminus comprises a DNA-binding moiety having any structure capable of noncovalently binding to the hexanucleotide repeat sequence GGGGCC;(b) the second terminus having any structure comprises a protein-binding moiety. Therefore in light of the specification, claims are broadly interpreted to comprise transcription of any gene comprising only 6 nucleotide is defined ( GGGCC) a hexanucleotide repeat sequence GGGGCC, the method comprising contacting a cell comprising the gene having any structure with an agent having any structure having a first terminus, a second terminus, and an oligomeric backbone having any structure , wherein:(a) the first terminus comprises a DNA-binding moiety having any structure capable of noncovalently binding to the hexanucleotide repeat sequence GGGGCC;(b) the second terminus having any structure comprises a protein-binding moiety and function capable of binding to a regulatory molecule that modulates the expression of the gene comprising the hexanucleotide repeat sequence GGGGCC.
The Court of Appeals for the Federal Circuit has recently 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." University of California v. Eli Lilly and Co., 1997 U.S. App. LEXIS 18221, at *23, quoting Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993). To fully describe a genus of genetic material, which is a chemical compound, applicants must (1) fully describe at least one species of the claimed genus sufficient to represent said genus whereby a skilled artisan, in view of the prior art, could predict the structure of other species encompassed by the claimed genus and (2) identify the common characteristics of the claimed molecules, e.g., structure, physical and/or chemical characteristics, functional characteristics when coupled with a known or disclosed correlation between function and structure, or a combination of these (paraphrased from Enzo Biochemical).University of Rochester v. G.D. Searle & Co. (69 USPQ2d 1886 (2004)) specifically points to the applicability of both Lilly and Enzo Biochemical to methods of using products, wherein said products lack adequate written description. While in University of Rochester v. G.D. Searle & Co. the methods were held to lack written description because not a single example of the product used in the claimed methods was described, the same analysis applies wherein the product, used in the claimed methods, must have adequate written description (see Enzo paraphrased above).
There is no structure-function correlation with regard to the members of the genus gene comprising only 6 nucleotide is defined ( GGGCC) a hexanucleotide repeat sequence GGGGCC, the method comprising contacting a cell comprising the gene having any structure with an agent having any structure having a first terminus, a second terminus, and an oligomeric backbone having any structure , wherein:(a) the first terminus comprises a DNA-binding moiety having any structure capable of noncovalently binding to the hexanucleotide repeat sequence GGGGCC;(b) the second terminus having any structure comprises a protein-binding moiety and function capable of binding to a regulatory molecule that modulates the expression of the gene comprising the hexanucleotide repeat sequence GGGGCC recited in the claims. Therefore one of skill in the art would not recognize from the disclosure that applicants were in possession of the claimed invention.
The genus of gene comprising only 6 nucleotide is defined ( GGGCC) a hexanucleotide repeat sequence GGGGCC, the method comprising contacting a cell comprising the gene having any structure with an agent having any structure having a first terminus, a second terminus, and an oligomeric backbone having any structure , wherein:(a) the first terminus comprises a DNA-binding moiety having any structure capable of noncovalently binding to the hexanucleotide repeat sequence GGGGCC;(b) the second terminus having any structure comprises a protein-binding moiety having any structure and function capable of binding to a regulatory molecule that modulates the expression of the gene comprising the hexanucleotide repeat sequence GGGGCC is an extremely large structurally and functionally variable genus. An argument can be made that any or more of the gene C90RF72 and DNA-binding moiety can cyclic polyamide and protein-binding moiety an acetyltransferase inhibitor, a histone deacetylase inhibitor and bind histone acetyltransferase (HAT), a histone deacetylase. However, the art clearly teaches there is a practical limits to predict function of a polypeptide based structural homology:
A. Devos et al., (Proteins: Structure, Function and Genetics, 2000, Vol. 41: 98-107), teach that the results obtained by analyzing a significant number of true sequence similarities, derived directly from structural alignments, point to the complexity of function prediction. Different aspects of protein function, including (i) enzymatic function classification, (ii) functional annotations in the form of key words, (iii) classes of cellular function, and conservation of binding sites can only be reliably transferred between similar sequences to a modest degree. The reason for this difficulty is a combination of the unavoidable database inaccuracies and plasticity of proteins (Abstract, page 98) and the analysis poses interesting questions about the reliability of current function prediction exercises and the intrinsic limitation of protein function prediction (Column 1, paragraph 3, page 99) and conclude that "Despite widespread use of database searching techniques followed by function inference as standard procedures in Bioinformatics, the results presented here illustrate that transfer of function between similar sequences involves more difficulties than commonly believed. Our data show that even true pair-wise sequence relations, identified by their structural similarity, correspond in many cases to different functions (column 2, paragraph 2, and page 105).
B. Whisstock et al., (Quarterly Reviews of Biophysics 2003, Vol. 36 (3): 307-340,) also highlight the difficulties associated with "Prediction of protein function from protein sequence and structure": "To reason from sequence and structure to function is to step onto much shakier ground", closely related proteins can change function, either through divergence to a related function or by recruitment for a very different function, in such cases, assignment of function on the basis of homology, in the absence of direct experimental evidence, will give the wrong answer (page 309, paragraph 4), it is difficult to state criteria for successful prediction of function, since function is in principle a fuzzy concept. Given three sequences, it is possible to decide which of the three possible pairs is most closely related. Given three structures, methods are also available to measure and compare similarity of the pairs. However, in many cases, given three protein functions, it would be more difficult to choose the pair with most similar function, although it is possible to define metrics for quantitative comparisons of different protein sequences and structures, this is more difficult for proteins of different functions (page 312, paragraph 5), in families of closely related proteins, mutations usually conserve function but modulate specificity i.e., mutations tend to leave the backbone conformation of the pocket unchanged but to affect the shape and charge of its lining, altering specificity (page 313, paragraph 4), although the hope is that highly similar proteins will share similar functions, substitutions of a single, critically placed amino acid in an active-site residue may be sufficient to alter a protein's role fundamentally (page 323, paragraph 1).
C. This finding is reinforced in the following scientific teachings for specific proteins in the art that suggest, even highly structurally homologous polypeptides do not necessarily share the same function and many functionally similar proteins will have little or no structural homology to disclosed proteins. For example, proteins having similar structure have different activities (structure does not always correlate to function); Witkowski et al., (Biochemistry 38:11643-11650, 1999) teaches that one conservative amino acid substitution transforms a beta -ketoacyl synthase into a malonyl decarboxylase and completely eliminates beta-ketoacyl synthase activity. The art also teaches that functionally similar molecules have different structures; Kisselev L., (Structure, 2002, Vol. 10: 8-9) teach that polypeptide release factors in prokaryotes and eukaryotes have same function but different structures.
As stated above, no information beyond the characterization of a few species; such as the gene C90RF72 and DNA-binding moiety can cyclic polyamide and protein-binding moiety an acetyltransferase inhibitor, a histone deacetylase inhibitor and bind histone acetyltransferase (HAT), a histone deacetylase has been provided by the applicants’, which would indicate that they had the possession of the claimed use of the genus gene comprising only 6 nucleotide is defined ( GGGCC) a hexanucleotide repeat sequence GGGGCC, the method comprising contacting a cell comprising the gene having any structure with an agent having any structure having a first terminus, a second terminus, and an oligomeric backbone having any structure , wherein:(a) the first terminus comprises a DNA-binding moiety having any structure capable of noncovalently binding to the hexanucleotide repeat sequence GGGGCC;(b) the second terminus having any structure comprises a protein-binding moiety and function capable of binding to any regulatory molecule that modulates the expression of the gene comprising the hexanucleotide repeat sequence GGGGCC recited in the claims. The claimed genera of genus of genes have widely variable structures and associated functions. As it is discussed above, a minor changes in structure may result in changes affecting function, since, the specification provided no additional information (species/variant/mutant) correlating structure with function, one skilled in the art cannot reasonably conclude that applicant had possession of the claimed invention at the time the instant application was filed. Furthermore, "Possession may not be shown by merely describing how to obtain possession of members of the claimed ,genus or how to identify their common structural features" (See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895). A definition by function, as we have previously indicated, does not suffice to define the genus because it is only an indication of what the .gene does (function), rather what it is (structure), see University of California v. Eli Lilly & Co., 43 USPQ2d 1938, thus above claims lack adequate written description.
Applicants' are referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov
Conclusion
Claims 178-190 are rejected and no claim is allowable.
Any inquiry concerning this communication or earlier communications from the
examiner should be directed to Mohammad Meah whose telephone number is 571-272-
1261. The examiner can normally be reached on 8:30-5PM.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s
supervisor, Robert Mondesi can be reached on 4089187584. The fax phone number
for the organization where this application or proceeding is assigned is 571-273-8300.
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/MOHAMMAD Y MEAH/Examiner, Art Unit 1652
Prosecution Insights