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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on May 12, 2026 has been entered.
DETAILED ACTION
Claims 1 – 3, 9, 26, 28, 33, 35, 40, 54, 72 – 73, 76, 84, 86, 89, and 123 – 141 are pending in this application, wherein claims 1, 9, and 72 are amended, claims 4 – 8, 10 – 25, 27, 29 – 32, 34, 36 – 39, 41 – 53, 55 – 71, 74 – 75, 77 – 83, 85, 87 – 88, and 90 – 122 are canceled, and claims 26, 28, 54, 76, 84, 86, 89, 126, 128 – 132, and 138 – 141 are withdrawn.
Claims 1 – 3, 9, 33, 35, 40, 72 – 73, 123 – 125, 127, and 133 – 137 are currently examined.
Priority
This application is a national stage application of PCT/US2019/055870, filed October 11, 2019, which claims benefit of domestic application of 62/745,136, filed October 12, 2018.
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 62/745,136, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. The domestic application 62/745,136 does not provide support for the limitation of “H336 mutation selected from the group consisting of H336A, H336C, H336D, H336E, H336F, H336G, H336I, H336K, H336L, H336M, H336M, H336T, H336V, H336W, H336Y, H336N, H336P, H336Q, H336R, H336S, and H336W” that recited in claim 73 and “H336R mutation” of claims 136 – 137. Thus, the priority date of claims 73 and 136 – 137 is October 11, 2019.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 06/29/2026 was filed after the mailing date of the previous Office Action on January 27, 2026. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Withdrawn Rejections
The rejection of claims 1 – 3, 33, 35, 40, 123 – 125, 127, and 133 – 134 in the previous Office Action, dated January 27, 2026, under 35 U.S.C. 102(a)(1) as being anticipated by Efcavitch et al. has been considered and is withdrawn in view of the amended claim 1.
The rejection of claims 1 – 3, 9, 33, 35, 40, 72 – 73, 123 – 125, 127, 133 – 134, and 136 – 137 in the previous Office Action, dated January 27, 2026, under 35 U.S.C. 103 as being unpatentable over Efcavitch et al. (US2016/0046974A1) in view of Lunde et al. has been considered and is withdrawn in view of the amended claim 1.
The rejection of 1 – 3, 33, 40, 123 – 125, and 134 – 135 in the previous Office Action, dated January 27, 2026, on the ground of nonstatutory double patenting as being unpatentable over claims 1 – 2, 5 – 6, and 8 of copending Application No. 18/285,014 (reference application) has been considered and is withdrawn in view of the amended claim 1.
Sequence Compliance
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application contains sequence disclosures in accordance with the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 - 1.825.
The sequence disclosures are located Figure 7B and claim 137.
Required response – Applicant must provide:
A "Sequence Listing" part of the disclosure, as described above in item 1); as well as
An amendment specifically directing entry of the "Sequence Listing" part of the disclosure into the application in accordance with 1.825(b)(2);
A statement that the "Sequence Listing" includes no new matter in accordance with 1.825(b)(5); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(b)(4).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter;
If the "Sequence Listing" part of the disclosure is submitted according to item 1) b), c), or d) above, Applicant must also provide:
A replacement CRF in accordance with 1.825(b)(6); and
Statement according to item 2) a) or b) above.
Responses to Applicant’s Remarks:
Applicant’s Remarks, filed May 12, 2026, have been fully considered. However, the requirements identified under Specific Deficiency IV remain outstanding. In particular, Applicant has not provided an amendment specifically directing entry of the “Sequence Listing” part of the disclosure into the application in accordance with 37 CFR 1.825(b)(2). Submission of a Sequence Listing file, by itself, does not satisfy this requirement absent an express amendment requesting that the Sequence Listing be entered as part of the disclosure. Applicant has also not provided the statement required by 37 CFR 1.825(b)(5) that the ”Sequence Listing” contains no new matter. Further, Applicant has not provided the statement required by 37 CFR 1.825(b)(4) identifying support for the amendment in the application as originally filed. Such statement should identify the specific portions of the originally filed application that provide support for the sequence information included in the Sequence Listing, for example, the applicable figure(s), claims(s), and/or specification paragraph(s).
Accordingly, Specific Deficiency IV is maintained, and Application is required to provide the above item in order to comply with the applicable sequence listing requirements.
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.
Claims 1 – 3, 9, 33, 35, 40, 72 – 73, 123 – 125, 127, and 133 – 137 are 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.
Claims 1 and 9 recite “(SEQ ID NO:3)”. The phrase is written within a parenthesis. It is unclear whether the parenthetical phrase is limiting and it intended to define the poly(U) polymerase or is merely providing non-limiting descriptive information. Thus, the metes and bounds of the claims are not clear and the phrase renders the claims indefinite. Claims 2 – 3, 33, 35, 40, 72 – 73, 123 – 125, 127, and 133 – 137 depends from claim 1 and are, therefore, indefinite.
Claim Rejections - 35 USC § 103
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 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:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. 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 – 3, 9, 33, 35, 40, 72 – 73, 123 – 125, 127, and 133 – 137 is/are rejected under 35 U.S.C. 103 as being unpatentable over Efcavitch et al. (US2016/0046974A1, cited in PTO-892 on January 27, 2026) in view of Lunde et al. (Nucleic Acids Research, 2012, Vol. 40, Issue 19, page 9815 – 9824, cited in PTO-892 on May 19, 2025) and Moritz (RNA, 2014, Vol. 20, Issue 3, page 421 – 427, PTO-892).
Efcavitch et al. teach improved methods for synthesizing polynucleotides, such as DNA and RNA, using renewable initiators coupled to a solid support (Abstract). Methods of the invention are directed to template-independent synthesis of polynucleotides, including DNA and RNA (para. [0054]) by using a nucleotidyl transferase enzyme to incorporate nucleotide analogs coupled to an inhibitor by a cleavable linker (para. [0004]). Thus, Efcavitch et al. teach template-independent synthesis of an oligonucleotide, which reads on the limitation “a method for template-independent synthesis of an oligonucleotide” of claim 1. The disclosed synthesis of RNA further reads on the limitation “the oligonucleotide is an RNA oligonucleotide” of claim 123, and the disclosed synthesis of polynucleotides reads on the limitation “the oligonucleotide is a polynucleotide” of claim 125.
Efcavitch et al. further teach that de novo synthesis begins with a nucleic acid initiator that is bound to a solid support. In the presence of suitable enzyme, nucleotide analogs are added to the nucleic acid initiator in order to create an oligonucleotide. It is preferable that the nucleotide analogs include removable terminating groups that cause the enzymatic addition to stop after the addition of one nucleotide. A removable terminating group can be linked to the base portion of the nucleic acid and/or to the 3’ hydroxyl of the nucleic acid. Deblocking of the terminating group and/or the 3’ blocking group is done and it creates a new active site that is a substrate for the enzyme. With subsequent addition of a new nucleotide or nucleotide analog, the oligonucleotide is extended (para. [0005]). Thus, Efcavitch et al. teach providing an initiator oligonucleotide, enzymatically incorporating a reversible terminator nucleotide, deprotecting the incorporated reversible terminator nucleotide, and thereafter incorporating another nucleotide or nucleotide analog, which read on the corresponding limitations “providing an initiator oligonucleotide”, “addition of the 2’- and/or 3’-O-protected reversible terminator nucleotide to the 3’-end of the initiator oligonucleotide”, and “deprotecting the oligonucleotide formed in step (c)” of claim 1. The subsequent addition of a new nucleotide or nucleotide analog following deblocking further reads on the limitation “adding one or more natural or modified nucleotides to the 3’end of the resulting oligonucleotide” of claim 3. The disclosed repeated addition/deblocking/extension process also provides the teaching relevant to “repeating steps (a)-(d)” of claim 2. Efcavitch et al. teach that the invention includes an apparatus. In some embodiments, the apparatus is designed to recycle nucleotide analog solutions by recovering the solutions after nucleotide addition and reusing solutions for subsequent nucleotide addition (para. [0007]). This disclosure further confirms that Efcavitch et al. contemplate subsequent nucleotide-addition operations following an initial nucleotide addition, consistent with the repeated nucleotide addition process recited in claim 2.
Efcavitch et al. further teach that, in some embodiments, the nucleotide analog is a 3’-O-blocked nucleotide analog, wherein the 3’-O-blocking groups are typically small and easily removed, thus allowing use with engineered enzyme having modified active sites, wherein the blocking group may be an allyl group (para. [0009]). Thus, Efcavitch et al. teach a reversible terminator nucleotide protected at the 3’-O position with an oxygen protecting group, which reads on the limitation of claim 33. Efcavitch et al. further teach that the 3’-O protecting group may be an allyl group, which reads on the “3’-O-allyl” alternative recited in claim 35. The 3’-O-blocked nucleotide analog may also be 3’-O-N3-dATP with the following structure (figure 21):
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with the circled moieties that address the limitations “X”, “Y”, RP”, “R”, and “Base” of claim 40. For synthesis of RNA polynucleotides, a nucleotidyl transferase like E. coli poly(A) polymerase can be used to catalyze the addition of ribonucleotides to the 3’ end of a ribonucleotide initiator. In other embodiments, E. coli poly(U) polymerase may be more suitable for use with the methods of the invention. These enzymes may be used with 3’unblocked reversible terminator ribonucleotide triphosphates (rNTPs) to synthesize RNA. In certain embodiments, RNA may be synthesized using 3’blocked, 2’blocked, or 2’-3’blocked rNTPs and poly(U) polymerase or poly(A) polymerase. These enzymes may have an amino acid sequence at least 99% in common with SEQ ID NO. 3 (para. [0080]). Thus, Efcavitch et al. teach providing a poly(U) polymerase and combining the poly(U) polymerase with a 2’- and/or 3’-protected reversible terminator ribonucleotide for addition to the 3’ end of the ribonucleotide initiator, which reads on the corresponding poly(U) polymerase, reversible terminator nucleotide, and 3’-end addition limitations of claim 1. In some embodiments, the initiator is a single-stranded oligonucleotide, such as pentamer, hexamer, septamer, or octamer (para. [0094]). Thus, Efcavitch et al. teach that the initiator oligonucleotide is single-stranded, which reads on the limitations “wherein the initiator oligonucleotide is single-stranded oligonucleotide” of claim 1 and “single-stranded RNA” of claim 124. The disclosed pentamer, hexamer, septamer, and octamer initiators contain 5, 6, 7, or 8 nucleotides, respectively, each of which falls within the claimed range of 5 – 20 nucleotides, thereby reading on the limitation “5 – 20 nucleotides in length” of claim 134.
Efcavitch et al. further teach that the initiator is preferably a universal initiator for the enzyme, such as a homopolymer sequence (para. [0052]). Thus, Efcavitch et al. teach a homopolymeric initiator oligonucleotide, which is relevant to the limitation of claim 135 requiring the initiator to be poly-rU, poly-rC, poly-rG, or poly-rA. An aqueous phase DNA synthesizer is used to produce desired polynucleotides in substantial quantities to capitalize the efficiency of the disclosed methods. Efcavitch et al. further teach that nucleotidyl transferases may polymerize both ribonucleotides and deoxyribonucleotides, and that some nucleotidyl transferases polymerize ribonucleotides and deoxyribonucleotides at approximately the same rate (para. [0077]). Efcavitch et al. further teach that terminal deoxynucleotidyl transferase (TdT) catalyzes addition of deoxyribonucleotides to the 3’ end of a nucleotide chain and may also catalyze addition of ribonucleotides, which may be useful in constructing site-specific DNA-RNA chimeric polynucleotides (para. [0078]). Thus, Efcavitch et al. teach a chimeric polynucleotide containing both ribonucleotide and deoxyribonucleotide residues, which reads on the limitation “modified RNA oligonucleotide containing one or more DNA nucleotides” of claim 127. In one embodiment, a synthesizer will include four wells of the described NTP analog reagents, i.e., dCTP, dATP, dGTP, and dTTP, as well as TdT at concentrations sufficient to effect polynucleotide growth (para. [0097]). Thus, Efcavitch et al. further teach the use of nucleotide analog reagents in enzymatic template-independent polynucleotide synthesis, consistent with the nucleotide- addition aspect of claim 1.
Furthermore, Efcavitch et al. teach another embodiment for using non-template dependent polymerase enzymes. Protein engineering or protein evolution is used to modify the enzyme to accept 3-blocked reversible terminators with high efficiency. Modifying either single or several amino acid in the active sites of the enzyme can allow the highly-efficient incorporation of 3’-blocked reversible terminators into a support bound initiator (para. [0085]). Efcavitch et al. teach that modified TdT proteins having changes at Arg336 and Arg454 may have enzymatic activity against 3’-O-blocked nucleotide analogs. Efcavitch et al. explain that the guanidinium group of Arg336 assists in stabilizing the cis-peptide bond conformation and that the stability provided by Arg336 may explain why substitutions at this position have a negative impact on the reactivity of modified TdT proteins (para. [0086]). Efcavitch et al. further teach that modification of Arg336 and Arg454 may change the binding interactions of 3’-O-modified dNTPs and that substitutions may be explored to result in improved steric interactions of 3’-O-modified dNTPs with TdT (para. [0087]).
However, Efcavitch et al. do not teach that the poly(U) polymerase is wild-type Schizosaccharomyces pombe poly(U) polymerase, as required by claims 1 and 9, or a mutated variant of wild-type Schizosaccharomyces pombe poly(U) polymerase as required by claim 72. Efcavitch et al. further do not teach H336 mutation recited in claims 73 and 136 – 137.
Lunde et al. teach that many metabolic pathways depend on nucleotidyl transferases to catalyze the template-independent addition of nucleotide monophosphates (NMP) at the 3’-end of RNA targets. These non-template-encoded nucleotides provide an additional layer of control in determining the fate of these RNA (page 9815, Left Col., para. 1). The best studied members of these polymerase, the poly(A) polymerases (PAPs), add poly (A) tails to the 3’-ends of RNA. In addition to the PAPs, poly(U) polymerases (PUPs) are identified to have catalytic effect on the addition of poly(U) tails to 3’-end of RNAs (page 9815, Right Col., para. 1). One of the first described PUPs is Schizosaccharomyces pombe Cid1. Cid1 is initially identified as a PAP with residual PUP activity. However, later work demonstrates that Cid1 is specific for poly(U) incorporation in vitro and in vivo, thus reclassifying it as a PUP. This was followed by the discovery that Cid1 plays a role in the degradation of polyadenylated mRNAs and its poly(U) activity forms the basis of a novel mRNA decay pathway in fission yeast that may be conserved in higher eukaryotes (page 9815, Right Col., para. 3). Thus, Lunde et al. teach a wild-type Schizosaccharomyces pombe poly(U) polymerase, which reads on the limitation requiring wild-type Schizosaccharomyces pombe poly(U) polymerase of claims 1 and 9. A feature that appears to be unique to Cid1 family proteins is their ability to be PUPs, PAPs, or potentially both depending on their context (page 9815, Right Col., para. 4). Moreover, Lunde et al. created the variant of Cid1, Cid1 (H336N) is found to have a significantly decreased apparent KM for ATP and the rate of catalysis has improved (page 9823, Left Col, para. 1). Thus, Lunde eta l. teach a mutated Schizosaccharomyces pombe poly(U) polymerase having a mutation at H336, which reads on the mutated variant alternative of claim 1 and the mutated Schizosaccharomyces pombe poly(U) polymerase limitation of claim 72. Because H336N is one of the H366 substitutions recited in claim 73, Lunde et al. further read on the H336 mutation limitation of claim 73.
Moritz teaches enzymatic incorporation of a chemical modified nucleotide analog into RNA using Schizosaccharomyces pombe Cid1. Specifically, Moritz teaches that both Cid1 and E.coli PAP, under optimized conditions, incorporated N6-biotin-AMP, and further reports that, whereas E.coli PAP incorporated only a small number of biotin-AMP residues, Cid1 unexpected polymerized the biotin-AMP to long tails (page 422, Left Col., para. 1; Figure 1). Moritz further confirms PAP-dependent biotinylation by binding the resulting biotinylated RNA to streptavidin (page 422, Left Col., para. 1; Figure 2). Figure 1 specifically describes the reaction as “RNA tailing with biotin-ATP by S.pombe Cid1 and E.coli PAP and identifies the modified substrate used with Cid1 as N6-biotin-ATP (page 422, Figure 1). Moritz further discloses in the reaction conditions that RNA is incubated with Cid1 in the presence of ATP or N6-ATP analog, identified as N6-[(6-amino)hexyl]-amino-ATP-biotin (page 425, Right Col., para. 4; page 426, Left Col., para. 1). Thus, Moritz demonstrates that S.pombe Cid1 is capable of accepting a chemically modified ATP analog as a substrate and incorporating the corresponding modified nucleotide into RNA during RNA tailing.
It would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the template-independent RNA synthesis method of Efcavitch et al. by substituting the poly(U) polymerase contemplated by Efcavitch et al. with the Schizosaccharomyces pombe Cid1 poly(U) polymerase in view of Lunde et al. because Efcavitch et al. explicitly teach template-independent RNA synthesis using poly(U) polymerase together with reversible terminator ribonucleotide triphosphates, including 2’-blocked, 3’-blocked, and 2’-, 3’-blocked rNTPs and Lunde et al. teach that Schizosaccharomyces pombe Cid1 is a poly(U) polymerase that catalyzes template-independent nucleotide addition to the 3’ end of RNA. Accordingly, substituting the poly(U) polymerase contemplated by Efcavitch et al. with the known Schizosaccharomyces pombe Cid1 poly(U) polymerase of Lunde et al. would have constituted the substitution of one known poly(U) polymerase for another known poly(U) polymerase for performing the same known function of template-independent extension of an RNA substrate. One of ordinary skill in the art would have been motivated to modify the template-independent RNA synthesis method of Efcavitch et al. by substituting the poly(U) polymerase contemplated by Efcavitch et al. with the Schizosaccharomyces pombe Cid1 poly(U) polymerase in view of Lunde et al. because Efcavitch et al. explicitly identify poly(U) polymerase as suitable for synthesis of RNA using protected reversible terminator rNTPs and Lunde et al. identify S.pombe Cid1 as a known poly(U) polymerase having the requisite template-independent RNA extension activity. The motivation to select Cid1 is further supported by Moritz because Moritz experimentally employs S.pombe Cid1 in an in-vitro RNA tailing reaction and demonstrates that Cid1 incorporates the chemically modified nucleotide N6-biotin-AMP and polymerizes the modified nucleotide into long RNA tails. Moritz further discloses use of the N6-modified ATP analog in the Cid1 reaction. Thus, Moritz provides an additional reason for one of ordinary skill in the art to select Cid1 for the in-vitro RNA synthesis method of Efcavitch et al. because Cid1 has already been demonstrated to function in an in-vitro RNA extension reaction using a chemically modified nucleotide substrate. One of ordinary skill in the art would have had a reasonable expectation of success in making the proposed modification because Efcavitch et al. teach that poly(U) polymerase may be used with 2’-, 3’-, and 2’-, 3’-blocked rNTPs for template-independent RNA synthesis, Lunde et al. establish that S.pombe Cid1 possesses the poly(U) polymerase activity required by Efcavitch et al., and Moritz demonstrates that S.pombe Cid1 retains RNA extension activity when presented with a chemically modified nucleotide substrate. Considered together, these teachings would have provided one of ordinary skill in the art with a reasonable basis to expect that S.pombe Cid1 would function as the poly(U) polymerase in the protected-rNTP RNA synthesis method of Efcavitch et al.
With respect to claims 72 – 73, Efcavitch et al. teach that non-template-dependent polymerases may be modified by protein engineering or protein evolution to improve their ability to accept 3’-blocked reversible terminators, including modification of one or more amino acids in the active site. Lunde et al. teach the mutated S.pombe Cid1 variant (H336N) and report that the H336N variant exhibits a significantly decreased apparent KM for ATP and an improved rate of catalysis. Thus, Lunde et al. demonstrate that H336 is a functionally significant position in Cid1 and that substitution at H336 produces an enzymatically active Cid1 variant having altered nucleotide-handling properties. Accordingly, one of ordinary skill in the art, having selected S.pombe Cid1 for use in the protected reversible terminator synthesis method of Efcavitch et al., would have been motivated to employ a known Cid1 variant having a mutation at H336 in view of the teachings of Efcavitch et al. to modify active site residues of non-template-dependent polymerases to facilitate incorporation of blocked nucleotide substrates. One of ordinary skill in the art would have had a reasonable expectation of success because Lunde et al. experimentally demonstrate that the H336N Cid1 variant remains catalytically active and exhibits improved catalytic characteristics.
Regarding claims 136 – 137, Lunde et al. teach that residue H336 of Schizosaccharomyces pombe Cid1 is a functionally significant and mutable position. Specifically, Lunde et al. create the Cid1(H336N) variant and found that H336N substitution resulted in a significantly decreased apparent KM for ATP and an improved rate of catalysis. Thus, Lunde et al. demonstrate that substitution at H336 of S.pombe Cid1 may be made while retaining enzymatic activity and may alter the nucleotide recognition and catalytic properties of the enzyme. Efcavitch et al. further teach that protein engineering or protein evolution may be used to modify non-template-dependent polymerase enzymes to accept 3’-blocked reversible terminators with high efficiency and that modification of one or more amino acids in the active site may permit highly efficient incorporation of such blocked nucleotide substrates. Efcavitch et al. further teach that modified TdT proteins having changes at Arg336 and Arg454 may have enzymatic activity against 3’-O-blocked nucleotide analogs, and explain that the guanidinium group of Arg336 assists in stabilizing the cis-peptide bond conformation. Efcavitch et al. additionally teach that modification of Arg336 and Arg454 may change the binding interactions of 3’-O-modified dNTPs and that substitutions may be explored to obtain improved steric interactions between 3’-O-modified dNTPs and the polymerase. It would therefore have been prima facie obvious for one of ordinary skill in the art, seeking to adapt the S.pombe Cid1 poly(U) polymerase of Lunde et al. for incorporation of the 3’-O-blocked reversible terminators taught by Efcavitch et al., to modify the known functionally significant H336 position of Cid1 and to consider arginine as a candidate substitution at that position. One would have been motivated to investigate the H336R substitution because Lunde et al. establish H336 as a residue whose substitution alters Cid1 nucleotide utilization while retaining catalytic activity, whereas Efcavitch et al. identify Arg336 as a functionally significant active-site residue in a non-template-dependent polymerase and specifically discuss residue 336 in connection with the binding and reactivity of 3’-O-blocked nucleotide analogs. One of ordinary skill in the art would have had a reasonable expectation of success that such substitution at H336 would retain enzymatic activity because Lunde et al. experimentally demonstrate that Cid1 tolerates substitution at H336 and that such substitution may result in improved catalytic characteristics. Further, Efcavitch et al. teach that active-site substitutions, including modifications involving residue 336, may be explored to alter interactions with 3’-O-modified nucleotide substrates. Accordingly, substitution of arginine for histidine at position 336 of S.pombe Cid1 would have been an obvious candidate within the known active-site engineering approach, thereby resulting in the H336R mutated S.pombe poly(U) polymerase recited in claims 136 – 137.
Responses to Applicant’s Remarks:
Applicant’s Remarks, filed May 12, 2026, have been fully considered and are found to be not persuasive in view of the rejection set forth herein.
Applicant argues that Efcavitch et al. do not teach the limitation “wild-type Schizosaccharomyces pombe poly(U) polymerase (SEQ ID NO: 3), or a mutated variant thereof, wherein the mutated variant of the wild-type Schizosaccharomyces pombe poly(U) polymerase comprises a mutation at one or more positions selected from the group consisting of N171, T172, and H336” of the amended claim 1. However, the argument is not persuasive because the rejection does not rely upon Efcavitch et al. alone for the recited Schizosaccharomyces pombe poly(U) polymerase. As discussed above, Efcavitch et al. teach the template-independent synthesis of an oligonucleotide using a non-template-dependent polymerase and protected reversible terminator nucleotides. Lunde et al. further teach that Schizosaccharomyces pombe Cid1 is a poly(U) polymerase capable of template-independent nucleotide addition to the 3’ end of RNA. Lunde et al. further teach a mutated S.pombe Cid1 polymerase at position H336, specifically Cid1(336N), and report that the H336N variant has a significantly decreased apparent KM for ATP and an improved rate of catalysis. Thus, Lunde et al. supply the Schizosaccharomyces pombe poly(U) polymerase and H336-mutated poly(U) polymerase teachings that Efcavitch do not explicitly disclose. Accordingly, the rejection is based upon the combined teachings of the references and does not require Efcavitch et al. alone to disclose every limitation of amended claim 1.
Applicant argues that there is no sufficient rationale or reasonable expectation of success for modifying the method of Efcavitch et al. with the poly(U) polymerase of Lunde et al. According to Applicant, the rejection assumes that E. coli poly(U) polymerase and S. pombe poly(U) polymerase are interchangeable merely because both perform template-independent uridylation. Applicant contends that Lunde et al. only describe the biological role of S. pombe Cid1 in post-transcriptional RNA uridylation within cellular mRNA decay pathways and does not teach or suggest use of the enzyme with 2’- and/or 3’-O-protected reversible terminator nucleotides, nor under conditions relevant to the claimed synthetic oligonucleotide extension methods. However, the argument is not persuasive. The rejection does not rely merely upon the fact that the respective enzymes perform template-independent uridylation. Efcavitch et al. teach the use of nucleotidyl transferases in template-independent polynucleotide synthesis and further teach the use of blocked reversible terminator nucleotide analogs in such synthesis. Efcavitch et al. additionally teach that protein engineering or protein evolution may be used to modify non-template-dependent polymerase enzymes to accept 3’-blocked reversible terminators with high efficiency and that modification of one or more amino acids in the active site may permit highly efficient incorporation of the blocked reversible terminators. Lunde et al. teach that nucleotidyl transferases catalyze template-independent nucleotide addition to the 3’ end of RNA and specifically identify S.pombe Cid1 as a poly(U) polymerase having such catalytic activity. Moreover, Moritz provides additional experimental support for the suitability of S.pombe Cid1 in an in vitro RNA extension reaction involving a chemically modified nucleotide. Moritz teaches that Cid1 incorporates N6-biotin-AMP and polymerizes the modified nucleotide into long RNA tails and identifies the modified nucleotide substrate as N6-[(6-amino)hexyl]-amino-ATP-biotin. Thus, Moritz demonstrates experimentally that S.pombe Cid1 is capable of functioning outside its naturally occurring cellular uridylation context to catalyze RNA extension using a chemically modified nucleotide substrate. Therefore, the propose combination is supported not merely by a similarity in enzyme designation or biological function, but by the teachings of the relevant template-independent catalytic activity of Lunde et al. and Moritz’s experimental demonstration of Cid1 activity with a modified nucleotide substrate.
Applicant further argues that Efcavitch et al. merely mention E. coli poly(I) polymerase as a candidate enzyme without experimental support demonstrating compatibility with protected reversible terminators. Thus, Applicant asserts there is no teaching in either reference linking naturally occurring uridylation activity to successful incorporation of modified nucleotides in iterative synthetic applications. However, the argument is not persuasive in view of the references relied upon in the present rejection. Efcavitch et al. teach the use of non-template-dependent polymerases with blocked reversible terminator nucleotide analogs and further teach engineering such polymerases to increase their ability to accept blocked reversible terminators. Lunde et al. establish that S.pombe Cid1 is a template-independent poly(U) polymerase. Moritz further provides the experimental link that Applicant contends is absent, because Moritz demonstrates that S.pombe Cid1 incorporates the chemically modified nucleotide N6-biotin-AMP and polymerizes the modified nucleotide into long RNA tails. Accordingly, the present rejection does not rely solely upon naturally occurring uridylation activity as a basis for predicting modified nucleotide incorporation. Instead, Moritz provides experimental support that S.pombe Cid1 may accept and incorporate a chemically modified nucleotide during in vitro RNA extension. Moritz is not relied upon as teaching the particular 2’ and/or 3’-O-protected reversible terminator nucleotide recited in claim 1. Efcavitch et al. supply the teaching of blocked reversible terminator nucleotide substrates, while Moritz demonstrate that S.pombe Cid1 possesses substrate tolerance extending to a chemically modified nucleotide. The teachings are therefore relied upon in combination.
Applicant further argues that the SEQ ID NO. 3 of Efcavitch et al. corresponds to E. coli poly(A) polymerase, not poly(U) polymerase, and therefore does not encompass S. pombe Cid1. Applicant argues that sequence similarity alone does not establish that structurally distinct enzymes from different organisms would function equivalently with 2’- and/or 3’-protected reversible terminator nucleotide. However, the argument is not persuasive. As discussed above with respect to the rejection under 35 U.S.C. 112(b), claim 1 is indefinite with respect to the recitation of “(SEQ ID NO:3)”. Accordingly, the broadest reasonable interpretation of the limitation is a wild-type S.pombe poly(U) polymerase. Lunde et al. teach S.pombe Cid1 poly(U) polymerase and its template-independent nucleotide transfer activity. Thus, Lunde et al. teach the wild-type S.pombe Cid1 poly(U) polymerase required under the broadest reasonable interpretation of claim 1. The present rejection therefore does not rely upon the SEQ ID NO:3 disclosed by Efcavitch et al. as being the claimed S.pombe SEQ ID NO:3, nor does the rejection rely upon sequence similarity alone to establish functional equivalence. Further, Moritz provides experimental support that S.pombe Cid1 itself is capable of incorporating a chemically modified nucleotide into RNA. Thus, the combination is based upon demonstrated catalytic properties of S.pombe Cid1, rather than an assumption that the Efcavitch and S.pombe sequences are equivalent.
Regarding Lunde et al., Applicant argues that Lunde et al. teach away from the proposed combination and undermine any expectation of success because the structural data of Lunde et al. indicates that the S. pombe poly(U) polymerase active site relies on critical interactions with the 2’- and 3’-hydroxyl groups of the incoming nucleotide. Specifically, Lunde et al. disclose that the 2’-hydroxyl forms a direct hydrogen bond with N171 and that the 3’-hydroxyl is contacted by T172 through a water-mediated bridge, with T172 also directly interacting with the 2’-hydroxyl. Lunde et al. further state that these contacts are “likely to be important for discriminating between UTP and dUTP”. Applicant contends that a person of ordinary skill in the art would therefore have expected that adding protecting groups at the 2’-O or 3’-O positions would disrupt these active-site interactions and prevent productive binding, thereby suggesting that S. pombe poly(U) polymerase would not accept 2’- or 3’-O-protected reversible terminator nucleotides. The argument is not persuasive. Lunde et al. explain that the interactions involving N171 and T172 and 2’- and 3’-hydroxyl groups are likely important for discrimination between UTP and dUTP. Thus, while the disclosed interactions involve the 2’- or 3’-hydroxyl groups, Lunde et al. does not establish that the presence of a protecting group at the 2’- or 3’-position necessarily prevents productive nucleotide incorporation by Cid1. Moreover, Moritz provides experimental support that Cid1 possesses tolerance for at least a chemically modified nucleotide substrate, demonstrating incorporation of N6-biotin-AMP and polymerization thereof into long RNA tails. Although the modification disclosed by Moritz is not a 2’- or 3’-O-protecting group, the reference demonstrates that Cid1 is not limited to incorporation of its natural unmodified nucleotide substrate. Additionally, Efcavitch et al. recognize that incorporation of blocked reversible terminators may be improved through protein engineering or protein evolution and teach modifying one or more amino acids in the active site of a non-template-dependent polymerase to permit highly efficient incorporation of 3’-blocked reversible terminators. Thus, the structural observations of Lunde et al., when considered together with Moritz and Efcavitch et al., do not constitute a teaching away from the proposed modification.
With the support of Winz et al. and WO‘820, Applicant argues that the experimental evidence in the art negates any reasonable expectation of success because contemporaneous studies directly test S. pombe Cid1 poly(U) polymerase with 2’- and 3’-modified azido-nucleoside triphosphates and report “mostly 0” incorporation of 2’-modified nucleotides and no detectable incorporation of 3’-modified nucleotides. Applicant contends that these experimental results confirm the structural concerns identified in Lunde et al. regarding the importance of the 2’- and 3’-hydroxyl interactions within the active site of S. pombe poly(U) polymerase. However, the argument is not persuasive. The reported reduced or absent incorporation of particular azido-modified nucleotide substrates that are structurally different from the 2’- and/or 3’-O-protected reversible terminator nucleotides recited in the claims. For example, Winz et al. test Cid1 PUP with 2’-N3-2’-deoxynucleoside triphosphates (page 5, Figure 1A; Table 3) and WO’820 depicts the corresponding 2’-azido-modified nucleotide residue incorporated at an RNA termius (Figure 21). In these structures, the azido modification is presented at the 2’ carbon rather than as a protecting group attached through the 2’- or 3’-oxygen as recited in the claims. Accordingly, the reduced or absent incorporation of these particular substrates does not establish that Cid1 would be incapable of incorporating the structurally different O-protected reversible terminators presently claimed. However, Efcavitch et al. explicitly recognize the problem of incorporating blocked reversible terminators and teach a solution to that problem, namely protein engineering or protein evolution of non-template-dependent polymerases to improve acceptance of 3’-blocked reversible terminators. Thus, reduced activity of an enzyme toward a particular modified substrate would have provided a reason to employ the enzyme-modification approach taught by Efcavitch et al., rather than necessarily discouraging further use of the enzyme. Further, Moritz demonstrates that S.pombe Cid1 may incorporate a chemically modified nucleotide and polymerize the modified nucleotide into RNA tails. Therefore, the prior art considered as a whole demonstrates that Cid1 substrate acceptance depends upon the particular nucleotide modification and does not establish that Cid1 is incapable of incorporating modified nucleotide substrates.
Applicant further argues that both Winz et al. and WO‘820 direct skilled artisans away from using poly(U) polymerase with modified nucleotides and therefore undermine any reasonable expectation that S. pombe poly(U) polymerase would successfully accept 2’- and/or 3’-O-protected reversible terminator nucleotides under the conditions recited in amended claim 1. The argument is not persuasive because a reference teaches away when it would have discouraged a person of ordinary skill from flowing the path taken by the Applicant, rather than merely identifying disadvantages or reduced performance associated with particular embodiments. The evidence relied upon by Applicant concerns poor incorporation of particular modified nucleotide substrates. In contrast, Efcavitch et al. teach modifying non-template-dependent polymerases to obtain efficient incorporation of blocked reversible terminators, while Moritz demonstrates that S.pombe Cid1 may accept a chemically modified nucleotide substrate. Accordingly, the teachings relied upon by Applicant do not negate the reason provided by Efcavitch et al. to modify a template-independent polymerase to accommodate a blocked nucleotide substrate, particularly where the art demonstrates that Cid1 retains catalytic activity toward at least some chemically modified nucleotide substrates.
Regarding Efcavitch et al., Applicant argues that the stated motivation to introduce an H366R mutation into S. pombe poly(U) polymerase of Lunde et al. rests on an incorrect reading of Efcavitch et al. Applicant contends that Efcavitch does not teach that adding arginine at position 336 increases reaction efficiency; rather, Efcavitch et al state that “substitutions at [Arg336] have a negative impact on the reactivity of modified TdT proteins”. Applicant argues that Efcavitch et al. therefore teach that disturbing the naturally occurring arginine at position 336 in TdT is detrimental, not that introducing arginine at position 336 into another enzyme would improve efficiency. However, the argument is not persuasive because the present rejection does not rely upon Efcavitch et al. for the proposition that introducing arginine at position 336 of S.pombe poly(U) polymerase necessarily increases reaction efficiency. Instead, Efcavitch et al. are relied upon for the broader teaching that active-site engineering of non-template-dependent polymerases may be used to improve incorporation of 3’-blocked reversible terminators and, more specifically, that residue 336 is a functionally significant position involved in interactions with 3’-O-blocked nucleotide analogs. Efcavitch et al. teach that modified TdT proteins having changes at Arg336 and Arg454 may have enzymatic activity against 3’-O-blocked nucleotide analogs, that the guanidinium group of Arg336 assists in stabilizing the relevant enzyme conformation, and that modifications at Arg336 and Arg454 may change the binding interactions of 3’-O-modified dNTPs. Lunde et al. provide the teaching specific to S.pombe Cid1. Lunde et al. Identify H336 as a functionally significant and mutable position in S.pombe Cid1 and experimentally demonstrate that the H336N substitution results in a significantly decreased apparent KM for ATP and an improved rate of catalysis. Thus, Lunde et al. establish that substitution at H336 of S.pombe Cid1 may alter nucleotide-recognition and catalytic properties while retaining enzymatic activity. Accordingly, the rejection does not depend upon an assertion that Efcavitch et al. teach that H336R in S.pombe Cid1 increases efficiency. Instead, the references are relied upon in combination, wherein Lunde et al. establish H336 as a known, functionally significant mutation site in S.pombe Cid1 and Efcavitch et al. identify Arg336 as a functionally significant active-site residue in a non-template-dependent polymerase and specifically discuss residue 336 in connection with interactions involving 3’-O-blocked nucleotide substrates. Thus, one of ordinary skill in the art seeking to engineer the known H336 position of Cid1 for use with blocked nucleotide substrates would have had reason to consider arginine among candidate substitutions at that position.
Applicant further argues that the examiner improperly extrapolates a TdT-specific teaching to S. pombe poly(U) polymerase without any structural, functional, or other basis. Applicant emphasizes that S. pombe poly(U) polymerase has histidine, not arginine, at position 336, and that TdT’s Arg336 serves a structural role unique to TdT’s TGSR motif, which does not exist in S. pombe poly(U) polymerase. Applicant therefore contends there is no rational basis to predict that introducing arginine at position 336 of S. pombe poly(U) polymerase would improve, rather than disrupt, enzymatic activity. However, the argument is not persuasive. The present rejection does not require extrapolating the specific structural function of TdT Arg336 to S.pombe Cid1. Lunde et al. independently identify H336 to S.pombe Cid1 as a functionally significant and mutable residue and experimentally demonstrate that substitution at H336 may improve relevant catalytic properties. Accordingly, the basis for considering modification at H336 arises directly from experimental modification of S.pombe Cid1 itself, rather than from an assumption that TdT and Cid1 possess identical structural motifs. Efcavitch et al. is relied upon for the separate teaching that residue 336 is a functionally significant active-site position in a non-template-dependent polymerase in the context of interactions with 3’-O-blocked nucleotide substrates. Efcavitch et al. further teach that modifications involving Arg336 may alter the binding interactions of 3’-O-modified dNTPs and that substitutions at active-site residues may be explored to improve steric interactions with such blocked substrates. Thus, one of ordinary skill in the art would have had a reason to consider arginine among the candidate substitutions when engineering that position for interaction with blocked nucleotide substrates.
Regarding unexpected results, Applicant argues that the claimed methods produce surprising and unexpected results because the specification demonstrates that S. pombe poly(U) polymerase, as well as mutated variants thereof, accepts 2’- and/or 3’-O-protected reversible terminator nucleotides and catalyzes their addition to the 3’ end of an initiator oligonucleotide. Applicant contends that this result is surprising and unexpected because the prior art reports that S. pombe Cid1 poly(U) polymerase is essentially inactive with 2’- and 3’-modified nucleotides, and therefore the discovery that S. pombe poly(U) polymerase accepts such protected reversible terminator nucleotides is contrary to what the prior art predicted. Applicant’s evidence and argument regarding unexpected results have been considered. Applicant contends that the claimed results are unexpected because the prior art reports that S.pombe Cid1 poly(U) polymerase is essentially inactive with 2’- and 3’-modified nucleotides. However, the cited prior art does not establish that S.pombe Cid1 is incapable of accepting chemically modified nucleotide substrates. Moritz demonstrates that S.pombe Cid1 is capable of accepting and incorporating a chemically modified nucleotide substrate. Thus, Moritz provides experimental support that modification of a nucleotide does not, by itself, render the nucleotide incapable of being accepted as a substrate by S.pombe Cid1. Moreover, Efcavitch et al. recognize the steric constraints associated with incorporation of 3’-blocked reversible terminators by non-template-dependent polymerases and teach modifying one or more amino acids in the active-site to permit highly efficient incorporation of such 3’-blocked reversible terminators. Efcavitch et al. further identify active-site residues as targets for modification to accommodate the steric bulk of 3’-O-blocking groups. Thus, the reduced activity of an unmodified polymerase toward particular modified nucleotide substrates would not have discouraged one of ordinary skill in the art from modifying the polymerase to accommodate such substrates; instead, Efcavitch et al. identify that incompatibility as a problem susceptible to active-site engineering.
Applicant further argues that the examiner’s prior position that the results “naturally flow” from the disclosure of Efcavitch et al. because Efcavitch et al. teach “each and every limitation” cannot apply to the claims as amended. Applicant notes that amended claim 1 requires “wild-type Schizosaccharomyces pombe poly(U) polymerase (SEQ ID NO: 3), or a mutated variant thereof, wherein the mutated variant of the wild-type Schizosaccharomyces pombe poly(U) polymerase comprises a mutation at one or more positions selected from the group consisting of N171, T172, and H336”. Applicant asserts that the examiner has not identified any passage in Efcavitch et la. that disclose S. pombe poly(U) polymerase by name of sequence, any mutation of S. pombe poly(U) polymerase, or any experimental data for a poly(U) polymerase with any blocked substrate. However, the argument is not persuasive because the rejection is no longer on the basis that Efcavitch et al. alone teach each and every limitation. The present rejection instead relies upon the combined teachings of Efcavitch et al., Lunde et al., and Moritz. Efcavitch et al. teach the template-independent synthesis method employing blocked reversible terminator nucleotide substrates and further teach engineering non-template-dependent polymerases to improve acceptance of such substrates. Lunde et al. teach S.pombe Cid1 poly(U) polymerase and demonstrate that H336 of Cid1 may be mutated while retaining, and in the case of H336N improving, relevant catalytic properties. Moritz further provides experimental evidence that S.pombe Cid1 may function in an in vitro RNA extension reaction using a chemically modified nucleotide substrate. Therefore, the rejection no longer depends upon the proposition that Efcavitch et al. alone disclose the newly added S.pombe limitations.
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, 9, 33, 40, 123 – 125 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 31, 34 – 35, 38, and 40 – 41 of copending Application No. 18/869,037 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of ‘037 anticipate the claimed invention.
‘037 claims a method for template-independent synthesis of an RNA oligonucleotide, wherein the method comprises (a) providing an initiator oligonucleotide, wherein the initiator oligonucleotide is single-stranded RNA; (b) providing a polymerase; (c) combining the initiator oligonucleotide, the polymerase, and an NTP under conditions sufficient for the addition of the NTP to the 3’ end of the initiator oligonucleotide (claim 34). The NTP comprises a 3’-reversible terminator group and the method further comprises (d) deprotecting the 3’-reversible terminator group at the 3’end of the oligonucleotide formed in step (c). The method further comprises (e) incorporating one or more nucleoside triphosphates to the 3’end of the RNA oligonucleotide formed in step (d) (claim 35). The polymerase is a poly(N) polymerase (claim 38), wherein the poly(N) polymerase is a poly(U) polymerase (claim 40), wherein the poly(U) polymerase is a wild-type Schizosaccharomyces pombe poly(U) polymerase (claim 41). The NTP has a structure of (claim 31):
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351
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.
For these reasons above, ‘037 anticipates the claimed invention.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1 – 3, 9, 33, 40, 72 – 73, and 123 – 125 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5 – 6, and 8 of copending Application No. 18/285,014 in view of Lunde et al. (Nucleic Acids Research, 2012, Vol. 40, Issue 19, page 9815 – 9824, cited in PTO-892 on May 19, 2025) and Moritz (RNA, 2014, Vol. 20, Issue 3, page 421 – 427, PTO-892).
‘014 claims a method of synthesizing a polynucleotide, the method comprises (a) providing, attached to a synthesis support, initiators with a free 3’-hydroxyl and (b) repeating in a reaction mixture including the synthesis support, until the polynucleotide is formed, cycles of (i) contacting under elongation conditions the initiators having free 3’-O-hydroxyls with a 3’-O-blocked nucleoside triphosphate and a template-independent polymerase so that the initiator are elongated by incorporation of a 3’-O-blocked nucleoside triphosphate to form 3’-O-blocked elongated fragments, and (ii) deblocking the elongated fragments (claim 1). The polynucleotide is an RNA and the template-independent polymerase is a poly(U) polymerase (claim 5). The 3’-O-blocked nucleoside triphosphate is a 3’-O-azidomethyl ribonucleoside triphosphate (claim 6). The length of the polyC oligonucleotide is in the range of from 2 to 20 nucleotides (claim 8).
However, ‘014 does not claim that the poly(U) polymerase is wild-type Schizosaccharomyces pombe poly(U) polymerase or mutated Schizosaccharomyces pombe poly(U) polymerase that comprises an H336N mutation.
Lunde et al. teach that many metabolic pathways depend on nucleotidyl transferases to catalyze the template-independent addition of nucleotide monophosphates (NMP) at the 3’-end of RNA targets. These non-template-encoded nucleotides provide an additional layer of control in determining the fate of these RNA (page 9815, Left Col., para. 1). The best studied members of these polymerase, the poly(A) polymerases (PAPs), add poly (A) tails to the 3’-ends of RNA. In addition to the PAPs, poly(U) polymerases (PUPs) are identified to have catalytic effect on the addition of poly(U) tails to 3’-end of RNAs (page 9815, Right Col., para. 1). One of the first described PUPs is Schizosaccharomyces pombe Cid1. Cid1 is initially identified as a PAP with residual PUP activity. However, later work demonstrates that Cid1 is specific for poly(U) incorporation in vitro and in vivo, thus reclassifying it as a PUP. This was followed by the discovery that Cid1 plays a role in the degradation of polyadenylated mRNAs and its poly(U) activity forms the basis of a novel mRNA decay pathway in fission yeast that may be conserved in higher eukaryotes (page 9815, Right Col., para. 3). Thus, Lunde et al. teach a wild-type Schizosaccharomyces pombe poly(U) polymerase, which reads on the limitation requiring wild-type Schizosaccharomyces pombe poly(U) polymerase of claims 1 and 9. A feature that appears to be unique to Cid1 family proteins is their ability to be PUPs, PAPs, or potentially both depending on their context (page 9815, Right Col., para. 4). Moreover, Lunde et al. created the variant of Cid1, Cid1 (H336N) is found to have a significantly decreased apparent KM for ATP and the rate of catalysis has improved (page 9823, Left Col, para. 1). Thus, Lunde eta l. teach a mutated Schizosaccharomyces pombe poly(U) polymerase having a mutation at H336, which reads on the mutated variant alternative of claim 1 and the mutated Schizosaccharomyces pombe poly(U) polymerase limitation of claim 72. Because H336N is one of the H366 substitutions recited in claim 73, Lunde et al. further read on the H336 mutation limitation of claim 73.
Moritz teaches enzymatic incorporation of a chemical modified nucleotide analog into RNA using Schizosaccharomyces pombe Cid1. Specifically, Moritz teaches that both Cid1 and E.coli PAP, under optimized conditions, incorporated N6-biotin-AMP, and further reports that, whereas E.coli PAP incorporated only a small number of biotin-AMP residues, Cid1 unexpected polymerized the biotin-AMP to long tails (page 422, Left Col., para. 1; Figure 1). Moritz further confirms PAP-dependent biotinylation by binding the resulting biotinylated RNA to streptavidin (page 422, Left Col., para. 1; Figure 2). Figure 1 specifically describes the reaction as “RNA tailing with biotin-ATP by S.pombe Cid1 and E.coli PAP and identifies the modified substrate used with Cid1 as N6-biotin-ATP (page 422, Figure 1). Moritz further discloses in the reaction conditions that RNA is incubated with Cid1 in the presence of ATP or N6-ATP analog, identified as N6-[(6-amino)hexyl]-amino-ATP-biotin (page 425, Right Col., para. 4; page 426, Left Col., para. 1). Thus, Moritz demonstrates that S.pombe Cid1 is capable of accepting a chemically modified ATP analog as a substrate and incorporating the corresponding modified nucleotide into RNA during RNA tailing.
It would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the method claimed in ‘014 by employing the S.pombe Cid1 poly(U) polymerase in view of Lunde et al. because ‘014 claims template-independent synthesis of an RNA polynucleotide using a poly(U) polymerase and repeated incorporation and deblocking of 3’-O-blocked nucleoside triphosphates and Lunde eta l. teach that S.pombe Cid1 is a poly(U) polymerase that catalyzes template-independent nucleotide addition to the 3’ end of RNA. Thus, one of ordinary skill in the art would have been motivated to employ the known S.pombe Cid1 poly(U) polymerase of Lunde et al. as the poly(U) polymerase in the method claimed in ‘014 because Cid1 performs the same template-independent RNA extension function required by ‘014. One of ordinary skill in the art would further have had a reasonable expectation of success that S.pombe Cid1 would remain catalytically functional in such an RNA extension method because Moritz demonstrates enzymatic incorporation of a chemically modified nucleotide analog into RNA using S.pombe Cid1. Specifically, Moritz teaches that Cid1 incorporates N6-biotin-AMP and polymerizes the modified nucleotide into long RNA tails. Thus, Moritz provides experimental support the S.pombe Cid1 may function in an in vitro RNA-extension reaction using a chemically modified nucleotide substrate.
With respect to claims 72 – 73, Lunde et al. further teach a mutated S.pombe Cid1 poly(U) polymerase, Cid1(H336N), and report that the H336N variant exhibits a significantly decreased apparent KM for ATP and an improved rate of catalysis. Accordingly, one of ordinary skill in the art would have had reason to employ the known H336N Cid1 variant where a mutated S.pombe poly(U) polymerase is desired, with a reasonable expectation of retaining enzymatic activity because Lunde et al. demonstrate that the H336N variant remains catalytically active. H336N is encompassed by the H336 substitutions recited in claim 73.
This is a provisional nonstatutory double patenting rejection.
Responses to Applicant’s Remarks:
Applicant’s Remarks, filed May 12, 2026, have been fully considered and have been addressed in the Advisory Action dated on June 2, 2026.
Conclusion
No claim is found to be allowable.
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/H.Y.L./Examiner, Art Unit 1693
/SCARLETT Y GOON/Supervisory Patent Examiner, Art Unit 1693
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