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 .
The examiner of your application in the PTO has changed. To aid in correlating any papers for this application, all further correspondence regarding this application should be directed to Brian Whiteman, Art Unit 1636.
Election/Restrictions
Any claim drawn to a non-elected invention was cancelled in the amendment filed on 12/30/24.
The amendment to the claims filed on 12/19/25 added new claim 26.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
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 specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, 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 Objections
Claim 13 is objected to because of the following informalities: there is no nexus between a mammalian cell isolated from a human patient because a human only has human cells not mammalian cells unless non-human mammalian cells were introduced into the patient. If this was the case, then the DNA binding protein would not be produced naturally from the human. Appropriate correction is required.
Response to Arguments
Applicant’s arguments, see pages, filed 12/19/25, with respect to the rejection(s) of claim(s) 1-11, 13-15, 17-20 and 22 under 103 have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of an updated search of the claimed invention.
Claim Rejections - 35 USC § 112
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.
Claim 7 is 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. Claim 7 depends on claim 2(1) and the limitation “some or all of the binding site(s) are located in the transcribed sequence” recited in claim 1 could limit the DNA binding sites for the DNA binding protein to the transcribed sequence (mRNA) of the expression cassette. However, claim 7 recites some or all of the binding sites are located in the protein coding sequence of the expression cassette which could embrace none of the binding sites being in the transcribed sequence of the cassette. Also see applicant’s arguments on pages 8-9 discussing the prior art teaching binding sites for DNA not located in the transcribed sequence. 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.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
NOTE: any limitation after the term “optionally (optional)” recited in the instant claims is not considered an active limitation of the claimed invention because it is optional. Therefore, the structural and/or functional limitations after the term are not required to be taught or suggested by the prior art.
While claim 1 contains a limitation that limits one or all the binding sites to the transcribed sequence of the reporter expression cassette, claim 7 (which is dependent on claim 1) embraces that one or all of the binding sites are located in the protein coding sequence of the reporter expression cassette. This limitation in claim 7 is broader than the limitation in claim 1 because the protein coding sequence encompasses the DNA coding strand and the mRNA transcript, whereas the transcribed sequence is limited to the mRNA.
The term “functionally active antagonist” in the pre-amble of independent claims 1 and 21 does not have patentable weight because carrying out the method steps does not have to result in a functionally active antagonist. In addition, even if the term carried patentable weight, when one of ordinary skill in the art carries out the methods steps of the claimed invention the method would produce either a functional or non-functional antagonist.
Claims 1-8, 10, 11, 13-15, 17, 19, 22, and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Guo et al. (WO2018025085, published 08 February 2018, EFD 03 August 2016) taken with Belmont (US 20110245326).
‘085 teach eukaryotic cell based screening method to identify aptamers that specifically bind a ligand or a ligand that specifically binds an aptamers comprising: (a) inserting a polynucleotide cassette into the protein coding region of the target gene, wherein the polynucleotide cassette comprises (i) a riboswitch; and (ii) an alternatively-spliced exon, wherein the alternatively-spliced exon is flanked by a 5' intron and a 3' intron, and wherein the alternatively-spliced exon comprises a stop codon that is in-frame with the target gene when the alternatively-spliced exon is spliced into the target gene mRNA; and wherein the riboswitch comprises an effector region comprising a stem, which includes the 5' splice site sequence of the 3' intron, and an aptamer; (b) introducing the target gene comprising the polynucleotide cassette into a cell; and (c) exposing the cell to a ligand that specifically binds the aptamer in an amount effective to induce expression of the target gene, wherein the alternatively-spliced exon is derived from exon 2 of human dihydrofolate reductase (DHFR) gene (pages 44-47). The polynucleotide can be inserted into a vector. The ligand can be a small molecule (drug), lipids, monosaccharides, second messengers, other natural products and metabolites, nucleic acids (pages 13-17). The ligand is produced by the eukaryotic cell (page 47). The eukaryotic cell can be from a bacteria (E. coli).
‘085 does not specifically teach using the engineered riboswitch in a cell or cell-free screening assay for an antagonist comprising providing a cell line or a test tube comprising the test compound, a DNA-binding protein, and a reporter expression construct comprising at least one binding site for the DNA binding protein, wherein the binding sites are bound to the DNA-binding protein and inhibits expression of the reporter expression construct, and wherein at least one or more of the binding sites are located in the transcribed sequence of the reporter expression cassette.
However, Belmont teaches an aptamer for inducible post-transcriptional regulation in vivo has been demonstrated that is predicated on a direct interaction between a tetracycline repressor protein and a RNA aptamer element (abstract and pages 1-31 and 38-39). These aptamer components can be integrated in any organism to regulate RNA translation of a gene of interest. A plasmid comprising a gene of interest, wherein the gene of interest comprises an open reading frame encoding a protein of interest, wherein said open reading frame is in operably combination with a DNA sequence encoding an aptamer. A system comprising a) an RNA sequence that is capable of binding to a protein target of interest thereby forming an aptamer; b) a repressor protein capable of binding to the aptamer; and c) a regulatory molecule capable of interacting with the repressor protein thereby altering the aptamer, wherein the regulatory RNA sequence is added to a 5’ or 3’ UTR of said gene (pages 3 and 16-17). A regulatory protein can be a transcription factor (page 3). A bacterial repressor protein (e.g., tetracycline repressor (TetR) protein, which is a ligand-inducible, sequence-specific DNA binding protein and is a transcription factor) (pages 17-19). The binding of TetR to aptamers can be reversed by the addition of anhydrotetracycline (aTc). This is an example of a DNA binding protein and a binding region in the aptamer and Belmont contemplates using any known pair in the construct.
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to use a DNA-binding protein bound to the aptamer in the riboswitch in the assay to screen for unknown or known compound (ligand, DNA sequence, small molecule) that reversed the binding of the DNA-binding protein to the binding sites and activated expression of the reporter cassette with a reasonable expectation of success because the prior art suggest detecting an agent in a cell using a reporter sequence having a riboswitch comprising an aptamer in its transcribed sequence. wherein the aptamer is bound to a DNA binding protein and expression of the reporter sequence is observed when the binding between the DNA binding protein and the aptamer is reversed due to the presence of an agent that binds to the DNA binding protein. See also MPEP 2132(I)F. It would have been obvious for one of ordinary skill in the art to use the method to screen for a ligand, which specifically binds the aptamer in an amount effective to induce expression of the target gene, wherein the alternatively-spliced exon is derived from exon 2 of human dihydrofolate reductase (DHFR) gene to observe expression of DHFR. Even though they are RNA aptamers, the binding sites located in the stem loop for the TetR taught by Belmont would read on DNA binding sites and the TetR would read on the DNA binding protein because TetR is a DNA binding protein that would bind to binding sites (which would inherently be the DNA binding sites for TetR) in the stem loop of the aptamers. In addition, as stated above, Belmont suggest making a plasmid comprising the aptamer which would suggest to one of ordinary skill in the art try a DNA binding protein and the binding sites for the DNA binding protein. It would have been a simple substitution to use an artificial riboswitch comprising a DNA aptamer in place of a riboswitch comprising an RNA aptamer in the assay to regulate transcription of the reporter cassette with a reasonable expectation of success. ‘085 teaches that the cells can be E. Coli cells or from a mammal. Belmont suggest using a method to detect an agent in a cell from a human wherein the DNA binding protein is endogenously expressed (pages 18 and 25). ‘085 teaches using a vector to deliver the DNA-binding protein to the cell to control expression of the DNA-binding protein. ‘085 teaches that the test compound can be a peptide or a small molecule. One of ordinary skill in the art would have been motivated to use a vector to deliver the DNA-binding protein to provide and regulate the DNA-binding protein in the assay. It would have been obvious to one of ordinary skill in the art to administer the test compounds extra-cellularly to control what compound is being tested. One of ordinary skill in the art could use a cell-free assay to save time from having to maintain a cell line comprising the DNA-binding protein and reporter cassette or delivering the test compound, DNA-binding protein and reporter cassette to the cell. Belmont make obvious inserting at least one binding site into the 5’ UTR of the expression cassette (pages 3 and 16-17).
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Claims 9, 18, and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Guo (‘085) and Belmont as applied to claims 1-8, 10, 11, 13-15, 17, 19, 22, and 26 above, and further in view of Moellering et al. (WO 2017190061, published 02 November 2017 and EFD 28 April 2016).
‘085 and Belmont do not specifically teach an assay using an expression cassette comprising an artificial riboswitch to screen for drugs that target a basic leucine zipper (bZIP) transcription factor or a DNA binding fragment thereof.
However, Moellering teaches DNA binding peptides and using them in therapeutic and research methods (abstract and pages 1-7, 39-122, and 124-129). Transcription factors are well-known in the prior art be involved in cellular function and involved in human diseases (pages 1-3). Transcription factors (e.g., Myc) are DNA-binding proteins that are characterized by adjacent “basic” helix-loop-helix and leucine zipper domains. Synthetic DNA binding domains can bind to a DNA molecule (DNA comprising an E-box or other DNA binding sites). Moellering further teaches that it would have been obvious for one of ordinary skill in the art to design and make more robust peptides as potential therapeutics to maintain the peptide’s unique conformation and secondary structure (page 1-2).
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to use an assay made obvious by ‘085 and Belmont to screen for compounds that act as dimerization disruptors or DNA-binding inhibitors of transcription factors, including bZIP, bHLH or bHLH-ZIP or DNA binding-fragment thereof for research and therapeutic purposes as taught by Moellering. A person of ordinary skill in the art could use the assay as a high through put screening assay for screening for a compound that when introduced displaces the transcription factor from the aptamer resulting in transcription of the expression cassette. Since transcription factors set forth in instant claim 9 bind E-box motifs, one of ordinary skill in the art can make DNA aptamers featuring the E-Box motif with a reasonable expectation of success and using either strand displacement or competitor switch for screening synthetic peptides as potential therapeutics or research purposes. In view of the teaching of Moellering, it would have been obvious for one of ordinary skill in the art to introduce a cross-linking agent into the cells to produce the helix-contained peptide for use in the assay with a reasonable expectation of success (pages 1-2).
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Claims 18 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Guo (‘085) and Belmont as applied to claims 1-8, 10, 11, 13-15, 17, 19, 22, and 26 above, and further in view of GENENTECH, INC. (WO 98/20036) and (Iyer, Current Medicinal Chemistry 2016, 23, 3025-3043).
Guo and Belmont do not specifically teach that test compound is peptide comprising a helix-constrained peptide, wherein the helix-constrained peptide comprises a cross-link between two amino acid residues.
However, GENENTECH, INC. discloses studying constrained helical peptides for HIV vaccines (pages 1-70 and 236-240). Helix-constrained peptides from a HIV polypeptide (gp120) were produced by cross-linking between two amino acid residues in an alpha helix of the HIV peptide. Furthermore, one of ordinary skill in the art would possess the knowledge that alpha-helices are ubiquitous in the proteome and important for protein-protein interactions (Iyer, page 3025). Helix-constrained peptides in drug screening ensure that the peptide binds in the correct conformation stays stable and can function in cells (Iyer, page 3025). See also MPEP 2141(II)C. Rationales to support rejections under 35 U.S.C. 103 recites, “Prior art is not limited to the references being applied, but includes the understanding of one of ordinary skill in the art.”
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to combine the teaching of Guo and Belmont taken with GENENTECH INC. and Iyer to use the assay made obvious by Guo and Belmont to study for possible HIV treatment in cells infected with HIV or protein-protein interaction in any desired cell. GENENTECH, INC and Iyer teach the method step for making the helix as set forth in instant claim 18 and it would have been obvious for one of ordinary skill in the art to introduce a cross-linking agent into the HIV infected cells to produce the helix-contained peptide with a reasonable expectation of success.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Conclusion
See attached PTO-326 for disposition of claims.
The art made of record and not relied upon is considered pertinent to applicant's disclosure.
Mol et al. (Nucleic Acids Research 2019, Vol. 47, e132) teaches a method that would suggest claims 1, 2, 6, 11, 15, 19, and 26. However, the journal article was published after the filing date of the certified application filed on 20 December 2018.
Boyne et al. (WO2016126747) teach a method of modulating the expression of a target gene, the method comprising: (a) inserting a polynucleotide cassette into the protein coding region of the target gene, wherein the polynucleotide cassette comprises (i) a riboswitch; and (ii) an alternatively-spliced exon, wherein the alternatively-spliced exon is flanked by a 5' intron and a 3' intron, and wherein the alternatively-spliced exon comprises a stop codon that is in-frame with the target gene when the alternatively-spliced exon is spliced into the target gene mRNA; and wherein the riboswitch comprises an effector region comprising a stem, which includes the 5' splice site sequence of the 3' intron, and an aptamer; (b) introducing the target gene comprising the polynucleotide cassette into a cell; and (c) exposing the cell to a ligand that specifically binds the aptamer in an amount effective to induce expression of the target gene, wherein the alternatively-spliced exon is derived from exon 2 of human dihydrofolate reductase (DHFR) gene (pages 62-66). The polynucleotide can be inserted into a vector. The ligand can be a small molecule (drug), lipids, monosaccharides, second messengers, other natural products and metabolites, nucleic acids (pages 14-15). ‘747 does not specifically teach using the engineered riboswitch in a cell or cell-free screening assay for an antagonist comprising providing a cell or test tube comprising the test compound, a DNA-binding protein, and a reporter expression construct comprising at least one binding site for the DNA binding protein, wherein the binding sites are bound to the DNA-binding protein and inhibits expression of the reporter expression construct, and wherein at least one or more of the binding sties are located in the transcribed sequence of the reporter expression cassette. ‘747 could be used as a 102(a)(1) reference in a 103 rejection, but there is a 102(a)(1) reference already cited in the 103 rejection of record that makes obvious the claimed invention.
Berens et al. (Biotechnology Journal 2015, 10, 246-257) teach using engineered riboswitches in eukaryotes for regulation of mRNA splicing, wherein an aptamer is integrated into an intron of an eukaryotic mRNA to control accessibility of the 5’ splice site (page 249, Figure 2B).
PNG
media_image1.png
315
956
media_image1.png
Greyscale
Hunsicker et al. (Chemistry & Biology 16, 173-180, 2009) discloses aptamers in a sequence that are targeted by TetR (transcription factor).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Brian Whiteman whose telephone number is (571)272-0764. The examiner can normally be reached on Monday thru Friday; 6:00 AM to 3:00PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached at (571)-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/BRIAN WHITEMAN/ Primary Examiner, Art Unit 1636
