DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
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, 5-6, 11, 13-14, 18-19, 25, 30-31, 34-36, 39, 44, 48, and 76 were previously pending.
Receipt is acknowledged of the amendments to the claims submitted on 27 May, 2026.
Claims 1-2, and 6 are amended. Claims 35-36, 39, 44, 48, and 76 are cancelled. Claims 77-79 are newly added.
Applicant’s election without traverse of the invention of group I drawn to an engineered nucleic acid vector comprising a stationary-phase-induced promoter and a primosome assembly site (PAS) (claims 1-3, 5-6, 11, 13-14) in the reply filed on 08 December, 2025 was previously acknowledged. The newly added claims 77-79 read on the elected invention.
Claims 18-19, 25, 30-31, and 34 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Therefore, claims 1-3, 5-6, 11, 13-14, and 77-79 are pending and under examination in the present Official Action.
Priority
The present application is a 35 U.S.C. 371 national stage filing of International Application No. PCT/US2021/035636, filed 03 June, 2021, which claims priority to United States Provisional Application No. 63035630, filed 05 June, 2020. Acknowledgment is made of applicant’s claim for priority.
The earliest possible priority for the instant application is 05 June, 2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 27 May, 2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Examiner’s Comment
It is noted that where reference is made to the instant disclosure in the following Official Action, the Examiner will be referring to the publication of the instant Application (US 2023/0287437).
Claim Objections
Claims 1-2, 6, 11,77, and 79 are objected to because of the following informalities: Because a SEQ ID NO is a placeholder and not a sequence in and of itself, the claims should refer to the sequences contained within the SEQ ID NO. For example, claim 1 should be amended to recite “70%-90% sequence identity to the prsA* sequence of SEQ ID NO: 23” and “95% sequence identity to the prsA* sequence of SEQ ID NO: 24,”, claim 2 should be amended to recite “wherein the SL4 has the nucleic acid sequence of SEQ ID NO: 29” and “wherein the PAS has the nucleic acid sequence of SEQ ID NO: 28,” claim 6 should be amended to recite “wherein the P(osmY) has the nucleic acid sequence of SEQ ID NO: 27,” claim 11 should be amended to recite “at least 70% sequence identity to any one of the nucleic acid sequences of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, or SEQ ID NO: 22,” claim 77 should be amended to recite identical language to that suggested for claim 1, and claim 79 should be amended to recite “comprising any one of the nucleic acid sequences of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, or SEQ ID NO: 22.” Appropriate correction is required.
Claims 1-3, 5-6, and 77 are objected to because of the following informalities: Abbreviations/acronyms need to be spelled out upon their first encounter in the claims (For example: prsA*, prsA, RNAII, SL4, P(osmY)). Appropriate correction is required.
Applicant is advised that should claim 77 be found allowable, claim 78 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Withdrawn Rejections in view of Applicant’s Amendments/Arguments
Claim Rejections - 35 USC § 112
The rejection of claims 2 and 6 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 is withdrawn in view of Applicant’s amendments to the claims.
Applicant has amended the claims to remove previously raised issues of indefiniteness.
Claim Rejections - 35 USC § 102
The rejection of claims 1, 5, 6, and 14 under 35 U.S.C. 102(a)(1) as being anticipated by Jaishankar, et al., Frontiers in microbiology 8 (2017): 2000, hereinafter “Jaishankar”, as evidenced by Standley, et al., Current genetics 65.1 (2019): 179-192, hereinafter “Standley”, Seufert, et al., Cell 48.1 (1987): 73-78, hereinafter “Seufert” and Lange, et al., Journal of bacteriology 175.24 (1993): 7910-7917, hereinafter “Lange” is withdrawn in view of Applicant’s amendments to the claims.
Applicant has amended claim 1 to recite “wherein the nucleic acid has 70%-99% sequence identity to prsA* (SEQ ID NO: 23) or wherein the nucleic acid encodes a protein having at least 95% sequence identity to prsA* (SEQ ID NO: 24).” Jaishankar does not teach this limitation.
Claim Rejections - 35 USC § 103
The rejection of claims 1, 2-3, and 13 under 35 U.S.C. 103 as being unpatentable over Jaishankar, et al., Frontiers in microbiology 8 (2017): 2000, hereinafter “Jaishankar”, in view of Standley, et al., Current genetics 65.1 (2019): 179-192, hereinafter “Standley”, and WO 2011/007005 (published: 20 January, 2011) (hereinafter “Grabherr”) is withdrawn in view of Applicant’s amendments to the claims.
Applicant has amended claim 1 to recite “wherein the nucleic acid has 70%-99% sequence identity to prsA* (SEQ ID NO: 23) or wherein the nucleic acid encodes a protein having at least 95% sequence identity to prsA* (SEQ ID NO: 24).” Jaishankar does not teach this limitation and none of the other prior art of record provides a teaching, suggestion, or motivation to use a nucleic acid sequence having 70-99% sequence identity to SEQ ID NO: 23 or a nucleic acid encoding a protein having 95% sequence identity to SEQ ID NO: 24 in an engineered nucleic acid vector comprising a stationary-phase-induced promoter and a primosome assembly site.
Maintained Rejections in view of Applicant’s Amendments/Arguments
Claim Rejections - 35 USC § 112
Claims 1-3, 5-6, 11, and 13-14 remain rejected and claims 77-79 are newly rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This rejection has been modified as necessitated by Applicant’s amendments to the claims.
The instant claims are broadly directed to a genus of engineered nucleic acid vectors defined only in that they comprise a stationary-phase-induced promoter, a primosome assembly site (PAS), and a nucleic acid sequence having 70-99% sequence identity to SEQ ID NO: 23 or a nucleic acid encoding a protein having 95% sequence identity to SEQ ID NO: 24 with the intended use of enhancing supercoiling of a plasmid (para [0103]). To the extent the instant claims define a sequence for the vector, claim 1 requires either a nucleic acid sequence having 70-99% sequence identity to SEQ ID NO: 23 or a nucleic acid encoding a protein having 95% sequence identity to SEQ ID NO: 24 (encompassing any vector sequence so long as it contains a nucleic acid sequence which can vary from SEQ ID NO: 23 by at least 284 of the 948 nucleic acids presented therein). Claim 2 requires either the SL4 or the PAS to have the sequence of SEQ ID NO: 28 or 28 respectively (it is noted that the SL4 isn’t required to be in the vector and, as written, the language “stem-loop on RNAII, SL4” doesn’t even clearly refer to the stem-loop, SL4, on RNAII). Claim 6 requires the P(osmY) promoter to have the sequence of SEQ ID NO: 27 and claim 11 requires the nucleic acid vector to have a sequence that is 70% identical to SEQ ID NO: 19, 20, 21, or 22. New claim 77 presents the same limitation of either a nucleic acid sequence having 70-99% sequence identity to SEQ ID NO: 23 or a nucleic acid encoding a protein having 95% sequence identity to SEQ ID NO: 24 and new claim 79 requires “a nucleic acid of any one of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, and SEQ ID NO: 22.” It is noted that “a nucleic acid” does not refer to the nucleic acid sequences listed for claim 79 and that claim 79 reads on any vector so long as there is “a nucleic acid” in common with one of the listed sequences. While the sequence-specific claim limitations are technically narrower than any vector, they still read on a massive genus of nucleic acid vectors (as discussed below). Further, while the claims do not specify any particular function for the nucleic acid vector, the specification teaches that the function of the nucleic acid vectors of the claimed invention is enhanced plasmid DNA production (Specification, [0003]) and supercoiling (para [0103]). The claims do not state with any specificity what structures are required within the engineered nucleic acid vector to impart onto said vector the function of enhanced plasmid DNA production, and even the sequence-specific claim 11 allows the nucleic acid vector to vary by about 1232 of the 4108 nucleotides for SEQ ID NO: 19, about 914 of the 3047 nucleotides for SEQ ID NO: 20, and about 1297 of the 4324 nucleotides for SEQ ID NOs: 21, and 22 with the sequence-specific limitations in claim 79 being even more broad by reading on virtually any nucleic acid vector.
Applicants are claiming a vast genus of nucleic acid vectors having a stationary-phase-induced promoter, a PAS, and either a nucleic acid sequence having 70-99% sequence identity to SEQ ID NO: 23 or a nucleic acid encoding a protein having 95% sequence identity to SEQ ID NO: 24, a subgenus of an undefined number of vectors having 70% identity to SEQ ID NO: 19, 20, 21, or 22, and entirely separate genus of vectors having any possible sequence (claim 79). The specification teaches that the vectors of the invention function to enhance plasmid DNA production (Specification [0003]). The specification teaches that such a vector can be a recombinant plasmid comprising a nucleic acid sequence with at least 70% identity to SEQ ID NO: 19 or 20 (Specification, [0014]-[0015]) or an engineered nucleic acid vector comprising a nucleic acid having at least 70% identity to SEQ ID NO: 21 or 22 (Specification [0032]-[0037]). The specification goes on to teach that the instant invention combines several modifications to plasmid structure to increase plasmid DNA yield and quality: replacing the native RNAII promoter with a stationary phase induced P(osmY) promoter, introducing point mutations on to RNAII causing the formation of a critical stem loop on RNAII, SL4, that is needed for plasmid DNA replication to begin, and/or incorporating a primosome assembly site on the plasmid backbone (Specification, [0098]). It is noted that these specific features that the specification teaches are connected to the function of enhanced plasmid DNA production and supercoiling are missing from the claims. Specifically, the specification teaches an enhanced plasmid having a PAS of SEQ ID NO:28 inserted on the plasmid backbone and having P(osmY) of SEQ ID NO: 27 in place of the native RNAII promoter (Plasmid 1), and four specific point mutations “encouraging” SL4 formation (Plasmid 2) where the SL4 has a sequence of SEQ ID NO: 29 (para [0006]) and teaches that these plasmids had significantly higher plasmid DNA yields and plasmid supercoiling relative to the control plasmid (Specification, [0098], [0099]). This disclosure is not deemed to be descriptive of the complete structure of a representative number of polypeptide sequences encompassed by the instant claims as one of skill in the art cannot envision all of the variants of Plasmid 1 and Plasmid 2 which would retain the function of enhanced plasmid DNA production. The working examples are specific to SEQ ID NO: 19 (Plasmid 1) and 20 (Plasmid 2) (Specification, TABLE 3), and there is no disclosure of any actual variants of these two humanized polypeptides. Further, where the working examples teach plasmid production and plasmid supercoiling relative to plasmid modifications specifically, they only provide two paragraphs (Specification, [0162]-[0163]). These two paragraphs teach modifications of the pUC origin of replication in a control plasmid (SEQ ID NO: 19). There is no attempt to connect the specific modifications to the particular PAS inserted on the plasmid backbone, P(osmY) in place of the native RNAII promoter, and four specific point mutations “encouraging” SL4 formation modifications taught elsewhere in the specification. Further, reference to SEQ ID NO: 19 as the control plasmid appears to conflict with prior description within the specification which taught SEQ ID NO: 19 as having the PAS inserted on the plasmid backbone, and P(osmY) in place of the native RNAII promoter modifications (see above). Further, while the specification teaches SEQ ID NO: 20 as having four point mutations which “encourage” SL4 formation, the specification stops short of teaching anywhere that said four mutations actually cause such a formation. The skilled artisan understands RNAII SL4 formation to be dependent on RNAI interaction and in the absence of any description of RNAII mutations which cause SL4 formation (for example in the absence of RNAI, or enhanced SL4 formation in the presence of RNAI), Applicant has not described any vector having point mutations causing the formation of a stem-loop, SL4 (See Standley, Fig. 1). To the extent that a structure/function relationship can be gleaned from the instant specification, it is with respect to the specific nucleic acid vectors having SEQ ID NO: 19 or 20 having the property of enhancing plasmid DNA production (Specification, TABLE 3, [0162]-[0163]). There is no teaching in the working examples of SEQ ID NO: 21 or 22 having the function of enhancing plasmid DNA production, nor is there a teaching anywhere in the specification of which residues within SEQ ID NO: 19-22 can be changed to retain the functional property, let alone which 1232 of the 4108 nucleotides for SEQ ID NO: 19, 914 of the 3047 nucleotides for SEQ ID NO: 20, or 1297 of the 4324 nucleotides for SEQ ID NOs: 21, and 22 can be changed while retaining the functional property.
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021). Further, A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that "only describe[d] one type of structurally similar antibodies" that "are not representative of the full variety or scope of the genus."). The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure "indicates that the patentee has invented species sufficient to constitute the gen[us]." See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) ("[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated."). See MPEP 2163(II)(A)(3)(a)(ii).
In disclosing only four nucleic acid vectors having the functional property of enhancing plasmid DNA production (SEQ ID NOs: 19-22), applicant has not disclosed a representative number of species for the entire genus claimed because the claimed genus covers species having any vector sequence with the narrower embodiments still covering species in which the nucleic acid vectors can vary by about 1232 of the 4108 nucleotides for SEQ ID NO: 19, about 914 of the 3047 nucleotides for SEQ ID NO: 20, and about 1297 of the 4324 nucleotides for SEQ ID NOs: 21, and 22, and the replaced nucleotides may be any nucleotides (including a contiguous string of guanosines or cytosines). A skilled artisan would understand that any protein having a substitution of between 914 and 1297 contiguous nucleotides to guanosines or cytosines would cease to have much in common with the unsubstituted variant, and that the same can be said for adenosines or thymidines, and that such nucleic acid vectors would have their plasmid DNA production by bacterial host strains impacted by such substitutions. Hence, the structure/function correlation of a nucleic acid vector is unpredictable, and a skilled artisan would recognize that the vast genus claimed encompasses vectors whose function would be hindered if not abolished by specific nucleotide substitutions.
The skilled artisan understands that one nucleotide change in a DNA molecule or one amino acid change in the polypeptide encodes by the DNA molecule could result in loss of it’s biological activity as demonstrated in the generation of sickle-cell anemia wherein one specific amino acid mutation gives rise to the inherited disease (Voet et al., Biochemistry, John Wiley and Sons, 1990, p. 126-129). Further, the skilled artisan also understands that the significance of particular amino acids within a peptide cannot be predicted a priori but must be determined from case to case by painstaking experimental study (Rudinger, J., Peptide Hormones. Palgrave, London, 1976. 1-7. (Page 6, “Conclusions”)) and that it is not known whether there exists an algorithm for predicting the structure of a given protein from its amino acid sequence alone (Ngo et al., The protein folding problem and tertiary structure prediction. Boston, MA: Birkhäuser Boston, 1994. 433-506. (page 492, second full paragraph)). The specification prophetically teaches that an undefined genus of vectors having 70% identity to SEQ ID NO: 19, 20, 21, or 22 will have the function of enhanced plasmid DNA production (Specification, [0014]-[0015], [0032]-[0037]). However, the specification is silent as to what residues within SEQ ID NO: 19-22 are responsible for the functional property aside from those which encode the PAS inserted on the plasmid backbone, and P(osmY) in place of the native RNAII promoter modifications. Thus, a skilled artisan would understand from the teachings of Voet, Rudinger, and Ngo that the results of changing any given nucleotide within SEQ ID NO: 19-22 would be unpredictable and that it would require significant experimentation to determine which variants of SEQ ID NO: 19-22 would still possess the desired function.
The claims encompass engineered nucleic acid vectors having any sequence (Claim 79). The specification has only disclosed four distinct vectors. Where the claims narrow from claiming any vector, they encompass sequences 70% identical to the full length of SEQ ID NO: 19-22, SEQ ID NO: 19 is 4108 nucleotides long, SEQ ID NO: 20 is 3047 nucleotides long, and SEQ ID NO: 21-22 are 4324 nucleotides long. That 30 percent variance results in a situation in which if a 1232-contiguous nucleotide region within SEQ ID NO: 19 were independently varied among the 4 different naturally occurring nucleotides, there would be 5.469 x 10741 (41232 ) different possible molecules. In fact, since variations could occur anywhere within SEQ ID NO: 19, the actual number of different molecules encompassed by the claims is orders of magnitude higher than 41232. For SEQ ID NO: 20, that 30 percent variance results in a situation in which if a 914-contiguous nucleotide region within SEQ ID NO: 20 were independently varied among the 4 different naturally occurring amino acids, there would be 1.9179 x 10550 (4914 ) different possible molecules. In fact, since variations could occur anywhere within SEQ ID NO: 20, the actual number of different molecules encompassed by the claims is orders of magnitude higher than 2098. Further, the same calculation done for SEQ ID NOs: 21-22 produces 7.44x10780 different molecules. Computer software may provide means for identification of such molecules, but it is not itself an adequate written description of the structure of the claimed invention. Thus, Applicant has not disclosed a representative number of species for the entire genus of sequences claimed.
Response to Arguments
Applicant argues against the instant rejection for lack of written description by asserting that the amended language requiring either a nucleic acid sequence having 70-99% sequence identity to SEQ ID NO: 23 or a nucleic acid encoding a protein having 95% sequence identity to SEQ ID NO: 24 satisfies the written description requirement because one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention (Remarks, at 7). This argument has been fully considered but has not been found persuasive for the following reasons.
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021). Further, A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014). Here, Applicant has added claim 79 which broadly reads on any engineered nucleic acid vector so long as there is a single nucleic acid in common with any of the listed SEQ ID NOs (covering a vast and broad genus containing virtually any engineered vector). Where Applicant has narrowed the claims further than this, they are still claiming a genus which covers, at its narrowest, 1.9179 x 10550 (4914 ) different possible molecules. Applicant has not addressed this latter point at all with their response. The amended language added to claim 1 allows for any possible vector sequence comprising a sequence 70% identical to SEQ ID NO: 23 which itself is 948 nucleic acids long. This limitation itself is still an undefined genus covering a vast swathe of possible vectors. Applicant has only described four specific nucleic acid vectors and has only even demonstrated functional properties for two of these vectors (see above). Accordingly, Applicant’s arguments have been fully considered but have not been found persuasive.
New Rejections Necessitated by Applicant’s Amendments to the Claims
Claim Rejections - 35 USC § 102
Claim 79 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Jaishankar, et al., Frontiers in microbiology 8 (2017): 2000, hereinafter “Jaishankar”.
New claim 79 recites “An engineered nucleic acid vector comprising a nucleic acid of any one of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, and SEQ ID NO: 22.” Thus, any engineered nucleic acid vector which has at least a single nucleic acid in common with any of those vectors (A, T, G, or C) falls within the broadest reasonable interpretation of claim 79. Jaishankar teaches at least 18 different engineered nucleic acid vectors, all comprised by A, T, G, and C nucleic acids (Jaishankar, Table 4). Therefore, Jaishankar anticipates the invention claimed in instant claim 79.
Additional Comments
None of the prior art of record teach or suggest a sequence having 100% identity to SEQ ID NO: 19-23. Therefore, the nucleotides of SEQ ID NOS: 19-23 are free of the prior art of record.
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 BRENDAN THOMAS TINSLEY whose telephone number is (703)756-5906. The examiner can normally be reached Mon-Fri 8:00-5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MARIA G LEAVITT can be reached at 571-272-1085. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BRENDAN THOMAS TINSLEY/Examiner, Art Unit 1634
/MARIA MARVICH/Primary Examiner, Art Unit 1634
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