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 .
Response to Amendment/Status of Claims
Claims 1,6,7,18,20,125-129,138,139,141,142,145 and 146 have been amended. Claims 5,9-14,16,19,21-25,27,29 and 32-124 were previously canceled. Claims 147-151 are new. Claims 1-4,6-8,15,17,18,20 and 125-152 are pending.
Applicant elected Group I (claims 1-4,6-8,15,17,18,20 and 125-146), NaM as the first unnatural base and TPT3 as the second unnatural base from Species A, and N6-((azidoethoxy)-carbonyl)-L-lysine (AzK) from Species B without traverse in the reply filed on 09/02/2025.
Claims 1-4,6-8,15,17,18,20 and 125-152 are under examination.
Priority
This application is a CON of PCT/US2020/053339, filed 09/29/2020 which claims benefit of 62/908,421, filed 09/30/2019.
Withdrawn Rejections
Applicant’s arguments and amendments, see pages 10-11, filed 02/12/2026, with respect to the 35 U.S.C. 101 rejection of claims 1-4,6-8,15,17,18,20 and 125-146 have been fully considered and are persuasive, due to the amendments to the claims to recite that the eukaryotic cell is an isolated cell which no longer reads on a human organism comprising a human cell. The 35 U.S.C. 101 rejection of claims 1-4,6-8,15,17,18,20 and 125-146 has been withdrawn.
The provisional nonstatutory double patenting rejections of Claims 1-4,6-8,15,17,18,20,125-134,136-140 and 143-146 as being unpatentable over claims 67-83 of copending Application No. 18/532,609 (‘609) in view of Romesberg et al.; claims 7,17,127,129 and 137 as unpatentable over claims 67-83 of ‘609 in view of Romesberg and further in view of Caffaro; claim 135 as unpatentable over claims 67-83 of ‘609 in view of Romesberg and further in view of Franze, and claims 141 and 142 as unpatentable over claims 67-83 of ‘609 in view of Romesberg and further in view of Liu and Caffaro, have been withdrawn as claims 67-83 of ‘609 are cancelled.
Claim Objections
Claims 1 and 145 are objected to because of the following informalities: Amended claims 1 and 145 recite, “wherein the codon is selected from….GYC, wherein X is an unnatural nucleotide comprising the first unnatural base” and recites “GXU, wherein Y is an unnatural nucleotide comprising the first unnatural base”. In the instance of GYC, it appears X is a typo and should be Y. In the instance of GXU, it appears Y is a typo and should be X. Appropriate correction is required.
Maintained Rejections-modified based on Amendments
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.
Claims 1-4,6-8,15,18,20,125,128,130-134,136,138-140,143-148 and 151 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (Nature, Vol. 551, 30 Nov 2017, pp. 644-647), cited on an IDS, in view of Romesberg et al. (US 20170029829, Published 2 Feb 2017).
Claim Interpretation: The preambles of claims 143-144 are not being treated as a claim limitation as the preambles do not limit the structure, and the body of the claims do not provide additional elements other than the limitations recited in claim 4.
Regarding claims 1,18 and 125, Zhang et al. teach a semi-synthetic organism strain transformed with mRNA comprising a codon comprising an unnatural base and wherein the mRNA encodes a polypeptide (a semi-synthetic organism strain with a plasmid encoding superfolder green fluorescent protein (sfGFP) with the native sfGFP codon 151 (TAC) replaced by the unnatural codon AXC (sfGFP(AXC)151; X denotes NaM)), and a transfer RNA comprising an anticodon comprising a second unnatural base (an E. coli tRNASer gene (serT) and the anticodon of serT replaced by the unnatural anticodon GYT (tRNASer(GYT); Y denotes TPT3) (page 644, left column, 2nd paragraph).
Zhang et al. also teach a GXC codon and the corresponding anticodon tRNAPyl (GYC) (page 644, right column, page 645, right column). Therefore, Zhang et al. teach NaM is the first unnatural base, and TPT3 is the second unnatural base, and dNaM and dTPT3 is an unnatural base pair (UBP) (Figure 1a). Zhang et al. teach in vivo transcription of DNA containing dNaM and dTPT3 into mRNAs with two different unnatural codons and tRNAs with cognate unnatural anticodons, and their efficient decoding at the ribosome to direct the site-specific incorporation of non-canonical amino acids into superfolder green fluorescent protein, and the results demonstrate that interactions other than hydrogen bonding can contribute to every step of information storage and retrieval. The resulting semi-synthetic organism both encodes and retrieves increased information and should serve as a platform for the creation of new life forms and functions (Abstract).
Zhang et al. do not teach the cell is an isolated eukaryotic cell.
Romesberg et al. cures this deficiency. Romesberg et al. taught that in vitro, the natural two-letter genetic alphabet has been expanded with chemically synthesized unnatural nucleotides that form unnatural base pairs (paragraph 0004) and the development of a third, unnatural DNA base pair and an expanded genetic alphabet is a central goal of synthetic and chemical biology and would increase the functional diversity of nucleic acids, providing tools for their site-specific labeling, increase the information potential of DNA, and lay the foundation of a semi-synthetic organism (paragraph 0010). Romesberg et al. taught that the limitation of only having four different base components (nucleotides) in standard nucleic acids restricts their functions and potential as compared to the 20 different amino acids in natural proteins, and that the UBPs and cells stably incorporating the UBPs described herein, offer numerous advantages and can be applied to a broad range of biotechnologies (paragraph 0011). Romesberg et al. taught the discovery that particular unnatural base pairs (UBPs) including but not limited to (d)5SICS-(d)NaM and (d)TPT3-(d)NaM can be amplified with natural base pair-like efficiency and fidelity….Thus, provided herein are methods, compositions, and kits, for increasing the genetic alphabet of cell or an organism. Also, provided herein are compositions, e.g., cells, comprising an expanded genetic alphabet, e.g., cells that stably propagate an expanded genetic alphabet. Also, provided herein are compositions, e.g., cells, comprising an expanded genetic alphabet, wherein neither the presence of unnatural triphosphates nor the replication of the UBP represents a significant growth burden on the cells (paragraph 00200). Romesberg et al. taught cells comprising a first unnatural nucleic acid, and comprising an unnatural base pair within the cell (paragraphs 0012-0013), and embodiments wherein the cell is a eukaryotic cell (paragraphs 0063,0133,0327,0347,0348).
Regarding claims 2,4,15 and 143-144, Zhang et al. also teach to demonstrate the encoding of non-canonical amino acids with UBPs, plasmids were constructed with the Methanosarcina mazei tRNAPyl (GYT) gene. tRNAPyl can be selectively charged by the Methanosarcina bakeri pyrrolysyl-tRNA synthetase with the ncAA N6-[(2-propynyloxy)carbonyl]L-lysine (PrK) (page 644, right column). Zhang et al. teach seryl-tRNA synthetase does not rely on anticodon recognition for tRNA aminoacylation, thus eliminating the potential complications of inefficient charging (Page 644, left column). Therefore, Zhang et al. teach the tRNA is charged with an unnatural amino acid (Prk), and which is a lysine analogue, and teach a tRNA synthetase.
Regarding claim 3, Zhang et al. teach that PrK (the unnatural amino acid) is specifically incorporated into sfGFP through decoding of the unnatural codons by tRNAs with an unnatural anticodon (page 645, right column).
Regarding the recited cells of claims 6,7,138-140 and 147, Zhang et al. does not teach the cell is a human cell or a mammalian cell or a non-human cell.
Romesberg et al. cures this deficiency. Romesberg et al. taught many cells can be used for transforming or genetically engineering, and the cell can be a eukaryotic cell which is a human cell or animal cell (paragraph 0347) or mammalian cell (paragraph 0353). Romesberg et al. taught the mammalian cells are 293, or CHO cells (paragraph 0353).
Regarding claim 8 and 136, Zhang et al. teach the first unnatural base is NaM, and the second unnatural base is TPT3 (the native sfGFP codon 151 (TAC) replaced by the unnatural codon AXC (sfGFP(AXC)151; X denotes NaM), and the anticodon of serT replaced by the unnatural anticodon GYT (tRNASer(GYT); Y denotes TPT3) (page 644, left column, 2nd paragraph; (Figure 1a).
Regarding claims 20 and 151, and the codon being GYC, and the anticodon being GXC, as stated above Zhang et al. teach GXC codon and the corresponding anticodon tRNAPyl (GYC) (page 644, right column, page 645, right column). Instant claims 1, 20 and 151 only require that Y is an unnatural nucleotide comprising a first unnatural base and X is an unnatural nucleotide comprising a second unnatural base, and therefore do not require a specific unnatural nucleotide comprising a first unnatural base or a specific unnatural nucleotide comprising a second unnatural base and does not require that the unnatural bases are different. For example see claim 134 which depends on claim 1 and recites the first and second unnatural base are the same. Therefore in these claims, X and Y do not appear to be structurally different. Whether the codon is GXC or GYC and whether the anticodon is GYC or GXC, does not appear to be structurally different based on the claims as long as there is an unnatural base in the middle of the codon and an unnatural base in the middle of the anticodon which is taught by Zhang et al. Therefore, Zhang et al. is considered to teach the limitations of claims 20 and 151.
Regarding claim 128, Zhang et al. teach the codon is GXC and the corresponding anticodon tRNAPyl (GYC) (page 644, right column, page 645, right column).
Regarding claims 130-131, Zhang et al. teach the tRNA synthetase is Methanosarcina barkeri pyrrolysyl-tRNA synthetase (page 644, right column).
Regarding claims 132-133, Zhang et al. teach the tRNA is Methanosarcina mazei tRNAPyl gene (page 644, right column).
Regarding claim 134, Zhang et al. do not teach the first unnatural base and the second unnatural base are the same.
Romesberg et al. cures this deficiency. Romesberg et al. taught the first unnatural nucleic acid is the same as the second unnatural nucleic acid (paragraphs 0041,0144).
Regarding claims 145-146 and 148, Zhang et al. teach the unnatural codon AXC (sfGFP(AXC)151; X denotes NaM)), as well as a GXC codon as described above regarding claim 1. Zhang et al. teach sfGFP and tRNA expression plasmids (p[sfGFP(gg)151 tRNASer(gg)], p[sfGFP(gg)151 tRNAPyl(gg)], and p[sfGFP(gg)151 tRNApAzF(gg)]) which are used to introduce natural or unnatural position 151 sfGFP codons and tRNA anticodons (Methods, Construction of sfGFP and tRNA expression plasmids). Zhang et al. teach an expression plasmid for M. barkeri pyrrolysyl-tRNA synthetase (Methods, Construction of synthetase expression plasmids). Zhang et al. teach tRNAPyl can be selectively charged by the Methanosarcina bakeri pyrrolysyl-tRNA synthetase with the ncAA N6-[(2-propynyloxy)carbonyl]L-lysine (PrK) (page 644, right column). Zhang et al. teach seryl-tRNA synthetase does not rely on anticodon recognition for tRNA aminoacylation, thus eliminating the potential complications of inefficient charging (Page 644, left column).
Zhang et al. does not teach a kit comprising the isolated eukaryotic cell.
Romesberg et al. cures this deficiency. Romesberg et al. taught compositions and kits, for increasing the genetic alphabet of cell or an organism. Also, provided herein are compositions, e.g., cells, comprising an expanded genetic alphabet, e.g., cells that stably propagate an expanded genetic alphabet. Also, provided herein are compositions, e.g., cells, comprising an expanded genetic alphabet, wherein neither the presence of unnatural triphosphates nor the replication of the UBP represents a significant growth burden on the cells (paragraph 00200). Romesberg et al. taught the cell is a eukaryotic cell (paragraphs 0063,0133,0327,0347,0348). Romesberg et al. taught the kits can utilize one or more endogenous or exogenous enzymes to stably integrate unnatural nucleic acids (Paragraph 0203). Romesberg et al. taught kits comprising various combinations of components set forth above in regard to exemplary reaction mixtures and reaction methods can be provided in kit form, and can include individual components that are separated from each other, and can include one or more sub-combinations being separated from other components in the kit, and sub-combinations can be combinable to create a reaction mixture (paragraphs 0369-0370). Romesberg et al. taught the kit of the invention provides a cell and a nucleic acid molecule containing a heterologous gene for introduction into the cell, for expression provides expression vectors comprising the nucleic acid of any of the embodiments (paragraph 0377), and recombinant expression is accomplished using an expression cassette that can be part of a vector, such as a plasmid (paragraph 0401).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date, to provide the mRNAs comprising an unnatural AXC or GXC codon comprising a first unnatural base and tRNAs comprising an anticodon comprising a second unnatural base, and the tRNA synthetase of Zhang et al. in an isolated eukaryotic cell as taught by Romesberg et al. with a reasonable expectation of success. There would be a reasonable expectation of success, because Romesberg et al. also pertains to unnatural bases and unnatural base pairs (UBPs) including but not limited to TPT3-(d)NaM and increasing the genetic alphabet of cell or an organism and that the organism can be a eukaryotic cell, including human and mammalian cells, and taught the in vitro expansion of the genetic alphabet using chemically synthesized unnatural nucleotides that form unnatural base pairs, and therefore, it would be obvious that the eukaryotic cell would be an isolated cell. One of ordinary skill in the art would have been motivated to provide the plasmid encoding the tRNASer gene (serT) and sfGFP with the native sfGFP codon 151 (TAC) replaced by the unnatural codon AXC (sfGFP(AXC)151; X denotes NaM), and the anticodon of serT replaced by the unnatural anticodon GYT (tRNASer(GYT); Y denotes TPT3 , or wherein the codon is GXC and the corresponding anticodon is GYC of Zhang et al. in the eukaryotic cell of Romesberg et al., because Romesberg et al. teach that the UBPs and cells stably incorporating the UBPs described herein, offer numerous advantages and can be applied to a broad range of biotechnologies (paragraph 0011), and the discovery that particular unnatural base pairs (UBPs) including TPT3-(d)NaM can be amplified with natural base pair-like efficiency and fidelity and provide methods, compositions, and kits, for increasing the genetic alphabet of cell or an organism, including cells comprising an expanded genetic alphabet, e.g., cells that stably propagate an expanded genetic alphabet, and that the cell is a eukaryotic cell, including a human cell or animal cell (paragraphs 0063,0133,0327,0347,0348) or mammalian cell (paragraph 0353), or 293 or CHO cells (paragraph 0353).
Accordingly, the limitations of claims 1-4,6-8,15,18,20,125,128,130-134,136,138-140,143,144,147,148 and 151 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
It would have been obvious to one of ordinary skill in the art before the effective filing date, to combine the mRNA of Zhang et al. in an expression vector and the tRNA of Zhang et al. in an expression vector with a eukaryotic cell of Romesberg et al. to form a kit as taught by Romesberg et al. with a reasonable expectation of success. It would also be obvious to provide the plasmid encoding tRNA synthetase of Zhang et al. in the kit of Romesberg et al. with a reasonable expectation of success. There would be a reasonable expectation of success, because Romesberg et al. also pertains to unnatural bases and unnatural base pairs (UBPs) including but not limited to (d)5SICS-(d)NaM and (d)TPT3-(d)NaM and increasing the genetic alphabet of cell or an organism. One of ordinary skill in the art would have been motivated to provide a kit comprising the eukaryotic cell of Romesberg et al., an expression vector comprising a nucleic acid encoding the mRNA of Zhang et al. and an expression vector comprising a nucleic acid encoding the tRNA of Zhang et al., as well as the plasmid encoding tRNA synthetase of Zhang et al. because Romesberg et al. teach kits comprising various combinations of components in regard to exemplary reaction mixtures and reaction methods can be provided in kit form, and can include individual components that are separated from each other, and can include one or more sub-combinations being separated from other components in the kit, and sub-combinations can be combinable to create a reaction mixture (paragraphs 0369-0370). Romesberg et al. teach the kit of the invention provides a cell and a nucleic acid molecule containing a heterologous gene for introduction into the cell, for expression provides expression vectors comprising the nucleic acid of any of the embodiments (paragraph 0377), and recombinant expression is accomplished using an expression cassette that can be part of a vector, such as a plasmid (paragraph 0401).
Accordingly, the limitations of claims 145 and 146 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claims 17,126,127,129,137,150 and 152 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. and Romesberg et al. as applied to claims 1-4,6-8,15,18,20,125,128,130-134,136,138-140,143-148 and 151 above, and further in view of Caffaro et al. (WO2020097325, effectively filed 08 Nov 2018).
The teachings of Zhang et al. and Romesberg et al. as applicable to claims 1-4,6-8,15,18,20,125,128,130-134,136,138-140,143-148 and 151 are described above.
Zhang et al. and Romesberg et al. do not teach that the at least one unnatural amino acid comprises N6-((azidoethoxy)-carbonyl)-L-lysine (AzK). While Zhang et al. and Romesberg et al. teach the codon is AXC, they do not teach wherein the anticodon is GYU, or wherein the codon is GXU and the anticodon is AYC, or wherein the codon is AGX, and the anticodon is YCU or XCU.
Caffaro et al. cures these deficiencies. Caffaro et al. taught modified IL-10 polypeptides comprising amino acid sequence comprising at least one unnatural amino acid and that the unnatural amino acid comprises N6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK) (paragraphs 0005,0011,0013-0018,0078,0091,0117,0121). Caffaro et al. taught a plasmid comprising a double-stranded oligonucleotide that encodes an IL-10 variant having a desired amino acid sequence and that contains a unnatural base pair comprising a first unnatural nucleotide and a second unnatural nucleotide to provide a codon at the desired position at which an unnatural amino acid, such as /V6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK), a plasmid encoding a tRNA derived from M. mazei and which comprises an unnatural nucleotide to provide a recognized anticodon (to the codon of the IL-10 variant) in place of its native sequence, and a plasmid encoding a M. barkeri derived pyrrolysyl-tRNA synthetase (Mb PylRS) (paragraph 0121). Caffaro et al. also taught the codon comprises an unnatural nucleotide such as NaM, and the anticodon comprises the unnatural nucleotide such as TPT3 (paragraph 0121). Caffaro et al. also taught the IL-10 polypeptides containing an unnatural amino acid are generated recombinantly by a host cell, which is a eukaryotic cell (e.g. mammalian cell, insect cells, yeast cells, or plant cell (paragraphs 0234-0235). Caffaro et al. also teach other suitable host cells include human 293T cells and CHO cells (paragraphs 0281-0282).
Caffaro et al. taught the unnatural amino acid is incorporated into the IL-10 polypeptide by a synthetic codon/anticodon pair comprising those listed in the Table below, and therefore teaches the AXC codon and GYU anticodon, GXU codon and AYC anticodon, and AGX codon and YCU or XCU anticodon, where X and Y are unnatural bases shown below (paragraph 0273, See table below, page 92).
PNG
media_image1.png
401
321
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Greyscale
PNG
media_image2.png
325
632
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Greyscale
Therefore, It would have been obvious to one of ordinary skill in the art before the effective filing date, to provide N6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK) as the unnatural amino acid in the mRNA encoding a polypeptide comprising at least one unnatural amino acid of Zhang et al., based on the teachings of Caffaro et al. There would be a reasonable expectation of success, as this would have amounted to simple substitution of one known unnatural amino acid for another known unnatural amino acid to obtain predictable results. One of ordinary skill in the art would have been motivated to provide N6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK) as the unnatural amino acid because Caffaro et al. lists multiple unnatural amino acids appropriate for use in a modified IL-10 polypeptide including Azk.
Accordingly, the limitations of claims 17 and 137 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
It would have been obvious to one of ordinary skill in the art before the effective filing date, to replace the codon and anticodons of Zhang et al. with the codons and anticodons taught by Caffaro et al. (AXC codon and GYU anticodon, GXU codon and AYC anticodon, and AGX codon and YCU or XCU anticodon) with a reasonable expectation of success. There would be a reasonable expectation of success as Caffaro et al. also pertains to polypeptides comprising unnatural amino acids, as well as mRNA comprising codons with unnatural bases and tRNA comprising anticodons with unnatural bases. One of ordinary skill in the art would be motivated to do so because Caffaro et al. teach the unnatural amino acid is incorporated into the IL-10 polypeptide by a synthetic codon/anticodon pair comprising UUX, UGX, CGX, AGX, GAX, and CAX codons, and would be motivated to provide when the codon is AXC, the anticodon is GYU, and when the codon is GXU, the anticodon is AYC and when the codon is AGX the anticodon is YCU or XCU because Caffaro et al. teach various codon and anticodon combinations including the AXC codon and GYU anticodon, and GXU codon and AYC anticodon and AGX codon and YCU or XCU anticodon (paragraph 0273, Table page 92).
Accordingly, the limitations of claims 126,127,129,150 and 152 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claim 135 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. and Romesberg et al. as applied to claims 1-4,6-8,15,18,20,125,128, 130-134,136,138-140,143-148 and 151 above, and further in view of Franze et al. (US 20110117087, Published 19 May 2011).
The teachings of Zhang et al. and Romesberg et al. as applicable to claims 1-4,6-8,15,18,20,125,128,130-134,136,138-140,143-148 and 151 are described above.
Zhang et al. and Romesberg et al. do not teach wherein the polypeptide translated from the mRNA comprises a eukaryotic glycosylation pattern.
Franze et al. cures this deficiency. Franze et al. taught immunoglobulin production in cells, whereby the glycosylation pattern of the produced immunoglobulin can be modified based on the cultivation conditions (paragraph 0002) and that posttranslational modifications such as the glycosylation pattern do have an influence on the efficacy, stability, immunogenic potential, binding etc. of an immunoglobulin (paragraph 0004), and it has been reported that the glycosylation pattern of immunoglobulins, i.e. the saccharide composition and number of attached glycostructures, has a strong influence on the biological properties (paragraph 0005). Franze et al. taught the amount of the mannose-5 glycostructure in the glycosylation pattern of a polypeptide produced by a eukaryotic cell can be modified based on the amount of glucose provided in the cell cultivation process (paragraph 0011). Franze et al. taught the introduction of glycostructures to polypeptides, e.g. immunoglobulins, is a post-translational modification, and due to incompleteness of the glycosylation procedure of the respective cell every expressed polypeptide is obtained with a glycosylation pattern comprising different glycostructures. Thus, a polypeptide is obtained from a cell expressing it in form of a composition comprising differently glycosylated forms of the same polypeptide, i.e. with the same amino acid sequence. The sum of the individual glycostructures is denoted as glycosylation pattern, comprising e.g. polypeptides with completely missing glycostructures, differently processed glycostructures, and/or differently composed glycostructures (paragraph 0061).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date, to substitute the GFP produced from the mRNA of Zhang et al. with the immunoglobulin produced by a eukaryotic cell and having a modified glycosylation pattern from the cell expressing it according to the teachings of Franze et al. for the purpose of modifying the biological properties of the produced immunoglobin. There would be a reasonable expectation of success, as this amounts to simple substitution of one known protein/polypeptide (GFP of Zhang et al.) for another (immunoglobin with modified glycosylation pattern produced by a eukaryotic cell of Franze et al.) to obtain predictable results. An ordinary artisan would be motivated to provide an mRNA comprising a codon comprising a first unnatural base and tRNAs comprising an anticodon comprising a second unnatural base of Zhang et al. in a eukaryotic cell as taught by Romesberg et al., and substitute the mRNA of Zhang et al. with the teachings of Franze et al. in order to produce an immunoglobulin as the polypeptide produced, and wherein the immunoglobulin has the glycosylation pattern of the eukaryotic cell that produced it, because Franze et al. teach that posttranslational modifications such as the glycosylation pattern have an influence on the efficacy, stability, immunogenic potential, binding etc. of an immunoglobulin and that the glycosylation pattern of a polypeptide produced by a eukaryotic cell can be modified based on the amount of glucose provided in the cell cultivation process and because a polypeptide is obtained from a cell expressing it in form of a composition comprising differently glycosylated forms of the same polypeptide.
Accordingly, the limitations of claim 135 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claim 141 and 149 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. and Romesberg et al. as applied to claims 1-4,6-8,15,18,20,125, 128,130-134,136,138-140,143-148 and 151 above, and further in view of Liu et al. (WO 2019010164, Published 10 Jan 2019).
The teachings of Zhang et al. and Romesberg et al. as applicable to claims 1-4,6-8,15,18,20,125,128,130-134,136,138-140,143-148 and 151 are described above.
Zhang et al. teach the codon is GXC and the corresponding anticodon tRNAPyl (GYC) (page 644, right column, page 645, right column). Zhang et al. teach the tRNA is Methanosarcina mazei tRNAPyl gene (page 644, right column). Zhang et al. teach the tRNA synthetase is Methanosarcina barkeri pyrrolysyl-tRNA synthetase (page 644, right column).
Zhang et al. and Romesberg et al. do not teach the pyrrolysyl tRNA synthetase is a chimeric pyrrolysyl tRNA synthetase.
Liu et al. cures this deficiency. Liu et al. taught evolved aminoacyl-tRNA synthetases (AARSs) that increase the utility of orthogonal translation systems and establish the capability of rapidly and continuously evolving orthogonal AARSs with high activity and amino acid specificity, and improved enzymatic efficiency compared to the wild type enzyme (paragraph 0005). Liu et al. taught chimeric pyrrolysyl-tRNA synthetase protein variant comprising a first portion of amino acid residues 1-149 of Methanosarcina bakeri PyIRS and a second portion comprising amino acid residues 185-454 of Methanosarcina mazei PyIRS (paragraph 0011). Liu et al. taught the chimeric pyrrolysyl-tRNA synthetase (chPylRS) variants have enhanced aminoacylation activity (paragraph 00030, Figs. 8A-8E). Liu et al. taught tRNA synthetase protein variants described by the disclosure exhibit improved activity (e.g., improved incorporation of target non-canonical amino acids (ncAAs) into tRNAs) or amino acid specificity (e.g., charging of preferred ncAAs) relative to the wild-type or variant tRNA synthetase protein from which they are derived. Some aspects of this disclosure provide fusion proteins, such as chimeric PylRS protein variants comprising an N-terminal domain of a bPylRS protein or bPylRS protein variant and a C-terminal domain of a mPylRS protein or MmPylRS protein variant (paragraph 00068).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date, to substitute the pyrrolysyl-tRNA synthetase of Zhang et al. with the chimeric pyrrolysyl tRNA synthetase of Liu et al. with a reasonable expectation of success. There would be a reasonable expectation of success as this would about to simple substitution of one known element (a known pyrrolysyl-tRNA synthetase of Zhang et al.) for another (the known chimeric pyrrolysyl tRNA synthetase of Liu et al.) to obtain predictable results. One of ordinary skill in the art would have been motivated to do so because Liu et al. teach a chimeric pyrrolysyl-tRNA synthetase protein variant comprising a first portion of amino acid residues 1-149 of Methanosarcina bakeri PyIRS and a second portion comprising amino acid residues 185-454 of Methanosarcina mazei PyIRS (paragraph 0011) and the benefits thereof include enhanced aminoacylation activity (paragraph 00030, Figs. 8A-8E), exhibit improved activity (e.g., improved incorporation of target non-canonical amino acids (ncAAs) into tRNAs) or amino acid specificity (e.g., charging of preferred ncAAs) relative to the wild-type or variant tRNA synthetase protein from which they are derived (paragraph 00068).
Accordingly, the limitations of claim 141 and 149 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claim 142 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al., Romesberg et al., and Liu et al. as applied to claim 141 and 149 above, and further in view of Caffaro et al., cited above.
The teachings of Zhang et al., Romesberg et al. and Liu et al. as applicable to claim 141 and 149 are described above.
Zhang et al., Romesberg et al. and Liu et al. do not teach wherein the at least one unnatural amino acid encoded by the codon is N6-((azidoethoxy)-carbonyl)-L-lysine (AzK).
Caffaro et al. cures these deficiencies. Caffaro et al. taught modified IL-10 polypeptides comprising amino acid sequence comprising at least one unnatural amino acid and that the unnatural amino acid comprises N6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK) (paragraphs 0005,0011,0013-0018,0078,0091,0117,0121). Caffaro et al. taught a plasmid comprising a double-stranded oligonucleotide that encodes an IL-10 variant having a desired amino acid sequence and that contains a unnatural base pair comprising a first unnatural nucleotide and a second unnatural nucleotide to provide a codon at the desired position at which an unnatural amino acid, such as /V6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK), a plasmid encoding a tRNA derived from M. mazei and which comprises an unnatural nucleotide to provide a recognized anticodon (to the codon of the IL-10 variant) in place of its native sequence, and a plasmid encoding a M. barkeri derived pyrrolysyl-tRNA synthetase (Mb PylRS) (paragraph 0121). Caffaro et al. also taught the codon comprises an unnatural nucleotide such as NaM, and the anticodon comprises the unnatural nucleotide such as TPT3 (paragraph 0121). Caffaro et al. also taught the IL-10 polypeptides containing an unnatural amino acid are generated recombinantly by a host cell, which is a eukaryotic cell (e.g. mammalian cell, insect cells, yeast cells, or plant cell (paragraphs 0234-0235).
It would have been obvious to one of ordinary skill in the art before the effective filing date, to provide N6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK) as the unnatural amino acid in the mRNA encoding a polypeptide comprising at least one unnatural amino acid of Zhang et al., based on the teachings of Caffaro et al. There would be a reasonable expectation of success because Caffaro et al. also pertains to polypeptides comprising unnatural amino acids, as well as mRNA comprising codons with unnatural bases and tRNA comprising anticodons with unnatural bases, and this would have amounted to simple substitution of one known unnatural amino acid for another known unnatural amino acid to obtain predictable results. One of ordinary skill in the art would have been motivated to provide N6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK) as the unnatural amino acid because Caffaro et al. lists multiple unnatural amino acids appropriate for use in a modified IL-10 polypeptide including Azk.
Accordingly, the limitations of claim 142 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Response to Arguments
Applicant's arguments filed 02/12/2026 have been fully considered but they are not persuasive.
Applicant argues on page 12 of response that they disagree with the obviousness rejections and to expedite prosecution have amended independent claims 1 and 145. Applicant argues that the recited codons provide unexpectedly superior results in eukaryotic cells compared to other codons in terms of producing proteins comprising an unnatural amino acid and would not have been expected by one of ordinary skill in the art based on the cited references.
Applicant points to Example 2 in which eukaryotic cells were transfected with mRNA encoding EGFP comprising one of nine codons- AXC, GXC, GXU, GYC, AYC, GYU, XCC, YCC or AGX encoding unnatural amino acid AzK and provided with the cognate unnatural tRNA and AzK (specification paragraph 00172). Applicant states that as shown in FIG. 6A, the codons AXC, GYC, GXC, GXU (GXT in the figure) and AGX now recited in claims 1 and 145, produced much stronger fluorescence signal per cell when provided with cognate unnatural tRNAs relative to that when not provided with cognate unnatural tRNAs, and would not have been predictable from the cited references. None of the cited references provides any suggestions or guidance that any of the particular recited codons (AXC, GYC, GXC, GXU and AGX) would be more useful for higher levels of production of proteins comprising an unnatural amino acid in a eukaryotic cell relative to other codons and therefore claims 1 and 145 as well as the claims that depend thereon are not obvious in view of the cited references.
This is not found persuasive for several reasons. Regarding Applicants argument that the recited codons provide unexpectedly superior results in eukaryotic cells compared to other codons in terms of producing proteins comprising an unnatural amino acid, the instant claims are product claims and do not recite a function regarding producing proteins. In addition, Applicant has not explained what the expected results should be to determine if the results are in fact unexpected.
Whether the unexpected results are the result of unexpectedly improved results or a property not taught by the prior art, the "objective evidence of nonobviousness must be commensurate in scope with the claims which the evidence is offered to support." In other words, the showing of unexpected results must be reviewed to see if the results occur over the entire claimed range. In re Clemens, 622 F.2d 1029, 1036, 206 USPQ 289, 296 (CCPA 1980) (Claims were directed to a process for removing corrosion at "elevated temperatures" using a certain ion exchange resin (with the exception of claim 8 which recited a temperature in excess of 100C). Appellant demonstrated unexpected results via comparative tests with the prior art ion exchange resin at 110C and 130C. The court affirmed the rejection of claims 1-7 and 9-10 because the term "elevated temperatures" encompassed temperatures as low as 60C where the prior art ion exchange resin was known to perform well. The rejection of claim 8, directed to a temperature in excess of 100C, was reversed.). See also In re Peterson, 315 F.3d 1325, 1329-31, 65 USPQ2d 1379, 1382-85 (Fed. Cir. 2003) (data showing improved alloy strength with the addition of 2% rhenium did not evidence unexpected results for the entire claimed range of about 1-3% rhenium); In re Grasselli, 713 F.2d 731, 741, 218 USPQ 769, 777 (Fed. Cir. 1983) (Claims were directed to certain catalysts containing an alkali metal. Evidence presented to rebut an obviousness rejection compared catalysts containing sodium with the prior art. The court held this evidence insufficient to rebut the prima facie case because experiments limited to sodium were not commensurate in scope with the claims.). Note: MPEP 716.02(d).
It is also noted that any differences between the claimed invention and the prior art may be expected to result in some differences in properties. The issue is whether the properties differ to such an extent that the difference is really unexpected. An unexpected property or result must actually be unexpected and of statistical and practical significance. The burden is on the applicant to establish the results are in fact unexpected, unobvious and of statistical and practical significance. See MPEP 716.02.
In addition as the Examiner noted above, the claims are drawn to a product. "The patentability of apparatus or composition claims depends on the claimed structure, not on the use or purpose of that structure." Catalina Mktg. Int'l, Inc. v. Coolsavings.com, Inc., 289 F.3d 801,809 (Fed. Cir. 2002). Note: MPEP 2111.02. In addition, See MPEP 2112.01: "Products of identical chemical composition cannot have mutually exclusive properties." A chemical composition and its properties are inseparable. Therefore, if the prior art teaches the identical chemical structure, the properties applicant discloses and/or claims are necessarily present. In re Spada, 911 F.2d 705,709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
Regarding Applicant’s argument that the recited codons provide unexpectedly superior results in eukaryotic cells compared to other codons in terms of producing proteins comprising an unnatural amino acid and would not have been expected by one of ordinary skill in the art based on the cited references, it is well settled that "any need or problem known in the field of endeavor at the time of invention and addressed by the patent can provide a reason for combining the elements in the manner claimed." KSR Int 'l Co. v. Teleflex Inc., 550 U.S. 398, 420 (2007). As long as some suggestion to combine the elements is provided by the prior art as a whole, the law does not require that they be combined for the reason or advantage contemplated by the inventor. In re Beattie, 974 F.2d 1309, 1312 (Fed. Cir. 1992); In re Kronig, 539 F.2d 1300, 1304 (CCPA 1976). MPEP 2143.01 and 2144 (IV). The reason or motivation to modify the reference may often suggest what the inventor has done, but for a different purpose or to solve a different problem. It is not necessary that the prior art suggest the combination to achieve the same advantage or result discovered by applicant. See, e.g., In re Kahn, 441 F.3d 977, 987, 78 USPQ2d 1329, 1336 (Fed. Cir. 2006) (motivation question arises in the context of the general problem confronting the inventor rather than the specific problem solved by the invention); Cross Med. Prods., Inc. v. Medtronic Sofamor Danek, Inc., 424 F.3d 1293, 1323, 76 USPQ2d 1662, 1685 (Fed. Cir. 2005) ("One of ordinary skill in the art need not see the identical problem addressed in a prior art reference to be motivated to apply its teachings."); In re Lintner, 458 F.2d 1013, 173 USPQ 560 (CCPA 1972) (discussed below); In re Dillon, 919 F.2d 688, 16 USPQ2d 1897 (Fed. Cir. 1990), cert. denied, 500 U.S. 904 (1991).
Therefore, as the claims are directed to a product, and the Examiner has provided motivation from the references for combining and/or modifying the references to arrive at the instant claims, the motivation does not need to be the same motivation or reason that the present inventors have done so.
Therefore, the Examiner is maintaining the above 35 U.S.C. 103 rejections as being unpatentable over the cited references above.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1-4,6-8,15,17,18,20,125-134,136-140,143-148 and 150-152
are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 10,513,706, Issued 24 Dec 2019, in view of Zhang et al. and Caffaro et al. (WO2020097325, effectively filed 08 Nov 2018).
Instant claims 1-3,143-146 recite an isolated eukaryotic cell comprising a mRNA comprising a codon comprising a first unnatural base, wherein the mRNA encodes a polypeptide comprising at least one unnatural amino acid encoded by the codon; and a transfer RNA comprising an anticodon comprising a second unnatural base, wherein the first and second unnatural bases are capable of forming an unnatural base pair in the eukaryotic cell and recites specific codons (AXC, GYC, GXC, GXU, AGX). Instant claim 4 adds a tRNA synthetase and claims 6 and 7 recite the eukaryotic cell is an isolated human cell, or an isolated mammalian cell; claims 138-140 recite the isolated cell is a HEK293T, hamster, CHO cell; instant claims 8 and 136 recite the first and second unnatural bases are NaM and TPT3; instant claims 15,17 and 137 recite the unnatural amino acid, Azk. Instant claims 125-129 and 150-152 recite specific codons and anticodons; instant claims 130-133 recite specific tRNA synthetases and tRNA (pyrrolysyl or tyrosyl) derived from specific cells.
Claims 1-12 of U.S. Pat. 10,513,706 recite an isolated cell comprising DNA comprising at least one unnatural base pair (UBP) the at least one UBP comprising a first unnatural nucleotide and a second unnatural nucleotide; and a heterologous nucleic acid encoding a nucleoside triphosphate transporter that is at least 85% identical to SEQ ID NO: 1, wherein the isolated cell is an Escherichia coli cell, and recites options for the first and second unnatural nucleotide, including some of the same unnatural bases as in instant claims 8 and 136.
U.S. Pat. 10,513,706 does not recite the cell is an isolated eukaryotic cell, and does not recite that the cell comprising mRNA comprising a codon comprising a first unnatural base and which encodes a polypeptide comprising an unnatural amino acid encoded by the codon, and a tRNA comprising an anticodon comprising a second unnatural base, or any specific codons or anticodons. U.S. Pat. 10,513,706 does not recite a tRNA synthetase or unnatural amino acids.
The teachings of Zhang et al. and Caffaro et al. have been described above in the 103 rejections.
It would have been obvious to one of ordinary skill in the art to have modified claims 1-12 of U.S. Pat. 10,513,706 with the teachings of Zhang et al. and Caffaro et al. to arrive at the instant claims with a reasonable expectation of success because both Zhang et al. and Caffaro et al. relate to unnatural base pairs formed by unnatural nucleotides and teach the same unnatural nucleotides as those recited in claims 1-12 of U.S. Pat. 10,513,706. One of ordinary skill in the art would have been motivated modify the claims of U.S. Pat. 10,513,706 to provide the plasmid encoding the tRNASer gene (serT) and sfGFP with the native sfGFP codon 151 (TAC) replaced by the unnatural codon AXC (sfGFP(AXC)151; X denotes NaM), and the anticodon of serT replaced by the unnatural anticodon GYT (tRNASer(GYT); Y denotes TPT3, or wherein the codon is GXC and the corresponding anticodon is GYC of Zhang et al., or the specific codon and anticodon combinations taught by Caffaro et al. in the eukaryotic cells of Caffaro et al. for the purpose of producing a polypeptide comprising an unnatural amino acid in a suitable host cell which is a eukaryotic host cell as taught by Caffaro et al.
It would have been obvious to one of ordinary skill in the art to provide N6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK) as the unnatural amino acid in the mRNA encoding a polypeptide comprising at least one unnatural amino acid of Zhang et al., based on the teachings of Caffaro et al. There would be a reasonable expectation of success, as this would have amounted to simple substitution of one known unnatural amino acid for another known unnatural amino acid to obtain predictable results. One of ordinary skill in the art would have been motivated to provide N6-((2-azidoethoxy)-carbonyl)-L-lysine (AzK) as the unnatural amino acid because Caffaro et al. lists multiple unnatural amino acids appropriate for use in a modified IL-10 polypeptide including Azk.
Accordingly, the limitations of claims 1-4,6-8,15,17,18,20,125-134,136-140,143-148 and 150-152 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claim 135 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 10,513,706, Issued 24 Dec 2019, in view of Zhang et al. and Caffaro et al. (WO2020097325, effectively filed 08 Nov 2018) and further in view of Franze et al. (US 20110117087, Published 19 May 2011).
The teachings of Zhang et al., Caffaro et al. and Franze et al. have been described in the 103 rejections above.
U.S. Patent No. 10,513,706, Zhang et al. and Caffaro et al. do not teach wherein the polypeptide translated from the mRNA comprises a eukaryotic glycosylation pattern.
Franze et al. cures this deficiency. The teachings of Franze et al. has been described in the above 103 rejection.
It would have been obvious to one of ordinary skill in the art before the effective filing date, modify U.S. Patent No. 10,513,706, Zhang et al. and Caffaro et al. by substituting the GFP produced from the mRNA of Zhang et al. with the immunoglobulin produced by a eukaryotic cell and having a modified glycosylation pattern from the cell expressing it according to the teachings of Franze et al. for the purpose of modifying the biological properties of the produced immunoglobin. There would be a reasonable expectation of success, as this amounts to simple substitution of one known protein/polypeptide (GFP of Zhang et al.) for another (immunoglobin with modified glycosylation pattern produced by a eukaryotic cell of Franze et al.) to obtain predictable results. An ordinary artisan would be motivated to do so in order to produce an immunoglobulin as the polypeptide produced, and wherein the immunoglobulin has the glycosylation pattern of the eukaryotic cell that produced it, because Franze et al. teach that posttranslational modifications such as the glycosylation pattern have an influence on the efficacy, stability, immunogenic potential, binding etc. of an immunoglobulin and that the glycosylation pattern of a polypeptide produced by a eukaryotic cell can be modified based on the amount of glucose provided in the cell cultivation process and because a polypeptide is obtained from a cell expressing it in form of a composition comprising differently glycosylated forms of the same polypeptide.
Accordingly, the limitations of claim 135 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claims 141,142 and 149 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 10,513,706, Issued 24 Dec 2019, in view of Zhang et al. and Caffaro et al. (WO2020097325, effectively filed 08 Nov 2018) and further in view of Liu et al. (WO 2019010164, Published 10 Jan 2019).
The teachings of Zhang et al. and Caffaro et al. have been described in the 103 rejections above.
U.S. Patent No. 10,513,706, Zhang et al. and Caffaro et al. do not teach the pyrrolysyl tRNA synthetase is a chimeric pyrrolysyl tRNA synthetase.
Liu et al. cures this deficiency. The teachings of Liu et al. have been described in the above 103 rejection.
It would have been obvious to one of ordinary skill in the art before the effective filing date, to modify the claims of U.S. Patent No. 10,513,706 with the teachings of Zhang et al. and Caffaro et al. and to substitute the pyrrolysyl-tRNA synthetase of Zhang et al. with the chimeric pyrrolysyl tRNA synthetase of Liu et al. with a reasonable expectation of success. There would be a reasonable expectation of success as this would about to simple substitution of one known element (a known pyrrolysyl-tRNA synthetase of Zhang et al.) for another (the known chimeric pyrrolysyl tRNA synthetase of Liu et al.) to obtain predictable results. One of ordinary skill in the art would have been motivated to do so because Liu et al. teach a chimeric pyrrolysyl-tRNA synthetase protein variant comprising a first portion of amino acid residues 1-149 of Methanosarcina bakeri PyIRS and a second portion comprising amino acid residues 185-454 of Methanosarcina mazei PyIRS (paragraph 0011) and the benefits thereof include enhanced aminoacylation activity (paragraph 00030, Figs. 8A-8E), exhibit improved activity (e.g., improved incorporation of target non-canonical amino acids (ncAAs) into tRNAs) or amino acid specificity (e.g., charging of preferred ncAAs) relative to the wild-type or variant tRNA synthetase protein from which they are derived (paragraph 00068).
Accordingly, the limitations of claims 141,142 and 149 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claims 1-4,6-8,15,17,18,20 and 125-152 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of U.S. Patent No. 11,834,689 (‘689), Issued 5 Dec 2023, in view of Romesberg et al. or over claims 1-28 of U.S. Patent No. 12,319,944 (‘944) Issued 3 June 2025, in view of Romesberg et al.
Instant claims 1-3,143-146 recite an isolated eukaryotic cell comprising a mRNA comprising a codon comprising a first unnatural base, wherein the mRNA encodes a polypeptide comprising at least one unnatural amino acid encoded by the codon; and a transfer RNA comprising an anticodon comprising a second unnatural base, wherein the first and second unnatural bases are capable of forming an unnatural base pair in the eukaryotic cell and recites specific codons (AXC, GYC, GXC, GXU, AGX). Instant claim 4 adds a tRNA synthetase and claims 6 and 7 recite the eukaryotic cell is an isolated human cell, or an isolated mammalian cell; claims 138-140 recite the isolated cell is a HEK293T, hamster, CHO cell; instant claims 8 and 136 recite the first and second unnatural bases are NaM and TPT3; instant claims 15,17 and 137 recite the unnatural amino acid, Azk. Instant claims 125-129 and 150-152 recite specific codons and anticodons; instant claims 130-133 recite specific tRNA synthetases and tRNA (pyrrolysyl or tyrosyl) derived from specific cells.
Claims 1-25 of ‘689 recite a cell comprising a nucleoside triphosphate transporter, a tRNA from Methanosarcina mazei or Methanococcous jannaschii comprising an anticodon and recites specific anticodon sequences and comprising a first unnatural nucleobase which are the same unnatural nucleobases recited in the instant claims; an aminoacyl tRNA synthetase, and an mRNA encoding the protein comprising the unnatural amino acid and comprising a codon and recites specific codon sequences which are the same as those in the instant claims, and wherein the codon comprises an unnatural nucleotide comprising a second unnatural nucleobase and which are the same unnatural nucleobases recited in the instant claims.
Claims 1-28 of ‘944 recite a method of producing a protein comprising an unnatural amino acid in a cell comprising contacting the cell with an unnatural amino acid, the cell comprising: a nucleoside triphosphate transporter; a tRNA from Methanosarcina mazei or Methanococcous jannaschii comprising an anticodon comprising a first unnatural nucleobase which are the same unnatural nucleobases recited in the instant claims; an aminoacyl tRNA synthetase that aminoacylates the tRNA with the unnatural amino acid; an mRNA encoding the protein comprising the unnatural amino acid and comprising a codon, the codon comprising an unnatural nucleotide comprising a second unnatural nucleobase and which are the same unnatural nucleobases recited in the instant claims. Claims 5 and 12 recite the same anticodons, GYU or GYC as in instant claims 1,126-128. Claims 18 and 24 recite the same codons, AXC or GXC as in instant claims 1 and 125.
‘689 and ‘944 do not recite the cell is a eukaryotic cell and ‘944 recites a method of producing a protein in a cell rather than the cell comprising the recited components.
Romesberg et al. cures the deficiencies regarding the eukaryotic cell. The teachings of Romesberg et al. has been described above in the 103 rejections.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date, to switch the cell of ’689 or ‘944 with the eukaryotic cell of Romesberg et al. with a reasonable expectation of success. There would be a reasonable expectation of success, because Romesberg et al. also pertains to unnatural bases and unnatural base pairs (UBPs) including but not limited to (d)5SICS-(d)NaM and (d)TPT3-(d)NaM and increasing the genetic alphabet of cell or an organism. A cell product comprising the tRNA, synthetase and mRNA and comprising the unnatural bases and unnatural amino acids is an obvious variant of the method of ‘944. One of ordinary skill in the art would have been motivated to do so because Romesberg et al. teach that the UBPs and cells stably incorporating the UBPs described herein, offer numerous advantages and can be applied to a broad range of biotechnologies (paragraph 0011), and the discovery that particular unnatural base pairs (UBPs) including but not limited to (d)5SICS-(d)NaM and (d)TPT3-(d)NaM can be amplified with natural base pair-like efficiency and fidelity and provide methods, compositions, and kits, for increasing the genetic alphabet of cell or an organism, including cells comprising an expanded genetic alphabet, e.g., cells that stably propagate an expanded genetic alphabet, and that the cell is a eukaryotic cell, including a human cell or animal cell (paragraphs 0063,0133,0327,0347,0348) or mammalian cell (paragraph 0353), or 293 or CHO cells (paragraph 0353).
Accordingly, the limitations of claims 1-4,6-8,15,17,18,20 and 125-152 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Response to Arguments
Applicant's arguments filed 02/12/2026 have been fully considered but they are not persuasive.
Applicant argues on pages 13-14 regarding the above Nonstatutory Double Patenting rejections over the claims of US Patent No. 10,516,706, US Patent No. 11,834,689, and US Patent No. 12,319,944 that the amendments render the rejections moot, as well as the remarks presented regarding the 103 rejections.
This is not found persuasive. The examiner has responded to the arguments regarding the 103 rejections above, and even with the amendments to the instant claims, the obviousness type nonstatutory double patenting rejections over the claims of the above Patents still stand and are addressed above.
Conclusion
Claims 1-4,6-8,15,17,18,20 and 125-152 are rejected.
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.
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/STEPHANIE L SULLIVAN/Examiner, Art Unit 1635
/ABIGAIL VANHORN/Primary Examiner, Art Unit 1636
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