APPARATUS AND METHOD FOR CONTINUOUS PRODUCTION OF RNA

DETAILED ACTION Notice of Pre-AIA or AIA Status The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . Priority This application is filed under 35 U.S.C. 371 as a national stage of international application PCT/US2022/032436, filed on Jun 7, 2022. Election/Restrictions Claims 14-16, 18, 22, 27-28, and 30-32, drawn to a method for continuous production of RNA, remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention. Election was made without traverse in the reply filed on 4th May, 2026. Amendments and Arguments This action is in response to papers filed 24th August 2026 in which claim 1, 3, 6, 14-15 were amended. All of the amendments have been thoroughly reviewed and entered. Applicant's arguments are directed to the previous rejections of the previous claims. The amendments made to the claims have overcome these previous rejections; the §112b rejection of claims 3 and 6, and the §112a written description of claim 3 is withdrawn. However, the current rejections are applicable to the current claims. Applicant's remarks have been fully considered but are moot because they do not specifically address the current rejections of the current claims. Any rejection or objection not reiterated herein has been overcome by amendment. Claim Interpretation Claims 1-3 and 5, drawn to a modular apparatus comprising a reaction module, control module, and an RNA separation system, that supports a method for continuous production of purified RNA, are interpreted as comprising an apparatus with the following features: A reaction module comprising a bioreactor operating in continuous mode A Control module comprising at least one sensor An RNA separation system comprising a capture module and a purification module Wherein: the reaction module: A. the bioreactor houses: a DNA template (a sequence encoding an open reading frame) used for in vitro transcription (IVT) to produce a sequence encoding an affinity tag, B. wherein the affinity-tagged RNA molecule is mRNA (claim 2); the sensor: A. at least one sensor that is in communication with other two modules (providing feedback control of the in vitro transcription mixture in the bioreactor and the transcription reaction product in the affinity column); wherein the sensor provides feedback control of the transcription mixture in the reaction module, by detecting concentration of at least one reactant in the in vitro transcription mixture such that the control module can determine the concentration of the reactant in the in vitro transcription mixture based on the data received from the sensor and controls input of the reactants to the bioreactor when the concentration of the reactant falls below the threshold level, and feedback control of a transcription reaction product in the RNA separation system, wherein the at least one sensor is configured to determine when maximum binding capacity of the affinity-tagged RNA molecule in the affinity column is reached, wherein the control module is configured to instruct elution of the affinity-tagged RNA molecule from the affinity column when the maximum binding capacity is reached. B. the sensor /a plurality of sensors independently monitor nucleotides, capping molecules, RNA polymerase, magnesium levels, or a combination thereof (claim 5). in the RNA separation system: A. the capture module houses i) an affinity column with an immobilized ligand (for binding the produced affinity-tagged RNA molecule from the transcription reaction product to the immobilized ligand); ii) wherein the affinity column comprises immobilized poly(A)-binding protein and the affinity tag is a poly(A) tail or equivalent (claim 3) (the bound affinity-tagged RNA molecule is then eluted from the affinity column and passed on to the purification module); B. the purification module is a continuous chromatography column (for passing the eluted affinity-tagged RNA molecule through to provide the purified RNA) that captures contaminants or impurities in the eluate. 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. Claim(s) 1-3 and 5-7 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wochner (WO 2015/188933 A1, previously cited), in view of Deutsch (US 2021/0040472 A1), Heartlein (US 20200318156 A1, IDS, previously cited) and Laustsen (US 2022/0185868 A1, claiming priority to PCT/EP2015/051797). Claim 3 is evidenced by Deo (Deo R, Bonanno J, Sonenberg N ...Cell, 98, 835-845, 1999, previously cited). This is a new rejection necessitated by amendment. Wochner teach in vitro transcription of RNA molecules from corresponding DNA molecules produced in a bioreactor in continuous mode (abstract). Regarding claims 1-2 and 5, Wochner teaches the modular apparatus (see abstract) comprises: a bioreactor that houses a reaction module that contains: a DNA template (a sequence encoding an open reading frame, used for in vitro transcription (IVT) to produce an RNA molecule which comprise a combination of a 5'UTR, open reading frame, 3'UTR and poly(A); see pg. 11, first para; i.e., an mRNA; bioreactor operating in continuous mode. See Fig. 18; wherein the bioreactor further comprises a control module which comprises at least one ion-selective electrode (sensor); see pg. 37, last para; allows the real-time measurement of the nucleotide concentration during the in vitro transcription reaction to monitor the progress of the in vitro transcription reaction; see pg. 35, first para; monitoring of the progress of the in vitro transcription reaction feeding additional amounts of the sequence-optimized NTP mix into the in vitro transcription reaction (NTP feed); see pg. 29. A receiving unit (RNA separation system) comprising a capture module and a filtration membrane wherein the produced RNA molecules can be dispensed from the bioreactor by means of an exit line or the like (not shown) to a receiving unit or the like, in which further RNA elution and purification can be carried out; see pg. 63, middle para. The receiving unit comprising: a capture module comprises means for eluting the captured transcribed RNA molecules; see pg. 37, middle para. a means for purification (Subsequently the mRNA was purified using PureMessenger® (CureVac, Tubingen, Germany; WO2008/077592A1); see pg. 49. As per the cited reference, this purification may be HPLC/Affinity purification; see pg. 2, line 19. Regarding claim 7, Wochner teaches means for feeding the bioreactor and a means for obtaining eluted products. See abstract: PNG media_image1.png 200 400 media_image1.png Greyscale With respect to the first supply, Wochner teach on top of pg. 64, with reference to Fig. 18: the feed of nucleotides, buffer components and/or enzymes into reaction module 2 from a feed tank 24 can be controlled and regulated by means of a feed pump 43, which allows performing the RNA transcription reaction in an optimal steady - state condition yielding high transcriptional performance. With respect to the first transfer line and a second supply line, Wochner teach on pg. 63, middle para: PNG media_image2.png 200 400 media_image2.png Greyscale Thus, the apparatus in Wochner’s invention read on instant apparatus except for the specific description of a capture/purification module that comprises an affinity tag - a poly(A) tail and a poly-A binding protein and the amendments relating to the control module. However, before the effective filing date of instant invention, Deutsch had taught an automated method of performing an in vitro transcription (IVT) reaction using a system comprising a plurality of fluid depots in communication with a microfluidic path device [0037] wherein concentrations are controlled by software [0179]. The system comprises a control module comprising at least one sensor wherein the sensor provides optical feedback such that the in vitro transcription reaction is automatically and continuously performed (The method of claim 1, wherein the system automatically and continuously performs the steps of forming the synthetic template, performing in vitro transcription from the template, and purifying the therapeutic polynucleotide with optical feedback from one or more sensors of system, claim 8; [0015]; [the optical data is used] to move material between the plurality of fluid depots, [0032]; mixing and reagent additions (both at the beginning and throughout the reaction) may be controlled to optimize levels [0275]). The system may include a controller to perform these methods, including, e.g., performing the steps of transporting reagents by deflecting one or more elastic layers within the microfluidic path device. These methods may include receiving, in a controller for the system, optical sensor data from one or more sensors of the system, wherein the controller controls the operation of the system based on the optical sensor data [0038]. The controller may monitor the fluid level and therefore the amount of each material in the fluid interface assembly [0224]. The control module is in communication with a downstream RNA separation system, the latter comprising: one or more purification reactor regions of the microfluidic path device [0037]. Thus, Deutsch’s sensor reads on instant provides feedback control of the transcription mixture in the reaction module, by detecting concentration of at least one reactant in the in vitro transcription mixture such that the control module can determine the concentration of the reactant in the in vitro transcription mixture based on the data received from the sensor and controls input of the reactants to the bioreactor, and feedback control of a transcription reaction product in the RNA separation system. Deutsch’s sensor results in transferring the therapeutic mRNA into a one or more purification reactor regions [0037]. Pure mRNA is eluted after impurities and side products are removed [0277]-[0278]. Deutsch does not explicitly teach controls input of the reactants to the bioreactor when the concentration of the reactant falls below the threshold level, Deutsch’s teachings on “concentrations are controlled by software [0179]”, “mixing and reagent additions”, “claim 8: wherein the system automatically and continuously performs the steps of forming the synthetic template, performing in vitro transcription from the template, and purifying the therapeutic polynucleotide with optical feedback from one or more sensors of system.”, and “to optimize levels [0275]” read on this instant limitation. It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the apparatus and method of Wochner and control the progress of the IVT reaction with sensors that determine concentrations and keep the reaction running in continuous mode as taught by Deutsch. The motivation being to use a fixed amount of resin to be used for processing an essentially unlimited amount of unpurified product for the purification of IVT-generated RNA, and to run such a system autonomously. In view of the detailed teachings, and the fact that it is being used for the very same purpose- to improve mRNA yield in a continuous method of operation of IVT, the ordinary artisan would have also had a most reasonable expectation of success in combining the teachings of Deutsch with those of Wochner. See MPEP 2144 A. Neither Wochner nor Deutsch teach affinity tagging the mRNA. However, before the effective filing date of instant invention, Heartlein had taught a method of IVT that included a step of purifying the RNA product that required synthesizing a polyA tag to the RNA product. See Example 1: Synthesis of mRNA: [0107] Firefly Luciferase (FFL) and human erythropoietin (EPO) mRNA were synthesized by in vitro transcription from a plasmid DNA template encoding each respective gene. In vitro transcription included addition of a 5′ cap structure, Cap1, which has a 2′-O-methyl residue at the 2′ OH group of the ribose ring of base 1, by enzymatic conjugation of GTP via guanylyl transferase. A 3′ poly(A) tail of approximately 200 nucleotides in length (as determined by gel electrophoresis) was incorporated through the addition of ATP in conjunction with PolyA polymerase The synthesis step is followed by a capture step. The capture agents are immobilized on to solid supports ([0075]; For example, in some embodiments, an mRNA is captured by its 3′ end (e.g., by hybridization of immobilized oligo-dT or polyA-binding protein to the polyA tail, [0082]). Regarding claim 3, Heartlein had taught that in some embodiments, a poly-A binding protein is used to capture the mRNA [0015, 0082]. Thus, Heartlein teaches an affinity based purification of the transcribed RNA wherein the affinity column comprises immobilized poly-A binding protein and affinity tag is a poly(A) tail. As evidenced by Deo (whole paper), poly-A binding protein and its ability to bind poly(A) tail was well-studied and known in the art. It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the method of Wochner and Deutsch and incorporate a poly(A) tail on the RNA and a cognate immobilized poly(A) Binding Protein to capture the RNA as taught by Heartlein because Wochner already taught the incorporation of sequence-optimized NTP mix into the in vitro transcription reaction, which could be programmed to provide the right quantities of ATP needed for the polyA tail and further this would allow for a possible alternative way of purifying the RNA produced even if it wasn’t mRNA that naturally has a polyA tail. One of skill would be motivated to use an immobilized poly(A) Binding Protein instead of PureMessenger® as used by Wochner, as such substitution would provide a cheaper alternative. See MPEP 2144 B. Regarding claim 6, the claim is being interpreted as the continuous chromatography column comprising an immobilized support for capturing the affinity-tagged RNA molecule. Deutsch Neither Wochner, Deutsch, nor Hertlein taught wherein the at least one sensor is configured to determine when maximum binding capacity of the affinity-tagged RNA molecule in the affinity column is reached, wherein the control module is configured to instruct elution of the affinity-tagged RNA molecule from the affinity column when the maximum binding capacity is reached. However, before the effective filing date of instant invention, Laustsen had taught a bioreactor arrangement for producing a biopolymer expressed by a cell and a continuous process for capturing the biopolymer employing two chromatography units operated in series or independently (abstract). Laustsen teach when a pre-determined level of binding capacity is reached, components are led in to the next unit in series [0035]. Specifically, regarding the eluting process (of the biopolymer), Laustsen teach in [0216]: medium comprising biopolymer and waste products are provided from the product harvest module (51) to the first and/or second chromatography units (2) and/or (3) and the biopolymer is captured by the affinity ligand e.g. resin or filter whereby binding sites for the absorbing biopolymer get occupied and the binding capacity decreases… When the first chromatography unit is loaded until a pre-determined level of binding capacity, it is detached from the second chromatography unit, washed and the biopolymer is eluted. The step of optimizing the binding is significant because Laustsen teach in [0010]: [0010] In such a typical downstream purification process it is commonly the chromatographic capturing step that is presenting significant challenges in terms of facility throughput since, due to the high cost of producing polypeptides including complex monoclonal antibodies … the affinity resin is often only saturated until 30-50% of its actual binding capacity during the capturing step to avoid pass through of costly product. In addition the affinity resin in itself is normally also a costly compound. Thus, there is a strong incentive to optimize the utilization of the capturing resin. About the pre-determined amount, Laustsen teach: [0218] The pre-determined levels of binding capacity may independently be set such that the resin for example is loaded to about 30%-100%,… It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the modular apparatus for performing IVT, taught by Wochner, Deutsch, and Hertlein, by adding a step of determining when maximum binding capacity of the affinity-tagged RNA molecule in the affinity column is reached, and then configure the control module to instruct elution of the affinity-tagged RNA molecule from the affinity column when the maximum binding capacity is reached, as taught by Laustsen, for a more efficient IVT modular apparatus. The cost-savings effect of such an approach offers motivation for a person of ordinary skill in the art to adopt such an approach under suitable circumstances, e.g. where costs prohibit including more than one affinity column. One of skill in the art would have reasonable expectation of success in doing so because, Wochner had a sensor in their IVT modular apparatus, and Deutsch had taught optically detecting the levels of reaction components with the sensor, and Laustsen had taught that a pre-determined amount can be set to a desired level; i.e., each step and component that would carry out that step was explicitly taught in the prior art, and on combining them there would be no change in the way each component functioned. See MPEP 2143 A and F. Regarding claim 6, the teachings of Wochner, in view of Deutsch, Heartlein, and Laustsen as discussed for claims 1-3, 5, and 7 above would result in impurities (not poly(A) tagged) being separated from the captured RNA molecules. Thus, Wochner in view of Deutsch, Heartlein, and Laustsen make obvious instant claims 1-3 and 5-7. Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Response to Arguments Applicant's arguments filed 24th August, 2026 to obviousness rejection of amended claims under 35 USC § 103 have been fully considered and are persuasive. Indeed, the applied reference of Wochner and others does not teach limitations as amended. However, the 35 USC § 103 rejection of claims in view of Wochner has been replaced with rejection based on Wochner and new secondary references of Deutsch and Laustsen and the previously cited secondary reference of Heartlein is retained in the new rejection for the teaching of affinity tagged mRNA. The new secondary references of Deutsch and Laustsen when combined with the primary reference of Wochner “provide sensor-based control of the interface between affinity-column loading and affinity-column elution” as argued (middle of pg.18 of arguments). Conclusion No claims are 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. Correspondence Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHABANA MEYERING, Ph.D. whose telephone number is (703)756-4603. The examiner can normally be reached M - F: 9am to 5pm EST. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. 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If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /SHABANA S MEYERING/Examiner, Art Unit 1635 /CATHERINE KONOPKA/Primary Examiner, Art Unit 1635