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 .
Status of Application/Amendment/Claims
This Office action is in response to the communications filed on May 19, 2026.
Currently, claims 1, 3-4, 6, 9, 11-12, 14, 16, 18, 21, 24-25, 27-30, 32-35, 42, 45, 54, 61, and 71-75 are pending in the instant application. Claims 9 and 42 are withdrawn from further consideration as being drawn to nonelected inventions. The newly amended claim, claims 4 and 6, are now drawn to NNX and XNN, which are drawn to nonelected species thus are withdrawn from consideration as being directed to non-elected species.
Accordingly, claims 1, 3, 11-12, 14, 16, 18, 21, 24-25, 27-30, 32-35, 45, 54, 61, and 71-75 are under examination on the merits in the instant application.
The following rejections are either newly applied or are reiterated and are the only rejections and/or objections presently applied to the instant application.
Response to Arguments and Amendments
Withdrawn Rejections
Any rejections/objections not repeated in this Office action are hereby withdrawn.
New Rejections Necessitated by Amendment
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, 3, 11-12, 14, 16, 18, 21, 24-25, 27-30, 32-35, 45, 54, 61, and 71-75 are rejected under 35 U.S.C. 103 as being unpatentable over Feldman et al. (JACS, 2019, 141:10644-10653, of record) in view of Zhang et al. (Nature, 2017, 551:644-647, of record), Suzuki et al. (Nature Chemical Biology, 2017, 13:1261-1266), Liu (US 2013/0078671 A1, of record), and Romesberg et al. (WO 2017/223528 A1, of record).
Feldman discloses a method of producing proteins in vivo comprising site-specific three “noncanonical amino acids (ncAAs)” that are “N6-(2-azidoethoxy)-carbonyl-L-lysine (AzK)” in a strain of E. coli constitutively expressing a nucleoside triphosphate transporter from P. tricornutum (PtNTT2), wherein the method comprises using a plasmid comprising three site-specific “AXC” (X is dNaM) for the codon template at codon positions 149, 151, and 153 and the base-pairing “GYT” (Y is dTPT3) for the anticodon template for M. mazei Pyl tRNA, which is charged with AzK by the M. barkeri pyrrolysyl-tRNA synthetase (PylRS), wherein the unnatural mRNA is transcribed by T7 RNAP and the protein with “incorporation of three AzK residues” is translated in E. coli. See pages 10644-10645 and 10649-10651; Figures 7A-7C.
Feldman discloses the RNA analogues of “NaM” and “TPT3” in Figures 4A-B as shown below.
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Feldman does not teach that the protein comprises four AzK residues are site-specifically incorporated. However, Feldman teaches a goal “to produce protein with a higher density of ncAAs.” See page 10652.
Feldman does not teach using two unnatural tRNA molecules each comprising a different unnatural anticodon of different nucleotide sequences and charging the tRNA molecules by two different tRNA synthetases comprising chPylRS and MjpAzFRS.
Zhang teaches producing a protein in E. coli comprising a site-specific noncanonical amino acid “N6-[(2-(propynyloxy)carbonyl]-L-lysine (PrK)” comprising a plasmid with the “GXC” codon (X denotes NaM) at position 151, the “GYC” anticodon (Y denotes TPT3), and “PylRS”, wherein the GXC-GYC pair produced a higher level (about 97.5%) of PrK incorporation compared to the AXC-GYT pair (about 96.2%). See pages 644-645; Figures 2c-2d.
Zhang teaches producing a protein in E. coli comprising a site-specific noncanonical amino acid “p-azido-phenylalanine (pAzF)” comprising a plasmid with the “GXC” codon (X denotes NaM) at position 151, the “GYC” anticodon (Y denotes TPT3), and “an evolved Methanococcus jannaschii TryRS-tRNATyr pair (pAzFRS-tRNApAzF)”, wherein See page 645; Figure 3b.
Zhang teaches that “the nucleoside triphosphate transporter from P. tricornutum (PtNTT2) is able to import both the deoxy- and ribotriphosphates of both unnatural nucleotides”. See page 644.
Suzuki discloses “a novel chimeric PylRS (chPylRS, encoded by chpylS)”, which as “improved solubility in vitro compared to that of nonchimeric proteins”. See page 1262.
Liu teaches a method of site-specifically incorporating a plurality of different noncanonical amino acids or “at least two different noncanonical amino acids” into a single target protein using multiple aminoacyl-tRNA synthetase/tRNA pairs, wherein the protein comprising different noncanonical amino acids is useful “to enhance functional studies of the proteins.” See paragraphs 0004-0008.
Romesberg teaches an “in vivo method of increasing the production of a nucleic acid molecule containing an unnatural nucleotide” such as dNaM forming a base pair with dTPT3, wherein the nucleic acid molecule is produced by an engineered E. coli cell utilizing a modified nucleoside triphosphate transporter from P. tricornutum (PtNTT2), which is SEQ ID NO:4. See paragraphs 0007-0010; claims 11, 18-22, 69-71, 79-80, and 88.
It is noted that Romesberg’s SEQ ID NO:4 is a truncated amino acid sequence of SEQ ID NO:1 claimed in the instant case and is at least 80% identical to SEQ ID NO:1 claimed in the instant case.
It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Feldman’s method of incorporating three AzK amino acid sites encoded by AXC codon paired with GYT anticodon by additionally incorporating at least one of Zhang’s PrK encoded by GXC codon paired with GYC anticodon. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success in order to produce a protein comprising a higher density of diverse, art-recognized noncanonical amino acids, thereby enhancing the functional understanding/studies of proteins because it was an art-recognized goal “to produce protein with a higher density of ncAAs” as expressly disclosed by Feldman, wherein producing a protein in E. coli comprising a site-specific noncanonical amino acid PrK, which is produced by a plasmid with the “GXC” codon (X denotes NaM) and the “GYC” anticodon (Y denotes TPT3) was already successfully practiced by Zhang.
It would also have been obvious to incorporate pAzF amino acid sites encoded by AXC paired with GYT in the presence of Zhang’s MjpAzFRS and to further incorporate Zhang’s PrK amino acid sties encoded by GXC codon paired with GYC anticodon in the presence of Suzuki’s chimeric PylRS in place of Zhang’s nonchimeric PylRS, wherein the total number of pAzF and PrK in combination is more than three. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success in order to produce a protein comprising a higher density of diverse, art-recognized noncanonical amino acids, thereby enhancing the functional understanding/studies of proteins because it was an art-recognized goal “to produce protein with a higher density of ncAAs”, wherein incorporation of three ncAAs using was already practiced in the art as evidenced by Feldman, which thus would have promoted one of ordinary skill in the art to increase the number of three ncAAs that were already practiced and deemed viable, and because producing a protein comprising site-specific incorporation of at least two different ncAAs using at least two different aminoacyl-tRNA synthetase/tRNA pairs was an art-recognized goal “to enhance functional studies of the proteins” as evidenced by Liu, wherein Suzuki’s “chimeric PylRS (chPylRS, encoded by chpylS)” was known to provide “improved solubility in vitro compared to that of nonchimeric proteins”.
It would have been obvious to one of ordinary skill in the art to replace the PtNTT2 used by both Feldman and Zhang with Romesberg’s SEQ ID NO:4, which is a truncated PtNTT2, because Romesberg’s SEQ ID NO:4 was suggested to be useful in an “in vivo method of increasing the production of a nucleic acid molecule containing an unnatural nucleotide” comprising dNaM base pairing with dTPT3, thereby suggesting a reasonable expectation that Romesberg’s SEQ ID NO:4 would be useful in increasing in vivo production of a protein comprising unnatural protein that is synthesized from the nucleic acid comprising the unnatural base pairs formed by dNaM and dTPT3.
Accordingly, claims 1, 3, 11-12, 14, 16, 18, 21, 24-25, 27-30, 32-35, 45, 54, 61, and 71-75 taken as a whole would have been prima facie obvious before the effective filing date.
Response to Arguments
Applicant's arguments filed on May 19, 2026 have been fully considered but they are not persuasive. Applicant argues that the claims as currently amended are not obvious because none of the cited references teaches using two different codon-anti-codon pairs. In response, it is noted that the prima facie obviousness of the currently amended claims drawn to using two different pairs of AXC-GYT and GXC-GYC to encode two different unnatural amino acids of Azk and AzF, respectively, is set forth in the rejection hereinabove.
Applicant argues that the claims are not obvious because of “results that are surprisingly better than” expected/predicted by a person of ordinary skill in the art by pointing out Figure 14, Table 2, and paragraph 00238 of the instant application, which together support a “significantly greater” and “more potent” protein production compared to a control “comprising only natural nucleotides” as in Liu. In response, applicant’s attention is directed to the fact that unexpected results must be compared with the closest prior art.
“When unexpected results are used as evidence of nonobviousness, the results must be shown to be unexpected compared with the closest prior art.” In re Baxter Travenol Labs., 952 F.2d 388, 392 (Fed. Cir. 1991).
Applicant’s argument that the claimed subject matter is surprising and unexpected compared to a control “comprising only natural nucleotides”, which are also used in Liu’s experiments, is thus found insufficient to support the asserted unexpected results provided by the claimed subject matter because the closest prior art in the instant rejection is Feldman’s method of producing a protein comprising using an unnatural codon-anti-codon pair encoding an unnatural amino acid, AzK.
In view of the foregoing, applicant’s arguments are not found persuasive.
Double Patenting
The text of the judicially created doctrine not included in this action can be found in a prior Office action.
Claims 45, 54, 61, and 71-75 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of U.S. Patent No. 11,834,689 B2 in view of Feldman et al. (JACS, 2019, 141:10644-10653, of record) in view of Zhang et al. (Nature, 2017, 551:644-647, of record), Suzuki et al. (Nature Chemical Biology, 2017, 13:1261-1266), Liu (US 2013/0078671 A1, of record), and Romesberg et al. (WO 2017/223528 A1, of record).
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims would have been obvious over the ‘689 patent claims drawn to a cell comprising at least two different tRNA synthetases, wherein the anticodon (“GYT or GYC”) of the tRNAs pairs with the codon (“AXC or GXC”) of the mRNA, wherein the Y is TPT3 and X is NaM, wherein the cell comprises a PtNTT. It would have been obvious to incorporate a plurality of UBPs because the terms “an anticodon” and “a codon” claimed in the ‘689 patent claims are defined to include a plurality as evidenced by the ‘689 specification’s definition that “the singular forms “a,” “an”, and “the” include plural referents unless the context clearly dictates otherwise.” It would have bene obvious to incorporate at least 4 UBPs into the cell of the ‘689 patent claims for the reasons stated in the §103 rejection above in view of the combined teachings of Feldman, Zhang, Suzuki, Liu, and Romesberg, which are set forth in the §103 rejection above, which is fully incorporated by reference herein, wherein the at least 4 UBPs are the combination of Zhang’s PrK (GXC-GYC) in the presence of Suzuki’s chimeric PylRS and pAzF (AXC and GYT), wherein the cell is further modified to comprise Romesberg’s SEQ ID NO:4 so as to provide increased “production of a nucleic acid molecule containing an unnatural nucleotide”.
Claims 1, 3, 11-12, 14, 16, 18, 21, 24-25, 27-30, 32-35, 45, 54, 61, and 71-75 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-28 of U.S. Patent No. 12,319,944 B2 in view of Feldman et al. (JACS, 2019, 141:10644-10653, of record) in view of Zhang et al. (Nature, 2017, 551:644-647, of record), Suzuki et al. (Nature Chemical Biology, 2017, 13:1261-1266), Liu (US 2013/0078671 A1, of record), and Romesberg et al. (WO 2017/223528 A1, of record).
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims would have been obvious over the ‘944 patent claims drawn to a method of producing a protein comprising an unnatural amino acid in an E. coli cell comprising at least two different tRNA synthetases that aminoacylate the tRNA with the unnatural amino acid, wherein the anticodon (“GYU or GYC”) of the tRNAs pairs with the codon (“AXC or GXC”) of the mRNA, wherein the Y is TPT3 and X is NaM, wherein the unnatural amino acid is pAzF or PrK, and “at least one unnatural nucleoside is introduced into the cell via the nucleoside triphosphate transporter”. It would have been obvious to incorporate a plurality of UBPs because the terms “an unnatural amino acid”, “an anticodon”, and “a codon” claimed in the ‘944 patent claims are defined to include a plurality as evidenced by the ‘944 patent specification’s definition that “the singular forms “a,” “an”, and “the” include plural referents unless the context clearly dictates otherwise.” It would have bene obvious to incorporate at least 4 UBPs into the cell of the ‘944 patent claims for the reasons stated in the §103 rejection above in view of the combined teachings of Feldman, Zhang, Suzuki, Liu, and Romesberg, which are set forth in the §103 rejection above, which is fully incorporated by reference herein, wherein use of Suzuki’s “chimeric PylRS (chPylRS, encoded by chpylS)” was known to provide “improved solubility”, and wherein Romesberg’s SEQ ID NO:4 was known for “increasing the production of a nucleic acid molecule containing an unnatural nucleotide”.
Claims 1, 3, 11-12, 14, 16, 18, 21, 24-25, 27-30, 32-35, 45, 54, 61, and 71-75 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55-76 of copending Application No. 19/196,915 in view of Feldman et al. (JACS, 2019, 141:10644-10653, of record) in view of Zhang et al. (Nature, 2017, 551:644-647, of record), Suzuki et al. (Nature Chemical Biology, 2017, 13:1261-1266), Liu (US 2013/0078671 A1, of record), and Romesberg et al. (WO 2017/223528 A1, of record).
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims would have been obvious over the ‘915 claims drawn to kit/method for “producing a protein comprising an unnatural amino acid” using the kit, wherein the kit comprises an E. coli cell comprising at least two different tRNA synthetases, wherein the mutant anticodon such as “GYU” and “GYC” of the tRNAs pairs with the mutant codon “AXC” and “GXC” of the mRNA, wherein the Y is TPT3 and X is NaM, wherein the cell further comprises PtNTT and unnatural amino acids pAzF and PrK. It would have been obvious to incorporate a plurality of UBPs because the terms “an unnatural amino acid”, “a mutant anticodon”, and “a mutant codon” claimed in the ‘915 claims are defined to include a plurality as evidenced by the ‘915 specification’s definition that “the singular forms “a,” “an”, and “the” include plural referents unless the context clearly dictates otherwise.” See paragraph 0039. It would have bene obvious to incorporate at least 4 UBPs into the cell of the ‘915 claims for the reasons stated in the §103 rejection above in view of the combined teachings of Feldman, Zhang, Suzuki, Liu, and Romesberg, which are set forth in the §103 rejection above, which is fully incorporated by reference herein, wherein use of Suzuki’s “chimeric PylRS (chPylRS, encoded by chpylS)” was known to provide “improved solubility”, and wherein Romesberg’s SEQ ID NO:4 was known for “increasing the production of a nucleic acid molecule containing an unnatural nucleotide”.
Response to Arguments
Applicant's arguments filed on May 19, 2026 have been fully considered but they are not persuasive. Applicant argues that the claims as currently amended are not obvious over the reference claims of the ‘689 patent claims, ‘944 patent claims, and the ‘915 application claims for the same reasons that the cited secondary references do not render the instant claims obvious. In response, the new ground of rejection under §103 necessitated by claim amendments is set forth hereinabove, which is different from the previous ground of rejection. Accordingly, applicant’s arguments are moot and unpersuasive.
Conclusion
No claim is allowed.
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 DANA H SHIN whose telephone number is (571)272-8008. The examiner can normally be reached Monday-Thursday: 8am - 6:30pm.
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/DANA H SHIN/Primary Examiner, Art Unit 1635
