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 10/29/2025. Claims 1-25 are currently pending. No claims are withdrawn from prosecution as being drawn to non-elected subject matter. Accordingly, claims 1-25 are examined herein.
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.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 10/29/2025 was filed after the mailing date of the non-final office rejection on 08/01/2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-25 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by U.S. Patent No. 12,385,035 B2 (of record; priority filing date, 05/14/2019; hereinafter PAT035).
The applied reference has a common assignee/inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Regarding claim 1, PAT035 teaches a prokaryotic cell which does not express first and second endogenous tRNAs and an endogenous release factor, wherein first and second types of sense codons as well as a stop codon have been recoded so that their associated tRNAs and the release factor are dispensable, and the cell expresses orthogonal tRNA-aminoacyl-tRNA-synthetase pairs capable decoding the recoded codons, and the cell expresses a polypeptide comprising non-canonical amino acids encoded by the recoded sense codons (claims 1-4, 6-11 and below):
(168) For instance, the synthetic prokaryotic genome of the present invention substantially or completely lacks one or more sense codons. Therefore, one or more tRNA or release factors may be deleted from the synthetic genome. For instance, a tRNA which decodes the one or more sense codons that have been replaced (or deleted) may be deleted from the synthetic prokaryotic genome. A tRNA which decodes one or more sense codons that have been replaced (or deleted) may be deleted and the synthetic prokaryotic genome will remain viable if the tRNA decodes only the one or more sense codons that have been replaced (or deleted); or alternatively if the tRNA decodes one or more sense codons that have been replaced (or deleted) and one or more sense codons that have not been replaced (or deleted), if the tRNA is dispensable for the one or more sense codons that have not been replaced (or deleted) (i.e. the one or remaining sense codons which the tRNA decodes are decoded by one or more alternative tRNAs). For example, if the synthetic prokaryotic genome lacks TCA sense codons, serT, encoding tRNA.sup.Ser.sub.UGA, may be deleted and/or if the synthetic prokaryotic genome lacks TCG sense codons, serU, encoding tRNA.sup.Ser.sub.CGA, may be deleted. The deletion of one or more tRNAs may be used, for instance, in combination with a reassigned, endogenous tRNA or an orthogonal aminoacyl-tRNA synthetase/tRNA pair to reassign the one or more sense codons to an alternative amino acid.
(189) In some embodiments the synthetic prokaryotic genome lacks genes encoding release factors (e.g. RF1) and/or the host cell lacks release factors (e.g. RF1) to increase the efficiency of incorporation of non-proteinogenic amino acids.
(245) We first designed a version of the E. coli MDS42 genome (Uniprot accession number AP012306.1) in which the serine codons TCG and TCA and the stop codon TAG in open reading frames (ORFs) are systematically replaced by their synonyms AGC, AGT, and TAA, respectively (FIG. 1A, FIG. 18, SEQ ID NO: 1).
PAT035 further teaches wherein the endogenous tRNAs/release factor are cognates for the first types of sense and stop codons, respectively, and wherein the genome comprises no occurrences of the first types of sense and stop codons (see above; relevant to claims 2-3, 6-8, 10-11, 17-18, and 22).
PAT035 further teaches wherein the first type of sense codon is TCA and first endogenous tRNA is tRNASerUGA; the second type of sense codon and second endogenous tRNA are TCG and tRNASerUGA; and the first type of stop codon is TAG and the endogenous release factor is RF-1 (see above; relevant to claims 4, 9, 12, 19 and 23).
PAT035 further teaches wherein all occurrences of the TCA codon have been replaced with AGT; all occurrences of the TCG codon have been replaced with AGC; and all occurrences of the TAG codon have been replaced with TAA (see above, relevant to claims 5 and 13).
PAT035 further teaches wherein the prokaryotic cell is a viable E. coli bacterial cell (MDS42, see above, relevant to claims 14-16, 20-21 and 24-25).
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:
Determining the scope and contents of the prior art.
Ascertaining the differences between the prior art and the claims at issue.
Resolving the level of ordinary skill in the pertinent art.
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 1-25 are rejected under 35 U.S.C. 103 as being unpatentable over Tharp et al. (Genetic Encoding of Three Distinct Noncanonical Amino Acids Using Reprogrammed Initiator and Nonsense Codons. bioRxiv 2020.12.07.415521.; posted on bioRxiv 12/08/2020) in view of Fredens et al. (Total synthesis of Escherichia coli with a recoded genome. Nature. 2019 May 01; 569(7757): 514–518, cited on an IDS).
Regarding claim 1, Tharp et al. teach a prokaryotic cell which expresses first, second and third aminoacyl-tRNA synthetases and first, second and third orthogonal tRNAs, such that each first/second/third respective synthetase and first/second/third tRNA form a pair and each tRNA is capable of decoding a different codon, wherein the cell expresses a polypeptide comprising three non-canonical amino acids encoded by their respective amino acids (§ABSTRACT):
Using itRNATy2AUA, in conjunction with its cognate tyrosyl-tRNA synthetase and two mutually orthogonal pyrrolysyl-tRNA synthetases, we demonstrate that
UAU can be reassigned along with UAG or UAA to encode two distinct ncAAs in the same protein. Furthermore, by engineering the substrate specificity of one of the pyrrolysyl-tRNA synthetases, we developed a triply orthogonal system that enables simultaneous reassignment of UAU, UAG, and UAA to produce proteins containing three distinct ncAAs at precisely defined sites.
Tharp et al. teach that a first type of sense codon and a first type of stop codon have been recoded (see ¶21 above).
Regarding claims 10-13, Tharp et al. teach that the cell is a bacterial cell which is E. coli, and that it is viable (p. 6 second ¶):
we devised a plasmid-based system for simultaneous incorporation of three distinct ncAAs. This three-plasmid system consisted of: (1) an accessory plasmids encoding AzFRS.2.t1, MaPylRS(N166S), and MatRNA(6)Pyl, (2) a second accessory plasmid encoding MmPylRS and MmtRNAPylUUA, and (3) a reporter plasmid encoding itRNATy2AUA and a triple-mutant sfGFP with a UAU mutation at position 1, a UAG mutation at position 135, and a UAA mutation at position 151 (Figure S15A). We measured sfGFP production E. coli DH10BΔmetZWV in the presence of pMeF, BocK, and mIF
Tharp et al. provide a teaching, suggestion or motivation to design cells capable of expressing proteins with non-canonical amino acids, because the technology has broad-ranging applications and can produce proteins with new functions (§Introduction p. 1):
Through the combined action of multiple, mutually orthogonal o-aaRS•o-tRNA pairs, proteins with multiple distinct ncAAs can be produced in living cells...This technology has broad-ranging applications, from introducing reactive
moieties into proteins for site-specific bioconjugation at multiple sites…to producing homogenously modified proteins featuring genetically encoded posttranslational modifications…An exciting prospect of GCE is the ability one day to produce completely unnatural polypeptides with new-to-Nature
functions.
Tharp et al. also note that one strategy to expand the genetic code (to produce polypeptides with non-canonical amino acids) is to, “reassign one of the 61 sense codons that normally encode a canonical amino acid” (§Introduction p. 1).
Tharp et al. do not teach that the reassigned (recoded) codons are a combination of a first type of sense codon, second type of sense codon, and first type of stop codon.
Fredens et al. teach total recoding of the E. coli genome to replace two sense codons and a stop codon (i.e., a prokaryotic cell wherein the first/second sense codons and stop codons have been recoded)(§Design of a recoded genome p. 514):
We designed a genome in which the serine codons TCG and TCA, and
the stop codon TAG, in open reading frames (ORFs) of MDS42 E. coli…are systematically replaced by their synonyms AGC, AGT and TAA, respectively
Tharp et al. do not teach that the cell does not express first and second endogenous tRNAs and does not express an endogenous release factor.
Fredens et al. teach wherein the cell does not express first and second endogenous tRNAs and a release factor, and that the endogenous tRNAs and release factor are dispensable (§Properties of Syn61 p. 516):
Co-translational incorporation of a non-canonical amino acid, using an orthogonal aminoacyl-tRNA synthetase/tRNACGA pair…targeted to TCG codons, was extremely toxic in MDS42 but non-toxic in Syn61; this validates the removal of TCG codons in Syn61 (Fig. 4b)…serT encodes the tRNASerUGA, which is the only tRNA predicted to decode TCA codons in E. coli and is therefore essential…Because Syn61 does not contain TCA codons, serT is dispensable in this strain…as expected. serU and prfA could also be deleted in Syn61…These data provide functional confirmation that we have removed the target codons from the genome, show that the cognate tRNAs and release factor can be removed in Syn61
Regarding claims 2-3 and 6-8, Fredens et al. teach that the first/second endogenous tRNAs are cognate tRNA for the first/second type of sense codon, respectively (see ¶29 above).
Further regarding claims 2-3 and 6-8, Fredens et al. teach that the essential genes of the prokaryotic cell genome do not contain occurrences of the first or second sense codons (§ABSTRACT):
Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome.
Regarding claims 4-5 and 9, Fredens teaches wherein the first type of sense codon is TCA or TCG, the first endogenous tRNA is tRNASerUGA or tRNASerCGA, and that TCA/TCG have been replaced with AGT/AGC, respectively (§Design of a recoded genome p. 514):
We designed a genome in which the serine codons TCG and TCA, and the stop codon TAG, in open reading frames (ORFs) of MDS42 E. coli…are systematically replaced by their synonyms AGC, AGT and TAA, respectively
Regarding claims 10-13, Fredens et al. teach wherein all occurrences of the TAG stop codon have been replaced with TAA (see ¶31 above), and the first endogenous release factor is its cognate factor, RF-1 (see Fig. 4a, STOP codon box, which shows RF-1 to be the cognate release factor for the TAG codon)
Regarding claims 14-16, Fredens et al. teach wherein the bacterial cell is viable and is an E. coli cell:
Conjugative assembly…enabled the synthesis of a synthetic E. coli that we named ‘Syn61’ (Assembly of a recoded genome p. 516)
Syn61 doubled only 1.6× slower than MDS42 in lysogeny broth (Properties of Syn61 p. 516)
Regarding newly added claims 17-25, these claims recite the same limitations addressed above, merely with different dependencies and combinations of limitations within claims, and are thus taught by the combined references as already described above.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the E.coli cell as taught by Tharp et al. by recoding additional sense codons, as taught by Fredens et al. Both Tharp et al. and Fredens et al. teach methods of engineering bacterial cells by recoding endogenous codons and introducing orthogonal tRNA/aaRs pairs, with the goal of producing polypeptides which contain non-canonical amino acids. The skilled artisan would have been motivated by Tharp et al.’s teachings that this recoding, or expansion of the genetic code, can produce proteins with new functions, and that reassignment of sense codons is one strategy to achieve that. Fredens et al. provide the means to recode sense codons in a way which produces a viable cell capable of expressing polypeptides with multiple distinct non-canonical amino acids. Based on the combined teachings of Tharp et al. and Fredens et al., which both produced viable cells expressing the desired polypeptides, the skilled artisan would have had a reasonable expectation of success.
Response to Arguments
Applicant's arguments filed 10/29/2025 have been fully considered but they are not persuasive for the reasons that follow.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Specifically, Applicant argues that Tharp discourages one skilled in the art from taking the Fredens approach of recoding sense codons by stating that the strategy is challenging and most often affords a heterogeneous product, thus expressing skepticism and disapproval (pp. 9-10 of the remarks). Applicant further argues that Tharp does the opposite of providing the requisite motivation to combine (p. 9). This argument is not convincing because, as discussed above and noted by the Applicant, Tharp notes that reassignment of sense codons has the advantage of expanding the genetic code to produce completely unnatural polypeptides with “new to nature” functions, thus providing a strong motivation to pursue both sense and nonsense codon reassignment to the full extent possible to produce these completely unnatural polypeptides (p. 2). While Tharp notes that the strategy of sense codon reassignment has the disadvantage that it is generically challenging, the disclosure that a given course of action often has simultaneous advantages and disadvantages does not necessarily obviate motivation to combine (MPEP 2143.01.V). Tharp also notes that “nonsense suppression can only provide three blank codons for GCE”. In this case, when weighing the strong motivation to reassign multiple codons simultaneously to produce completely unnatural polypeptides against the limited number of available stop codons and the challenges of sense codon reassignment, the skilled artisan would have been motivated to investigate sense codon reassignment in spite of its challenges due to the potential advantages and the dearth of alternatives. Fredens then demonstrates that reassignment of certain specific sense codons, coupled with the deletion of their endogenous cognate aminoacyl-tRNAs, successfully overcame the challenges described by Tharp. When combined, the references provide a motivation to seek a path forward (Tharp), and a specific, predictable path forward (Fredens).
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.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-3, 6-8, 10-11, 14-16, 17-18, 20-22, and 24-25 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 56-57 and 123-130 of copending Application No. 18/288,340. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims recite a composition (the prokaryotic cell) while the copending claims recite a method using that compound. Per 804.01(B)(1), "The portion of the specification of the reference that describes subject matter that falls within the scope of a reference claim may be relied upon to properly construe the scope of that claim. In particular, when ascertaining the scope of the reference’s claim(s) to a compound, the examiner should consider the reference’s specification, including all of the compound’s uses that are disclosed." In this case, the copending specification states that the, “prokaryotic cells are suitable for the production of polymers containing non-canonical amino acids.” (p. 3 ln 9-10).
The instant and copending claims are compared below:
19/092,488
18/288,340
1. A prokaryotic cell, wherein the prokaryotic cell:…expresses a polypeptide encoded by a nucleic acid, wherein the polypeptide comprises first, second and third non-canonical amino acids encoded by the first and second sense codons and first stop codon.
56. A method of synthesizing a polymer, comprising provided an Escherichia coli (E. coli) cell…introducing into said E. coli cell a nucleic acid sequence encoding a polymer, said nucleic acid sequence comprising the first type of sense codon and the second sense codon…whereby the polymer is synthesized, including incorporation of the first and second non-canonical amino acid monomers
57. The method of claim 56, wherein: the E. coli cell further comprises…the nucleic acid sequence comprises a first stop codon…the third non- canonical amino acid monomer is incorporated into the polymer
1. A prokaryotic cell, wherein the prokaryotic cell:…does not express first and second endogenous tRNAs and does not express a first endogenous release factor
56. …wherein the gene encoding the first endogenous tRNA is not expressed and the gene encoding the second endogenous tRNA is not expressed
123. The method according to claim 57, wherein, in the genome of the E. coli cell, the release factor that reads the first stop codon is not expressed.
1. A prokaryotic cell, wherein the prokaryotic cell…comprises a genome wherein a first type and a second type of sense codon have been recoded such that the first and second endogenous tRNAs are dispensable, and a first stop codon has been recoded such that the first release factor is dispensable
17. (New) The prokaryotic cell of claim 1 wherein the genome comprises 5, 4, 3, 2, 1, or no occurrences of the first type of sense codon and 5, 4, 3, 2, 1, or no occurrences of the second type of sense codon, andthe first endogenous tRNA is a cognate tRNA for the first type of sense codon and the second endogenous tRNA is a cognate tRNA for the second type of sense codon.
18. (New) The prokaryotic cell of claim 1, wherein the genome comprises 5, 4, 3, 2, 1, or no occurrences of the first type of sense codon; 5, 4, 3, 2, 1, or no occurrences of the second type of sense codon; and 5, 4, 3, 2, 1, or no occurrences of the first type of stop codon; andthe first endogenous tRNA is a cognate tRNA for the first type of sense codon; the second endogenous tRNA is a cognate tRNA for the second type of sense codon; and the first endogenous release factor is a cognate release factor for the first type of stop codon.
22. (New) The prokaryotic cell of claim 1, wherein:the essential genes of the prokaryotic cell genome do not contain occurrences of the first type of sense codon, the second type of sense codon, or the first type of stop codon; andthe first endogenous tRNA is a cognate tRNA for the first type of sense codon, the second endogenous tRNA is a cognate tRNA for the second type of sense codon, and the first endogenous release factor is a cognate release factor for the first type of stop codon.
56. …wherein the first sense codon has been recoded such that a first endogenous tRNA is dispensable and the second sense codon has been recoded such that a second endogenous tRNA is dispensable
130. The method of claim 56, wherein the recoded E. coli cell comprises no occurrences of each of the first sense codon, the second sense codon, and the first stop codon.
1. A prokaryotic cell, wherein the prokaryotic cell…expresses first, second, and third orthogonal aminoacyl-tRNA synthetases and first,second, and third orthogonal tRNAs, such that the first orthogonal aminoacyl-tRNA synthetase and the first orthogonal tRNA form a first orthogonal aminoacyl-tRNA synthetase - tRNA pair, and the first orthogonal tRNA is capable of decoding the first type of sense codon, the second orthogonal aminoacyl-tRNA synthetase and the second orthogonal tRNA form a second orthogonal aminoacyl- tRNA synthetase - tRNA pair, and the second orthogonal tRNA is capable of decoding a second type of sense codon, and the third orthogonal aminoacyl-tRNA synthetase and the third orthogonal tRNA form a third orthogonal aminoacyl-tRNA synthetase - tRNA pair, and the third orthogonal tRNA is capable of decoding the first type of stop codon
56. …which expresses a first orthogonal aminoacyl-tRNA synthetase pair suitable for decoding a first sense codon and a second orthogonal aminoacyl-tRNA pair suitable for decoding a second, different sense codon
57. …the E. coli cell further comprises a third orthogonal aminoacyl-tRNA synthetase - tRNA pair and the nucleic acid sequence comprises a first type of stop codon
2. The prokaryotic cell of claim 1, wherein: the essential genes of the prokaryotic cell genome do not contain occurrences of the first type of sense codon, and the first endogenous tRNA is a cognate tRNA for the first type of sense codon.
3. The prokaryotic cell of claim 1, wherein: the prokaryotic cell genome comprises 5, 4, 3, 2, 1, or no occurrences of the first type of sense codon, and the first endogenous tRNA is a cognate tRNA for the first type of sense codon
56. …which expresses a first orthogonal aminoacyl-tRNA synthetase pair suitable for decoding a first sense codon
130. The method of claim 56, wherein the recoded E. coli cell comprises no occurrences of each of the first sense codon, the second sense codon, and the first stop codon.
6. The prokaryotic cell of claim 1, wherein:the essential genes of the prokaryotic cell genome do not contain occurrences of the second type of sense codon, and the second endogenous tRNA is a cognate tRNA for the second type of sense codon.
7. The prokaryotic cell of claim 1, wherein:the essential genes of the prokaryotic cell genome do not contain occurrences of the first tvpe of sense codon or the second type of sense codon, andthe first endogenous tRNA is a cognate tRNA for the first type of sense codon and second endogenous tRNA is a cognate tRNA for the second type of sense codon.
8. The prokaryotic cell of claim 6, wherein:the prokaryotic cell genome comprises 5, 4, 3, 2, 1, or no occurrences of the second type of sense codon, and the second endogenous tRNA is a cognate tRNA for the second type of sense codon.
130. The method of claim 56, wherein the recoded E. coli cell comprises no occurrences of each of the first sense codon, the second sense codon, and the first stop codon.
56. …a second orthogonal aminoacyl-tRNA pair suitable for decoding a second, different sense codon
10. The prokaryotic cell of claim 1, wherein the essential genes of the prokaryotic cell genome do not contain occurrences of the first type of stop codon, and the first endogenous release factor is a cognate release factor for the first type of stop codon.
11. The prokaryotic cell of claim 10, wherein the genome comprises 5, 4, 3, 2, 1, or no occurrences of the first type of stop codon, andthe first endogenous release factor is a cognate release factor for the first type of stop codon.
130. The method of claim 56, wherein the recoded E. coli cell comprises no occurrences of each of the first sense codon, the second sense codon, and the first stop codon.
123. The method according to claim 57, wherein, in the genome of the E. coli cell, the release factor that reads the first stop codon is not expressed.
14. The prokaryotic cell of claim 1, wherein the prokaryotic cell is a bacterial cell.
15. The prokaryotic cell of claim 14, wherein the bacterial cell is an Escherichia coli cell.
16. The prokaryotic cell of claim 1, wherein the prokaryotic cell is viable.
20. (New) The prokaryotic cell of claim 18, wherein the prokaryotic cell is an Escherichia coli cell.
21. (New) The prokaryotic cell of claim 20, wherein the prokaryotic cell is viable.
24. (New) The prokaryotic cell of claim 22, wherein the prokaryotic cell is an Escherichia coli cell.
25. (New) The prokaryotic cell of claim 24, wherein the prokaryotic cell is viable.
56. A method of synthesizing a polymer, comprising: i) providing an Escherichia coli (E. coli) cell
Please note that insofar as the copending application recites tRNA-synthetase pairs suitable for decoding codons, those pairs are assumed to be cognate for the codons which they decode. Regarding claim 16, insofar as the copending claims recite a method for synthesizing a polymer comprising incubating the E. coli cell and expressing a nucleic acid sequence in the cell, it is assumed that a cell capable of growth and gene expression is necessarily viable.
Additionally, it is noted that the instant application is a continuation of copending application 18/288,340, but is not a divisional application . MPEP 804.01 states that, "the protection afforded by section 121 to applications (or patents issued therefrom) filed as a result of a restriction requirement is limited to divisional applications."
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-3, 6-8, 10-11, 14-16, 17-18, 20-22, and 24-25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims1-4 and 6-11 of U.S. Patent No. 12,385,035 B2 in view of Fredens (cited above).
The instant and patented claims are compared below:
19/092,488
12,385,035 B2
1. A prokaryotic cell, wherein the prokaryotic cell:…expresses a polypeptide encoded by a nucleic acid, wherein the polypeptide comprises first, second and third non-canonical amino acids encoded by the first and second sense codons and first stop codon.
7. A method for production of polypeptides comprising one or more non-proteinogenic amino acids, the method comprising culturing the E. coli host cell according to claim 6 under conditions and for a time sufficient for production of polypeptides comprising one or more non-proteinogenic amino acids.
1. A prokaryotic cell, wherein the prokaryotic cell:…does not express first and second endogenous tRNAs and does not express a first endogenous release factor
2. The prokaryotic cell of claim 1, wherein: the essential genes of the prokaryotic cell genome do not contain occurrences of the first type of sense codon, and the first endogenous tRNA is a cognate tRNA for the first type of sense codon.
1. …the synthetic E. coli genome further lacks a functional gene encoding an endogenous cognate tRNA for at least one of the serine codons
8. The synthetic E. coli genome of claim 2 or 4, wherein the synthetic E. coli genome lacks a functional serT gene.
9. The synthetic E. coli genome of claim 2 or 4, wherein the synthetic E. coli genome lacks a functional serU gene.
11. The synthetic E. coli genome of claim 10, wherein the synthetic E. coli genome lacks a functional prfA gene.
1. A prokaryotic cell, wherein the prokaryotic cell…comprises a genome wherein a first type and a second type of sense codon have been recoded such that the first and second endogenous tRNAs are dispensable, and a first stop codon has been recoded such that the first release factor is dispensable
1. A synthetic E. coli genome comprising 5 or fewer occurrences of one or two serine codons, wherein the synthetic E. coli genome further lacks a functional gene encoding an endogenous cognate tRNA for at least one of the serine codons and wherein each of the serine codons has been recoded such that the endogenous cognate tRNA for the serine codon is dispensable
4. The synthetic E. coli genome according to claim 3, wherein…(iv) the synthetic E. coli genome comprises 10 or fewer occurrences, or no occurrences, of the amber stop codon (TAG)
3. A synthetic E. coli genome derived from a parent E. coli genome, wherein the synthetic E. coli genome comprises 10% or less of the occurrences of one or two serine codons, relative to the parent E. coli genome, wherein the synthetic E. coli genome further lacks a functional gene encoding an endogenous cognate tRNA for at least one of the serine codons and wherein each of the serine codons has been recoded such that the endogenous cognate tRNA for the serine codons is dispensable; and wherein an E. coli comprising the synthetic E. coli genome is viable.
3. The prokaryotic cell of claim 1, wherein: the prokaryotic cell genome comprises 5, 4, 3, 2, 1, or no occurrences of the first type of sense codon, and the first endogenous tRNA is a cognate tRNA for the first type of sense codon
4. The synthetic E. coli genome according to claim 3, wherein…(v) 99.9% or more of the occurrences of one or two serine codons in the parent E. coli genome are replaced with synonymous sense codons
6. The prokaryotic cell of claim 1, wherein:the essential genes of the prokaryotic cell genome do not contain occurrences of the second type of sense codon, and the second endogenous tRNA is a cognate tRNA for the second type of sense codon.
7. The prokaryotic cell of claim 1, wherein:the essential genes of the prokaryotic cell genome do not contain occurrences of the first tvpe of sense codon or the second type of sense codon, andthe first endogenous tRNA is a cognate tRNA for the first type of sense codon and second endogenous tRNA is a cognate tRNA for the second type of sense codon.
8. The prokaryotic cell of claim 6, wherein:the prokaryotic cell genome comprises 5, 4, 3, 2, 1, or no occurrences of the second type of sense codon, and the second endogenous tRNA is a cognate tRNA for the second type of sense codon.
17. (New) The prokaryotic cell of claim 1 wherein the genome comprises 5, 4, 3, 2, 1, or no occurrences of the first type of sense codon and 5, 4, 3, 2, 1, or no occurrences of the second type of sense codon, andthe first endogenous tRNA is a cognate tRNA for the first type of sense codon and the second endogenous tRNA is a cognate tRNA for the second type of sense codon.
4. The synthetic E. coli genome according to claim 3, wherein…(v) 99.9% or more of the occurrences of one or two serine codons in the parent E. coli genome are replaced with synonymous sense codons
10. The prokaryotic cell of claim 1, wherein the essential genes of the prokaryotic cell genome do not contain occurrences of the first type of stop codon, and the first endogenous release factor is a cognate release factor for the first type of stop codon.
11. The prokaryotic cell of claim 10, wherein the genome comprises 5, 4, 3, 2, 1, or no occurrences of the first type of stop codon, and the first endogenous release factor is a cognate release factor for the first type of stop codon.
4. The synthetic E. coli genome according to claim 3, wherein…(iv) the synthetic E. coli genome comprises 10 or fewer occurrences, or no occurrences, of the amber stop codon (TAG)
11. The synthetic E. coli genome of claim 10, wherein the synthetic E. coli genome lacks a functional prfA gene.
14. The prokaryotic cell of claim 1, wherein the prokaryotic cell is a bacterial cell.
15. The prokaryotic cell of claim 14, wherein the bacterial cell is an Escherichia coli cell.
16. The prokaryotic cell of claim 1, wherein the prokaryotic cell is viable.
20. (New) The prokaryotic cell of claim 18, wherein the prokaryotic cell is an Escherichia coli cell.
21. (New) The prokaryotic cell of claim 20, wherein the prokaryotic cell is viable.
24. (New) The prokaryotic cell of claim 22, wherein the prokaryotic cell is an Escherichia coli cell.
25. (New) The prokaryotic cell of claim 24, wherein the prokaryotic cell is viable.
6. An E. coli host cell comprising the synthetic E. coli genome according to claim 1 or claim 3.
3. A synthetic E. coli genome derived from a parent E. coli genome, wherein the synthetic E. coli genome comprises 10% or less of the occurrences of one or two serine codons, relative to the parent E. coli genome, wherein the synthetic E. coli genome further lacks a functional gene encoding an endogenous cognate tRNA for at least one of the serine codons and wherein each of the serine codons has been recoded such that the endogenous cognate tRNA for the serine codons is dispensable; and wherein an E. coli comprising the synthetic E. coli genome is viable.
18. (New) The prokaryotic cell of claim 1, wherein the genome comprises 5, 4, 3, 2, 1, or no occurrences of the first type of sense codon; 5, 4, 3, 2, 1, or no occurrences of the second type of sense codon; and 5, 4, 3, 2, 1, or no occurrences of the first type of stop codon; and the first endogenous tRNA is a cognate tRNA for the first type of sense codon; the second endogenous tRNA is a cognate tRNA for the second type of sense codon; and the first endogenous release factor is a cognate release factor for the first type of stop codon.
22. (New) The prokaryotic cell of claim 1, wherein:the essential genes of the prokaryotic cell genome do not contain occurrences of the first type of sense codon, the second type of sense codon, or the first type of stop codon; andthe first endogenous tRNA is a cognate tRNA for the first type of sense codon, the second endogenous tRNA is a cognate tRNA for the second type of sense codon, and the first endogenous release factor is a cognate release factor for the first type of stop codon.
4. The synthetic E. coli genome according to claim 3, wherein…(iv) the synthetic E. coli genome comprises 10 or fewer occurrences, or no occurrences, of the amber stop codon (TAG); (v) 99.9% or more of the occurrences of one or two serine codons in the parent E. coli genome are replaced with synonymous sense codons
While the patented claims do not recite wherein the cell expresses first, second and third orthogonal aminoacyl-tRNA synthetase pairs, Fredens, as discussed above, teaches engineering the cell to express these components. It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have engineered the cell to express the required orthogonal aminoacyl-tRNA synthetase pairs because, as taught by Fredens, these components are required for decoding of the reassigned codons and expression of the polypeptide comprising the ncAAs
Response to Arguments
Applicant requests that the rejection be held in abeyance pending an indication of allowable subject matter. Per MPEP 804(I)(B)(1), a complete response to a nonstatutory double patenting (NSDP) rejection is either a reply by applicant showing that the claims subject to the rejection are patentably distinct from the reference claims, or the filing of a terminal disclaimer in accordance with 37 CFR 1.321 in the pending application(s) with a reply to the Office action (see MPEP § 1490 for a discussion of terminal disclaimers). Such a response is required even when the nonstatutory double patenting rejection is provisional. As filing a terminal disclaimer, or filing a showing that the claims subject to the rejection are patentably distinct from the reference application’s claims, is necessary for further consideration of the rejection of the claims, such a filing should not be held in abeyance. Only compliance with objections or requirements as to form not necessary for further consideration of the claims may be held in abeyance until allowable subject matter is indicated.
Conclusion
No claims are allowed.
Applicant's submission of an information disclosure statement under 37 CFR 1.97(c) with the timing fee set forth in 37 CFR 1.17(p) on 10/29/2025 prompted the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 609.04(b). 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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/A.M.Z./ Examiner, Art Unit 1636
/BRIAN WHITEMAN/Primary Examiner, Art Unit 1636