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
The amendment and reply of 09/15/2025 is acknowledged. Regarding the Office action mailed 06/18/2025:
The rejection of claims 1-20 under 35 USC 112(b) over the terminology “3’ engineered translation initiation site” is withdrawn in view of the amendment. The additional rejection of claim 11 is withdrawn in view of Applicant’s arguments, pointing to the discussion of upstream ORF (uORF) in the specification. After further investigation, uORF is a term of art as described, e.g., in Wu et al. (EMBO J. 39:e104763, 3 August 2020).
The rejection under 35 USC 102(a)(1) over Farhadi (Science 365:1469-1475 (2019)) is withdrawn in view of the amendment to incorporate the limitations of claim 6 into claim 1.
For the same reason, the rejection under 35 USC 102(a)(1) over Ho (J Biotechnol 157:130-139 (2012)) is withdrawn.
For the same reason, the rejection under 35 USC 102(a)(1) over Lutz (US 2021/0170017) is withdrawn.
For the same reason, the rejections under 35 USC 103 based on Farhadi (Science 365:1469-1475 (2019)) are withdrawn.
After further search and consideration, new grounds of rejection are set forth below. This Office action is non-final.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 9 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The language of claim 9 does not make sense. How can the steady state level of the first unit payload protein and the second unit payload protein be some fold greater than the steady state level of the same two proteins? For purposes of prior art, the Examiner will make the assumption that the intent of the claim is that the steady state level of the first unit payload protein is greater than the steady state level of the second unit payload protein by the recited amounts, or vice versa.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-5, 7-12, 15 and 18 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by GenBank Accession M25464 [online] 29 Feb 2008 [retrieved on 25 Dec 2025] retrieved from https://www.ncbi.nlm.nih.gov/nuccore/M25464, as evidenced by McCarthy (Mol Microbiol 4(8):1233-1240 (1990)).
GenBank disclosed the nucleic acid composition, i.e. a segment of the genome from the bacterium Escherichia coli encoding the atp operon. McCarthy provides evidence that this nucleic acid meets the limitations of the claims. In the following discussion, the terms eTIS (engineered translation initiation site” and TIR (translation initiation region) are used interchangeably.
McCarthy describes the atp operon of Escherichia coli. The following discussion will show that this operon meets the limitations of the claims. Firstly, the term “payload protein” is not defined in the specification in any way that limits the structure of the payload protein, and therefore does not distinguish over any protein, even those which are natural. Secondly, the term “engineered translation initiation site” is not defined in the specification in any way that limits the structure of the engineered translation initiation site, and therefore does not distinguish over any translation initiation site, even those which are natural. The term “engineered” simply implies it was “designed”. However, whether designed by nature or by man, the structure is not limited. Therefore, the term “engineered” represents a “product-by-process” situation; see MPEP 2113. Finally, the term “three-nucleotide tunable element” would encompass any of the 64 possible triplets made from natural nucleotides (in fact, see claims 7 and 8, which lists every possible 64 triplet deoxyribonucleotides and ribonucleotides, respectively). Therefore, any nucleotide triplet upstream of a start codon is a “tunable element” (tunable because any such triplet could be changed into some other triplet by standard molecular biologic mutagenesis techniques). Given these assertions, the atp operon meets the claim limitations as follows.
Claim 1:
A nucleic acid composition,
comprising: a promoter operably linked to a polynucleotide comprising a first nucleic acid unit and a second nucleic acid unit,
McCarthy page 1233, last paragraph (citations omitted): “The major promoter of the atp operon initiates transcription 73 base pairs upstream of atpI and there is a ρ-independent terminator downstream of atpC. Thus transcription can support the synthesis of a message of maximally 7 kb which encode all of the H+-ATPase subunits.” See also McCarthy Fig. 2 and figure legend detailing the organization of the atp operon. For purposes of this discussion, the atpB gene (encoding the F0 “a” subunit) and the atpE gene (encoding the F0 “c” subunit) correspond to the “first” and “second” nucleic acid units, respectively.
wherein the first nucleic acid unit encodes one or more first unit payload protein(s),
See McCarthy Fig. 2 and figure legend: the atpB gene (encoding the F0 “a” subunit). Referring back to the GenBank disclosure, page 1 refers to this as subunit “A” and indicates the coding sequence starts at nucleotide 566 and ends at nucleotide 1381.
wherein the second nucleic acid unit encodes one or more second unit payload protein(s),
See McCarthy Fig. 2 and figure legend: the atpE gene (encoding the F0 “c” subunit). Referring back to the GenBank disclosure, page 1 refers to this as subunit “C” and indicates the coding sequence starts at nucleotide 1428 and ends at nucleotide 1667.
wherein the first nucleic acid unit and the second nucleic acid unit each comprise an engineered translation initiation site (eTIS)
McCarthy page 1238, section titled “The molecular basis of translational control” (citations omitted): “Experiments were performed using mRNA transcribed in vitro from DNA fragments varying from 237 to 432 base pairs bearing the TIRs of atpB, atpE and atpG, respectively. The TIR of atpE supports efficient translational initiation and is predicted to have a relatively open structure. The other two TIRs specify poor rates of translation.”
comprising a three-nucleotide tunable element immediately upstream of a start codon,
Turning to the GenBank disclosure, the start codon for subunit “A” begins at 566. The three nucleotides immediately upstream of this are “atc”. The start codon for subunit “C” begins at 1428. The three nucleotides immediately upstream of this are “gtc”.
wherein the promoter is capable of inducing transcription of the first nucleic acid unit and the second nucleic acid unit to generate a polycistronic transcript,
McCarthy page 1233, last paragraph (citations omitted): “The major promoter of the atp operon initiates transcription 73 base pairs upstream of atpI and there is a ρ-independent terminator downstream of atpC. Thus transcription can support the synthesis of a message of maximally 7 kb which encode all of the H+-ATPase subunits.”
wherein the polycistronic transcript is capable of being translated to generate the one or more first unit payload protein(s) and the one or more second unit payload protein(s),
McCarthy page 1233, last paragraph: “Thus transcription can support the synthesis of a message of maximally 7 kb which encode all of the H+-ATPase subunits.”
and wherein the eTIS of each of the first nucleic acid unit and the second nucleic acid unit is configured to achieve a predetermined stoichiometry of the one or more first unit payload protein(s) and one or more second unit payload protein(s) in a cell or cell-like environment,
McCarthy page 1233, last paragraph: “Thus transcription can support the synthesis of a message of maximally 7 kb which encode all of the H+-ATPase subunits. The rates of synthesis of these subunits differ substantially from each other, and are indeed matched reasonably well to the requirements of assembly of a functional H+-ATPase complex.” See also Fig. 2 and figure legend indicating the stoichiometry of the subunits in the complex. Note that there are roughly 12 subunits of the “c” subunit (product of the atpE gene) per 1 subunit of the “a” subunit (product of the atpB gene).
and wherein the strength of the eTIS of the second nucleic acid unit is greater than the strength of the eTIS of the first nucleic acid unit,
McCarthy page 1238, section titled “The molecular basis of translational control” (citations omitted): “Experiments were performed using mRNA transcribed in vitro from DNA fragments varying from 237 to 432 base pairs bearing the TIRs of atpB, atpE and atpG, respectively. The TIR of atpE supports efficient translational initiation and is predicted to have a relatively open structure. The other two TIRs specify poor rates of translation.”
and thereby the eTIS of the second nucleic acid unit efficiently captures the ribosomal translational activity that fails to initiate at the eTIS of the first nucleic acid unit.
This is considered to be an inherent result of the fact that the TIR of atpE is stronger than the TIR of atpB.
Claim 2:
The coding sequence of each of the atp genes within the atp operon constitutes an open reading frame.
Claim 3:
Given that any three-nucleotide sequence can be a “tunable element”, this is considered to be an inherent property of the “tunable elements” of the atp operon disclosed by GenBank.
Claims 4 and 5:
McCarthy provides evidence that the TIR of atpE is stronger than the TIR of atpB. This is the only requirement specified in claim 1. Given that, and given that Applicant has not disclosed any other requirement to achieve the properties recited in claims 4 and 5, these are considered inherent properties. See MPEP 2112(III) and (V), and MPEP 2112.01(I) and (II). Should Applicant choose to argue that these properties are not inherent for any operon comprising two or more open reading frames, each with its own TIR, where the TIR of a downstream open reading frame is stronger than the TIR of the immediately upstream open reading frame, Applicant should be prepared to explain how Applicant’s disclosure permits one of ordinary skill in the art to predict in which situations the properties would be possessed by a particular nucleic acid, and in which situations they would not (without resorting to experimentation to find out). Otherwise, a rejection under the written description requirement of 35 USC 112(a) would be appropriate.
Claim 7:
As noted above, the “tunable element” for atpB (encoding the “A” subunit) is “atc”, while the “tunable element” for atpE (encoding the “C” subunit) is “gtc”.
Claim 8:
GenBank discloses the DNA sequence of the E. coli operon. However, implicit in this disclosure is the sequence of the corresponding RNA transcript, in which all “t” nucleotides would be “u” nucleotides. Thus, GenBank implicitly discloses the “tunable element” for atpB (encoding the “A” subunit) as “auc”, and the “tunable element” for atpE (encoding the “C” subunit) is “guc”.
Claims 9 and 10:
Notwithstanding the awkward language of claim 9, as evidenced by McCarthy (see discussion of claim 1), the steady state levels/stoichiometry of the “c” subunit is about 12-fold higher than the “a” subunit (or, “about 10-fold”). See McCarthy Fig. 2.
Claim 11:
The atp operon of E. coli does not contain an “upstream ORF (uORF)” as that term is described in the specification. Moreover, the “first unit payload protein” (i.e. the “A” subunit, encoded by the atpB gene) is more than 30 amino acids; see amino acid sequence at the top of page 2 of the GenBank disclosure.
Claim 12:
Both the “A” subunit and the “C” subunit comprise only native amino acid residues (see first two amino acid sequences on page 2 of the GenBank disclosure).
Claim 15:
The term “synthetic protein circuit” is not defined in the specification in such a way as to distinguish over the atp operon disclosed by GenBank. While the term “synthetic” implies something man-made, the term does not structurally limit the claimed nucleic acid composition. Therefore, “synthetic” is a product-by-process limitation.
Claim 18:
The atp operon comprises supplemental nucleic acid units encoding the “b”, “δ”, “α”, “γ”, “β” and “ε” subunits (see McCarthy Fig. 2 and GenBank page 2). Each comprises a TIR and a “tunable element” immediately upstream of its start codon. The properties recited in claim 18 regarding the inverse proportionality between the expression of a given unit and the strength of the TIR of the unit upstream thereof is considered an inherent property of a polycistronic transcript, given that the claimed nucleic acid composition is not structurally limited (given that there is not particular sequence required and given that any three-nucleotide sequence can be the “tunable element”). Should Applicant choose to argue that these properties are not inherent for any polycistronic transcript, each expressed nucleic acid unit within the transcript having its own TIR, Applicant should be prepared to explain how Applicant’s disclosure permits one of ordinary skill in the art to predict in which situations the properties would be possessed by a particular nucleic acid, and in which situations they would not (without resorting to experimentation to find out). Otherwise, a rejection under the written description requirement of 35 USC 112(a) would be appropriate.
Claim(s) 1-5, 7-12, 15, 18 and 19 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Dower (Nucleic Acids Research 16(13):6127-6145 (1988)) as evidenced by GenBank Accession M25464 [online] 29 Feb 2008 [retrieved on 25 Dec 2025] retrieved from https://www.ncbi.nlm.nih.gov/nuccore/M25464, and as evidenced by McCarthy (Mol Microbiol 4(8):1233-1240 (1990)).
Dowe disclosed E. coli transformed with plasmids pUC18 and pBR322 (hence, “engineered cells”). E. coli contains within its genome the atp operon, which, as evidenced by the disclosures of GenBank Accession M25464 and McCarthy, meets the limitations recited in claims 1-5, 7-12, 15 and 18 (see separate rejection under 35 USC 102(a)(1) above. Therefore, the engineered E. coli cells meets the limitations of these claims, as well as claim 19.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-5, 7-12, 15 and 18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural product without significantly more. The claim(s) recite(s) a nucleic acid composition. As set forth in the rejection under 35 USC 102(a)(1) above, the claims encompass a naturally occurring polynucleotide, that being the atp operon within the genome of the bacterium E. coli. This judicial exception is not integrated into a practical application because there are no additional elements to the claim beyond the polynucleotide itself. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because there are no additional elements to the claim beyond the polynucleotide itself.
Conclusion
Claims 13, 14, 16, 17 and 20 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SAMUEL C WOOLWINE whose telephone number is (571)272-1144. The examiner can normally be reached 9am-5:30pm.
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/SAMUEL C WOOLWINE/ Primary Examiner, Art Unit 1681