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 .
Application Status
This action is written in response to applicant' s correspondence received March 10, 2026. Claims 95-115 and 117-141 are currently pending. Claim 116 is canceled. Claims 108, 109, 138, 139, and 141 are withdrawn from prosecution as being drawn to non-elected subject matter. Accordingly, Claims 95-107, 110-115, 117-137 and 140 are examined herein. The restriction requirement mailed November 21, 2024 is still deemed proper. Applicant's elected Claim 107 and Claim 123 without traverse in the reply filed May 20, 2025.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Claim Rejections - 35 USC § 102
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 (i.e., changing from AIA to pre-AIA ) 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim 130 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lin, S., et. al., Molecular Cell, Vol. 62, p. 335-345, May 5, 2016.
Regarding Claim 130, Lin teaches a conjugate comprising a polypeptide comprising a RNA regulatory domain, METTL3, linked to a nucleic acid comprising a RNA targeting molecule with at least one hairpin structure, MS2 hairpins: “To directly test the possible role of METTL3 in promoting translation … we performed tethering experiments using a luciferase reporter mRNA containing two MS2-binding sites located just downstream of the stop codon. …. Intriguingly, we found that directly tethering FLAG-MS2-METTL3 to the 3′ UTR robustly enhanced translation efficiency by around 1.8 fold without changing the mRNA level” (p. 338, col. 2). The system taught by Lin forms the conjugate through a fusion protein comprising METTL3 and MS2 hairpin binding domain, in which the MS2 hairpin binding domain binds to the MS2 hairpins in the RNA targeting molecule. Therefore, Claim 130 is anticipated by Lin.
Response to Applicant’s Arguments - 35 USC § 102
Regarding Claim 130, Claim 130 was previously rejected under 102. Applicant has amended Claim 95 by incorporating Claim 116 (Applicant Argument, p. 9). However, Claim 130 is an independent claim and has not been amended. Therefore, the previous rejection is maintained.
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 95-97, 99, 100, 103, 110-114, 119, 125, 126, 129, 134-137 and 140 are rejected under 35 U.S.C. 103 as being unpatentable over Lin, S., et. al., Molecular Cell, Vol. 62, p. 335-345, May 5, 2016, Blakeley, B. and McNaughton, B., ACS Chemical Biology, Vol. 9, p. 1320-1329, Mar 17, 2014, and Freire, J. et. al., PLOS ONE, Vol. 8, Issue 12, p. 1-10, Dec. 5, 2013.
Regarding Claim 95, Lin teaches a RNA regulatory system comprising of (i) a polypeptide comprising of a MS2 hairpin binding domain, (ii) a nucleic acid comprising a RNA targeting molecule comprising a RNA targeting region and at least one hairpin structure, MS2 hairpins, which specifically bind to the RNA hairpin binding domain, and (iii)a polypeptide comprising a RNA regulatory domain, METTL3: “To directly test the possible role of METTL3 in promoting translation … we performed tethering experiments using a luciferase reporter mRNA containing two MS2-binding sites located just downstream of the stop codon. …. Intriguingly, we found that directly tethering FLAG-MS2-METTL3 to the 3′ UTR robustly enhanced translation efficiency by around 1.8 fold without changing the mRNA level” (p. 338, col. 2).
Lin does not teach a RNA hairpin binding domain that is human-derived and a stabilizer polypeptide.
Blakeley teaches a U1A/TAR system with a U1A hairpin binding domain, which is human-derived, and a TAR hairpin: “U1A-derived proteins bind TAR with single-digit micromolar dissociation constants” and “our findings represent the first synthetic RRMs that selectively bind a disease-relevant RNA hairpin and may represent a general approach for achieving sequence-selective recognition of RNA hairpins, which are the focus of therapeutic discovery and basic research” (p. 1320, Abstract).
Freire teaches stabilizer peptides, a class of cationic polypeptides that non-specifically bind to nucleic acids: “[T]his class of proteins [supercharged proteins] with unusually high net positive charge is frequently found among … capsid proteins” (p. 1, Abstract) and “Viral capsid proteins, in particular, are optimized for interacting with nucleic acids” (p. 1, col. 1). Freire teaches that one skilled in the art may seek to use viral capsid proteins for cell delivery: “[S]tudies … reported that supercharged proteins may serve as potent drug delivery systems into a wide variety of mammalian cells and tissues” (p. 1, col. 1)
Regarding Claim 95, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have performed a simple substitution and combination with the teachings of Lin, Blakeley, and Freire to create the invention of Claim 95 by substituting the U1A/TAR system taught by Blakeley for the MS2 system taught by Lin and combining the stabilizer peptides taught by Freire.. Lin teaches the elements of Claim 95 with MS2 hairpins and MS2 binding domains, and Blakeley teaches TAR hairpins with the U1A hairpin binding domain, both functions were known in the art and serve the same function of RNA hairpin and hairpin binding domain, and therefore the results of the substitution would have been predictable. Blakeley teaches an advantage of their invention as it allows for selective recognition of RNA hairpins for basic research. The elements of Lin and Freire are known within the art and perform the same function separately and in combination. Freire teaches an advantage of their invention as it may serve as potent drug delivery systems in mammalian cells. Therefore, Claim 95 is obvious over Lin, Blakeley and Freire.
Regarding Claim 96, the FLAG-MS2-METTL3 construct is a RNA hairpin binding domain, MS2 linked to a RNA regulatory domain, METTL3. Therefore, Claim 95 is obvious over Lin, Blakeley and Freire.
Regarding Claim 97, the FLAG-MS2-METTL3 construct is linked in a single polypeptide. Therefore, Claim 95 is obvious over Lin, Blakeley and Freire.
Regarding Claim 99, the FLAG-MS2-METTL3 construct is under 98 kDA per Figure 3C (p. 338), which is less than 150 kDA. Therefore, Claim 95 is obvious over Lin, Blakeley and Freire.
Regarding Claim 100, Lin teaches, “METTL3 (as well as the other complex components) are observed predominantly in nuclear speckles” (p. 335, col. 1) and “its nuclear localization, METTL3 protein” (p. 337, col. 2), which reads on METTL3 containing nuclear localization signals. Therefore, Claim 95 is obvious over Lin, Blakeley and Freire.
Regarding Claim 103, the system taught by Lin expresses more than two molecules each of the polypeptide comprising the RNA binding domain and RNA regulatory domain and the nucleic acid comprising the RNA targeting molecule. Therefore, Claim 103 is anticipated by Lin.
Regarding Claim 110, Lin teaches the luciferase reporter mRNA used has two MS2 hairpins. Therefore, Claim 110 is obvious over Lin, Blakeley and Freire.
Regarding Claim 111, Lin teaches “METTL3 is a methyltransferase that has “METTL3 is an RNA methyltransferase … through N6-methyladenosine” (p. 335, Summary) and therefore modifies nucleotides when bound. Therefore, the luciferase reporter mRNA would have a modified oligonucleotide, and therefore, Claim 111 is obvious over Lin, Blakeley and Freire.
Regarding Claim 112, Lin teaches a system using luciferase reporter mRNA containing two MS2-binding sites, which reads as mRNA capable of hybridizing tRNA, a possible target RNA. Lin further teaches their system in “[h]uman lung cancer cell lines (A549, H1299, H1792), HeLa, and HEK293T cells” (p. 343, Cell Culture and Cell Lines”, which reads as teaching the use in eukaryotic cells. Therefore, Claim 112 is obvious over Lin, Blakeley and Freire.
Regarding Claim 113, the luciferase reporter mRNA is longer than 12 nucleotides and capable of hybridizing to an RNA; “The pGL3c_TK luciferase reporter containing two MS binding sites (FLuc-MS2bs)” (p. 343, Plasmids and Molecular Cloning).
Regarding Claim 114, Lin teaches a linker between the luciferase reporter mRNA and the hairpins in Figure 5A (p. 340). Therefore, Claim 114 is obvious over Lin, Blakeley and Freire.
Regarding Claim 119, Freire teaches a stabilizer polypeptide that is viral. Therefore, Claim 119 is obvious over Lin, Blakeley, and Freire.
Regarding Claim 125, Lin teaches that “our results illuminate an important role of METTL3
in directly enhancing translation” (p. 340, Col. 2) and has “m6A catalytic activity” (p. 339, col. 1), which reads as Lin teaching a methylase and translational activator for the RNA regulatory domain. Therefore, Claim 125 is obvious over Lin, Blakeley and Freire.
Regarding Claim 126, Lin teaches METTL3 is a methyltransferase that modifies the nucleotide A to m6A, which modifies the base sequence. Therefore, Claim 126 is obvious over Lin, Blakeley and Freire.
Regarding Claim 129, Lin teaches a system with a “MS2-METTL3 expression plasmid” (p. 343, col. 1), which is a nucleic acid encoding a polypeptide comprising a RNA regulatory domain and RNA hairpin binding domain, and a “pGL3c_TK luciferase reporter containing two MS binding sites … plasmid”, which is a nucleic acid encoding a mRNA capable of binding RNA with two hair pin structures, (p. 343, Plasmids and Molecular Cloning).
Lin does not teach a human derived RNA hairpin binding domain and a stabilizer polypeptide.
Blakeley teaches a RNA hairpin binding domain that is human derived.
Freire teaches a stabilizer polypeptide.
Therefore, Claim 129 is obvious over Lin, Blakeley and Freire as described above in Claim 95.
Regarding Claim 134, Lin teaches “MS2-METTL3 expression plasmid” (p. 343, col. 1), which is a nucleic acid encoding a polypeptide comprising a RNA regulatory domain, which is not CRISPR/Cas, and RNA hairpin binding domain. Therefore, Claim 134 is obvious over Lin, Blakeley and Freire.
Regarding Claim 135, Lin teaches that the “[t]ransfection of plasmids was performed using Lipofectamine 2000” (p. 343, col. 1) into cells , which is a delivery vehicle for the plasmids of Claim 95. Therefore, Claim 135 is obvious over Lin, Blakeley and Freire.
Regarding Claim 136, the composition of a system is components of the system used together. Lin teaches the transfection of expression plasmids within a cell containing the system of Claim 95, which reads as a composition. Therefore, Claim 136 is obvious over Lin, Blakeley and Freire.
Regarding Claim 137, Lin teaches their system within a cell: “… we performed tethering experiments using a luciferase reporter mRNA containing two MS2-binding sites located just downstream of the stop codon … in … cells” (p. 338, col. 2). Therefore, Claim 137 is obvious over Lin, Blakeley and Freire.
Regarding Claim 140, a kit may be a collection of the components of a system. Lin teaches the expression plasmids and cells for the system of Claim 95, which reads a kit. Therefore, Claim 140 is obvious over Lin, Blakeley and Freire.
Claims 98, 104, 132, and 133 are rejected under 35 U.S.C. 103 as being unpatentable over Lin, S., et. al., Molecular Cell, Vol. 62, p. 335-345, May 5, 2016, Blakeley, B. and McNaughton, B., ACS Chemical Biology, Vol. 9, p. 1320-1329, Mar 17, 2014, and Freire, J. et. al., PLOS ONE, Vol. 8, Issue 12, p. 1-10, Dec. 5, 2013 as applied to Claims 95 and 96 above, and further in view of Chen, F. and Davis, G., US 2017/0191082 A1, published Jul 6, 2017.
Regarding Claims 98, 104, 132, and 133, Claim 96 is obvious over Lin, Blakeley and Freire.
Lin does not teach the RNA regulatory and the RNA hairpin binding domains are dimers, linked through non-covalent interactions or dimerization.
Chen teaches linking polypeptides through dimerization and non-covalent interactions: “In one aspect, the fusion proteins can function as dimers thereby increasing the length of the target site and increasing the likelihood of its uniqueness in the genome” (p. 3, [0016]), which reads as linking the domains through non-covalent bonds.
Regarding Claims 98 and 104, it would have been obvious to one skilled in the art before the effective filing date to combine the system of Lin, Blakeley and Freire with the teachings of Chen to create the system of Claim 95 including the polypeptides comprising the RNA hairpin binding and RNA regulatory domain, with two domains that may be dimerized. One would be motivated to do so because it increases the specificity towards a target sequence. It would have been predictable because Chen teaches in an example successful use of a dimer fusion protein (Fig 1A, p. 2, [0010]). Therefore, Claims 98 and 104 are obvious over Lin, Blakeley and Freire in further view of Chen.
Claims 105-107 are rejected under 35 U.S.C. 103 as being unpatentable over Lin, S., et. al., Molecular Cell, Vol. 62, p. 335-345, May 5, 2016, Blakeley, B. and McNaughton, B., ACS Chemical Biology, Vol. 9, p. 1320-1329, Mar 17, 2014, and Freire, J. et. al., PLOS ONE, Vol. 8, Issue 12, p. 1-10, Dec. 5, 2013 as applied to Claims 95 and 96 above, and further in view of Chen, F. and Davis, G., US 2017/0191082 A1, published Jul 6, 2017 as applied to Claim 104 above, and further in view of Juillerat, A., et. al., WO 2017/032777 A1, published Mar 2, 2017.
Regarding Claims 105-107, Claim 104 is obvious over Lin, Blakeley and Freire in further view of Chen.
Lin does not teach the system of Claim 104, wherein the dimerization is inducible, ligand-induced, and the use of PYL1 and ABI1 with ABA.
Juillerat teaches “a system where controlled variations in the conformation of the extracellular portion of a CAR containing the antigen-binding domain could be obtained upon addition of small molecules” (p. 2, lines 16-18). Juillerat teaches, “the first multimerizing ligand-binding domain and second multimerizing ligand-binding domain are selected from the pairs of multimerizing ligand-binding domains consisting of: FK506 binding protein (FKBP12):FKBP-rapamycin binding domain of mTOR (FRB), FKBP12:FKBP12, … and PYL1:ABI1” (p. 11). On pages 8 and 9, Juillerat teaches in a table that FKBP12:FRB dimerizes with rapamycin, FKBP12:FKBP12 dimerizes with FK1012, and PYR1:ABI1 dimerizes with ABA. Juillerat also teaches that use of ligand-inducible domains “ provides for novel more controlled and potentially safer engineered CAR endowed immune cells” (p. 2, lines 22-23).
Regarding Claims 105 and 106, it would have been obvious to one skilled in the art before the effective filing date to combine the teachings of Lin, Blakeley, Freire and Chen to create the system of Claim 95 with each domain linked through dimerization and to try the teachings of Juillerat to select for potential ligand induced dimerization domains with. Chen teaches a need in the art for better sequence targeting and provides a potential solution in dimerization. Juillerat teaches an identified list of predictable potential solutions for dimerization that haven been well characterized allowing for a reasonable expectation of success. One skilled in the art would be motivated to try the list of ligand inducible dimerization domains because ligand induced dimers allow for more control and better targeting. Therefore, Claims 105 and 106 are obvious over Lin, Blakeley and Freire in further view of Chen and Juillerat.
Regarding Claim 107, Juillerat teaches in their table of ligand inducible domains to try a first and second dimerization domain comprising PYL1 and ABI1 with the ligand ABA. Therefore, Claim 107 is obvious over Lin, Blakeley and Freire in further view of Chen and Juillerat.
Regarding Claims 98, 104, 132, and 133, Claim 96 is obvious over Lin, Blakeley and Freire.
Lin does not teach the RNA regulatory and the RNA hairpin binding domains are dimers, linked through non-covalent interactions or dimerization.
Chen teaches linking polypeptides through dimerization and non-covalent interactions: “In one aspect, the fusion proteins can function as dimers thereby increasing the length of the target site and increasing the likelihood of its uniqueness in the genome” (p. 3, [0016]), which reads as linking the domains through non-covalent bonds.
Regarding Claims 98 and 104, it would have been obvious to one skilled in the art before the effective filing date to combine the system of Lin, Blakeley and Freire with the teachings of Chen to create the system of Claim 95 including the polypeptides comprising the RNA hairpin binding and RNA regulatory domain, with two domains that may be dimerized. One would be motivated to do so because it increases the specificity towards a target sequence. It would have been predictable because Chen teaches in an example successful use of a dimer fusion protein (Fig 1A, p. 2, [0010]). Therefore, Claims 98 and 104 are obvious over Lin, Blakeley and Freire in further view of Chen.
Claims 101 and 102 are rejected under 35 U.S.C. 103 as being unpatentable over Lin, S., et. al., Molecular Cell, Vol. 62, p. 335-345, May 5, 2016, Blakeley, B. and McNaughton, B., ACS Chemical Biology, Vol. 9, p. 1320-1329, Mar 17, 2014, and Freire, J. et. al., PLOS ONE, Vol. 8, Issue 12, p. 1-10, Dec. 5, 2013 as applied to Claim 95 above, and further in view of Cook, J. and Charlesworth, A., Protein Engineering, Design and Selection, Vol. 30, Issue 4, p. 313-319, Jan 27, 2017..
Regarding Claims 101 and 102, Claim 95 is obvious over Lin, Blakeley and Freire.
Lin does not teach an amino acid linker between the RNA regulatory and RNA hairpin binding domains.
Cook teaches, “Linkers between recombinant fusion domains are crucial for protein folding, stability and bioactivity, and yet are often overlooked… Studies of linkers in natural proteins have been performed to inform construction of recombinant fusion proteins grouped inter-domain linkers of natural proteins into three sizes: small (~4 aa), medium (~9 aa) and large (~21 aa)..” (p. 314, col. 1), which provides a need in the art to examine the use of linkers in fusion proteins. Cook teaches a method for evaluating linkers: “In this study, we tested if extending the linker and/or inserting rigid linkers improved fusion protein expression and bioactivity” (p. 314, col. 1). Cook specifically teaches a “inter-domain linker that is … ~12 amino acid (aa) residues in length” (p. 314, col. 1)
It would have been obvious to one skilled in the art before the effective filing date to try the method taught by Cook to improve the system taught by Lin, Blakeley, and Freire to create the system of Claim 95 with a linker between the fusion protein and to create a linker that is at least 5 amino acids in length. Cook has a finding that linkers are often ignored for optimization for protein folding, stability and bioactivity. Cook teaches a range of amino acids to try, 4-21 amino acids, which includes linkers 5 amino acids or longer. One of ordinary skill in the art would have pursued the method of Cook to improve the system taught by Lin and had a reasonable expectation of success because linkers are naturally found between different domains in proteins and may improve their bioactivity. Therefore, Claims 101 and 102 are obvious over Lin, Blakeley and Freire in further view of Cook.
Claim 115 is rejected under 35 U.S.C. 103 as being unpatentable over Lin, S., et. al., Molecular Cell, Vol. 62, p. 335-345, May 5, 2016, Blakeley, B. and McNaughton, B., ACS Chemical Biology, Vol. 9, p. 1320-1329, Mar 17, 2014, and Freire, J. et. al., PLOS ONE, Vol. 8, Issue 12, p. 1-10, Dec. 5, 2013 as applied to Claim 114 above, and further in view of Koehn, et. al., US 2004/0077082 A1, published Apr 22, 2004.
Regarding Claim 115, Claim 114 is obvious over Lin, Blakeley and Freire.
Lin does not teach the linker is between 2 to 5 nucleotides.
Koehn teaches “oligonucleotides include a targeting region, and a hairpin loop” (p. 15, [0020). Koehn further teaches “the single hairpin loop, or either or both of the hairpin loops in the dual-hairpin oligonucleotides may be coupled to the targeting sequence of the oligonucleotides by linker sequences” and “[s]uch linker sequences generally each have a length of from about 1 to about 10 nucleotides in length” (p. 15, [0025]). This reads on teaching a nucleic acid with a targeting region and a hairpin loop with a linker 1 to 10 nucleotides in length, which includes 2 to 5 nucleotides in length.
It would have been obvious to one skilled in the art before the effective filing date to substitute into the teachings of Lin which include a nucleic acid comprises a RNA targeting region and hairpin structures with a linker with the teaching of Koehn for a linker with length 2 to 5 nucleotides in length. The results would be predictable as Lin uses a linker successfully and Koehn identifies a narrow range that includes 2 to 5 nucleotides. Therefore, Claim 115 is obvious over Lin, Blakeley and Freire in further view of Koehn.
Claims 95, 117, and 118 are rejected under 35 U.S.C. 103 as being unpatentable over Lin, S., et. al., Molecular Cell, Vol. 62, p. 335-345, May 5, 2016, Blakeley, B. and McNaughton, B., ACS Chemical Biology, Vol. 9, p. 1320-1329, Mar 17, 2014, Cronican, J., et. al., Chemistry & Biology, Vol. 18, p. 833-838, Jul 29, 2011; and Marcovitz, A. and Levy, Y., PNAS, Vol. 108, Issue 44, p. 17957-17962, Nov 1, 2011.
Regarding Claim 95, Lin teaches a RNA regulatory system comprising of (i) a polypeptide comprising of a MS2 hairpin binding domain, (ii) a nucleic acid comprising a RNA targeting molecule comprising a RNA targeting region and at least one hairpin structure, MS2 hairpins, which specifically bind to the RNA hairpin binding domain, and (iii)a polypeptide comprising a RNA regulatory domain, METTL3: “To directly test the possible role of METTL3 in promoting translation … we performed tethering experiments using a luciferase reporter mRNA containing two MS2-binding sites located just downstream of the stop codon. …. Intriguingly, we found that directly tethering FLAG-MS2-METTL3 to the 3′ UTR robustly enhanced translation efficiency by around 1.8 fold without changing the mRNA level” (p. 338, col. 2).
Lin does not teach a RNA hairpin binding domain that is human-derived and a stabilizer polypeptide.
Blakeley teaches a U1A/TAR system with a U1A hairpin binding domain, which is human-derived, and a TAR hairpin: “U1A-derived proteins bind TAR with single-digit micromolar dissociation constants” and “our findings represent the first synthetic RRMs that selectively bind a disease-relevant RNA hairpin and may represent a general approach for achieving sequence-selective recognition of RNA hairpins, which are the focus of therapeutic discovery and basic research” (p. 1320, Abstract).
Cronican teaches “a class of naturally occurring human proteins with unusually high net positive charge that can potently deliver proteins in functional form into mammalian cells both in vitro … in vivo” (p. 833, Summary), which reads on teaching the use of highly positively charged or cationic polypeptides. Cronican teaches on page 834 in Figure 1A, that HBEGF and β-defensin-3 are amongst that class. Cronican also teaches, “Our results reveal that potent vehicles for macromolecule delivery into mammalian cells in vivo already exist within the human body in the form of naturally supercharged proteins … they could serve as a new set of biologic delivery agents with a diversity of important properties such as charge, structure, molecular weight, immunogenicity, stability, and in vivo half-life” (p. 836-837, Significance), which provides motivation for their use.
Marcovitz teaches, “ nonspecific interactions are mostly dominated by electrostatic interactions between the positively charged protein side chains and the negatively charged DNA backbone” (p. 17957, col. 2), which reads on positively charged polypeptides bind DNA non-specifically.
Regarding Claim 95, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have performed a simple substitution and combination with the teachings of Lin, Blakeley, Cronican and Marcovitz to create the invention of Claim 95 by substituting the U1A/TAR system taught by Blakeley for the MS2 system taught by Lin and combining the stabilizer peptides taught by Cronican.. Lin teaches the elements of Claim 95 with MS2 hairpins and MS2 binding domains, and Blakeley teaches TAR hairpins with the U1A hairpin binding domain, and therefore both functions were known in the art and serve the same function. Blakeley teaches their invention allows for selective recognition of RNA hairpins for basic research and therefore the results of the substitution would have been predictable. The elements of Lin and Cronican are known within the art and perform the same function separately and in combination. Therefore, Claim 95 is obvious over Lin, Blakeley and Cronican and Marcovitz.
Regarding Claim 117, Cronican teaches a system with human derived positively charged polypeptides. Therefore, Claim 117 is obvious over Lin, Blakeley and Cronican and Marcovitz.
Regarding Claim 118, Cronican teaches that HBEGF and β-defensin-3 are human derived positively charged polypeptides. Therefore, Claim 118 is obvious over Lin, Blakeley and Cronican and Marcovitz.
Claims 95, 127 and 128 are rejected under 35 U.S.C. 103 as being unpatentable over Kennedy, E. et. al., Cell Host & Microbe, Vol. 19, p. 675-685, May 11, 2016, Blakeley, B. and McNaughton, B., ACS Chemical Biology, Vol. 9, p. 1320-1329, Mar 17, 2014, and Freire, J. et. al., PLOS ONE, Vol. 8, Issue 12, p. 1-10, Dec. 5, 2013.
Regarding Claims 95, 127 and 128, Kennedy teaches a RNA regulatory system through controlling the expression of YTHDF proteins: “Reducing YTHDF expression inhibited, while YTHDF overexpression enhanced, HIV-1 protein and RNA expression, and virus replication in CD4+ T cells”. Kennedy further teaches a polypeptide comprising (i) a RNA regulatory domain and (iii) a RNA hairpin binding domain, wherein the RNA regulatory system is not related to CRISPR/Cas: “[F]usion proteins consisting of the amino-terminal effector domains of YTHDF1, YTHDF2 and YTHDF3 linked to the bacteriophage MS2 coat protein” (p. 679, col 2). Kennedy teaches a nucleic acid comprising (ii) a RNA targeting molecule comprising a RLuc mRNA, which can target a complementary RNA sequence, and at a MS2 hairpin: “an RLuc indicator plasmid containing MS2 coat protein binding sites” (p. 679, col. 2).
Kennedy further teaches that YTHDF proteins are m6A readers: “The three YTHDF proteins all contain a conserved carboxy-terminal YTH domain that binds m6A” (p. 675, Col 2).
Kennedy does not teach a RNA hairpin binding domain that is human-derived and a stabilizer polypeptide.
Blakeley teaches a U1A/TAR system with a U1A hairpin binding domain, which is human-derived, and a TAR hairpin: “U1A-derived proteins bind TAR with single-digit micromolar dissociation constants” and “our findings represent the first synthetic RRMs that selectively bind a disease-relevant RNA hairpin and may represent a general approach for achieving sequence-selective recognition of RNA hairpins, which are the focus of therapeutic discovery and basic research” (p. 1320, Abstract).
Freire teaches stabilizer peptides, a class of cationic polypeptides that non-specifically bind to nucleic acids: “[T]his class of proteins [supercharged proteins] with unusually high net positive charge is frequently found among … capsid proteins” (p. 1, Abstract) and “Viral capsid proteins, in particular, are optimized for interacting with nucleic acids” (p. 1, col. 1). Freire teaches that one skilled in the art may seek to use viral capsid proteins for cell delivery: “[S]tudies … reported that supercharged proteins may serve as potent drug delivery systems into a wide variety of mammalian cells and tissues” (p. 1, col. 1)
Regarding Claim 95, it would have been obvious to one skilled in the art before the effective filling date of the claimed invention to have performed a simple substitution and combination with the teachings of Kennedy, Blakeley, and Freire to create the invention of Claim 95 by substituting the U1A/TAR system taught by Blakeley for the MS2 system taught by Kennedy and combining the stabilizer peptides taught by Freire.. Kennedy teaches the elements of Claim 95 with MS2 hairpins and MS2 binding domains, and Blakeley teaches TAR hairpins with the U1A hairpin binding domain, and therefore both functions were known in the art and serve the same function. Blakeley teaches their invention allows for selective recognition of RNA hairpins for basic research and therefore the results of the substitution would have been predictable. The elements of Kennedy and Freire are known within the art and perform the same function separately and in combination. Therefore, Claim 95 is obvious over Kennedy, Blakeley and Freire.
Regarding Claims 127 and 128, Kennedy teaches a RNA regulatory system comprising of a polypeptide with a RNA regulatory domain and a hairpin binding domain and a polynucleotide with a RNA targeting region and at least one hairpin structure that binds the hairpin binding domain, in which the RNA regulatory domain comprises of a m6A reader including YTHDF1 and YTHDF2. Therefore, Claims 127 and 128 are obvious over Kennedy, Blakeley and Freire.
Claims 131 is rejected under 35 U.S.C. 103 as being unpatentable over Lin, S., et. al., Molecular Cell, Vol. 62, p. 335-345, May 5, 2016, and Blakeley, B. and McNaughton, B., ACS Chemical Biology, Vol. 9, p. 1320-1329, Mar 17, 2014.
Lin teaches a RNA regulatory system comprising of (i) a polypeptide comprising of a MS2 hairpin binding domain, (ii) a nucleic acid comprising a RNA targeting molecule comprising a RNA targeting region and at least one hairpin structure, MS2 hairpins, which specifically bind to the RNA hairpin binding domain, and (iii)a polypeptide comprising a RNA regulatory domain, METTL3: “To directly test the possible role of METTL3 in promoting translation … we performed tethering experiments using a luciferase reporter mRNA containing two MS2-binding sites located just downstream of the stop codon. …. Intriguingly, we found that directly tethering FLAG-MS2-METTL3 to the 3′ UTR robustly enhanced translation efficiency by around 1.8 fold without changing the mRNA level” (p. 338, col. 2).
Lin does not teach a RNA hairpin binding domain that is human-derived.
Blakeley teaches a U1A/TAR system with a U1A hairpin binding domain, which is human-derived, and a TAR hairpin: “U1A-derived proteins bind TAR with single-digit micromolar dissociation constants” and “our findings represent the first synthetic RRMs that selectively bind a disease-relevant RNA hairpin and may represent a general approach for achieving sequence-selective recognition of RNA hairpins, which are the focus of therapeutic discovery and basic research” (p. 1320, Abstract).
Regarding Claim 131, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have performed a simple substitution with the teachings of Lin, and Blakley to create the invention of Claim 131 by substituting the U1A/TAR system taught by Blakeley for the MS2 system taught by Lin.. Lin teaches the elements of Claim 131 with MS2 hairpins and MS2 binding domains, and Blakeley teaches TAR hairpins with the U1A hairpin binding domain, and therefore both functions were known in the art and serve the same function. Blakeley teaches their invention allows for selective recognition of RNA hairpins for basic research and therefore the results of the substitution would have been predictable. Therefore, Claim 131 is obvious over Lin and Blakeley
RE: Applicant’s Arguments
Applicant argues Lin, Cronican, and Marcovitz do not teach every limitation in the present claims due to amendment in Claim 95 of a stabilizer polypeptide (p. 10). Claim 95 is rejected under 103 for obviousness over Lin, Blakeley and Freire, in which Freire is cited for the stabilizer polypeptide.
Applicant argues the office action has failed to provide “(1) a reasoned stated as to why an ordinarily skilled artisan (POSA) would combine and/or modify the cited references to arrive at the claimed subject matter; and (2) an explanation as to why the POSA would have had a reasonable expectation of success to modify and/or combine the cited references to arrive at the claimed subject matter” (p. 11-12). The applicant’s argument is not persuasive because the office action addresses why a POSA would substitute and modify Lin and have a reasonable expectation of success. Claim 95 is rejected as obvious over Lin, Blakeley and Freire. The rejection states Blakeley teaches a benefit of their invention which allows for selective recognition of RNA hairpins. The rejection also states Freire teaches a benefit of their invention allow for potent delivery to mammalian cells. The rejection states a POSA would have a reasonable expectation of success because Lin and Blakeley use similar systems, a RNA hairpin and hairpin binding domain, and the structure and function of both are known. The rejection also states a POSA would have a reasonable expectation of success because the elements of Lin and Freire serve the same function together and in combination.
Applicant argues unexpected results with the CIRTS system for a range of functions (p. 13). MPEP 716.02(b) establishes the burden of the applicant to show "that the differences in results are in fact unexpected and unobvious and of both statistical and practical significance" and “[A]ppellants have the burden of explaining the data in any declaration they proffer as evidence of non-obviousness.” The argument provided does not explain what elements are unexpected and what values or results are different from the prior art. Further, Claim 95 is not limited to the CIRTS system and allows for any RNA hairpin binding domain, any nucleic acid with a hairpin, any polypeptide comprising a RNA regulatory domain, and any stabilizer protein provided that one hairpin binding domain or hairpin is human or human-derived. This claim is much broader than the CIRTS system, and the dependent claims do not limit the claims to the CIRTS system.
Allowable Subject Matter
Claim 120 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
The following art is cited below: Chopin, M., et. al., Journal of Bacteriology, Vol. 184, No. 7, p. 2030-2033, April 2002.
Claim 119 is obvious over Lin, Blakeley and Freire.
Lin, Blakeley and Freire do not teach the use of viral ORF5 polypeptide.
Freire teaches stabilizer peptides, a class of cationic polypeptides that non-specifically bind to nucleic acids: “[T]his class of proteins [supercharged proteins] with unusually high net positive charge is frequently found among … capsid proteins” (p. 1, Abstract) and “Viral capsid proteins, in particular, are optimized for interacting with nucleic acids” (p. 1, col. 1)
Chopin teaches viral ORF5 polypeptide (p. 2032, Figure 5). Chopin does not teach ORF5 as a supercharged protein with a positive charge, but rather a mix of charges.
It would not have been obvious to one skilled in the art to use the teachings of Chopin in conjunction with the teachings of Freire to use ORF5 because Freire requires a supercharged positive protein, and Chopin does not teach ORF5 to be a supercharged protein.
Therefore, Claim 120 is allowable over the prior art.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 Krishna Nuggehalli Ravindra whose telephone number is (571)272-2758. The examiner can normally be reached M-Th, alternate F, 8a-5p est.
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/K.N.R./Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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