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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 04/21/2026 has been entered.
Response to Arguments
Applicant's arguments filed 04/21/2026 have been fully considered and they are persuasive. Arguments pertaining to any remaining rejections are addressed in this Office Action. The previous §103 rejection has been withdrawn. However, upon further consideration, new rejections not necessitated by amendment have been presented in this Office Action.
Election/Restrictions
Claims 26 and 32-33 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected groups, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 8/13/2024.
However, Applicants have cancelled withdrawn claims.
Thus, the restriction requirement is moot.
Status of the Claims
This action is in response to papers filed 04/21/2026 in which claims 26 and 32-33 were canceled new claims 35-38 added and claims 1, 4, 6, 8, 11, 18, 20, 23, and 29 were amended.
Claims 1-4,6,8,11,13-15,17-18,20,23,25, 29 and 35-38 are under prosecution.
Claim Objections
Claim 1 is objected to because of the following informalities: the use of the term “encoding” in lines 3 and 9 is improper because 1) the term “encoding” is duplicative and 2) it doesn’t make sense that a nucleic acid sequence would “encode” a recognition sequence that is a nucleic acid. Applicants may consider:
(i) A sensor circuit comprising a first … promoter operably linked to a nucleic acid sequence comprising (a) a nucleic acid sequence encoding… and (b) one or more target sequences…, and (ii) a signal circuit comprising a second… promoter operably linked to a nucleic acid sequence comprising (a) a repressor recognition sequence… and (b) a nucleic acid sequence encoding an output molecule.
Appropriate correction is required.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
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 Interpretation:
Repressor: instant application defines repressors as "protein[s] or nucleic acid molecule[s] that [are] capable of inhibiting translation of an RNA, pg. 8, lines 21-22. Therefore, claim 1 is being interpreted as: a sensor circuit that encodes a translational inhibitor and a signal circuit that carries within it a sequence recognizable by that translational inhibitor. The claim further requires that the translational inhibitor be either an endoribonuclease or a ribozyme. Therefore, an RNA sequence may be made but its further translation is prohibited.
Claims 1-4,6,8,11, 17-18,20,23,25, 29 and 35-38 are rejected under 35 U.S.C. 103 as being unpatentable over Matsuura (Matsuura, S., Ono, H., Kawasaki, S. et al. Nat Commun 9, 4847, 2018) in view of Liang and Loque (US 20200332304, pub. 10/22/2020) where claim 1 is evidenced by Registry of Standard Biological Parts (<https://parts.igem.org/Promoters/T7/Constitutive/Overview> accessed 07/02/2026, 1 pg.).
Regarding claim 1, Matsuura teaches all-RNA synthetic gene circuits in mammalian cells that perform Boolean logic operations using microRNA (miRNA)-responsive mRNAs as decision-making controllers (whole paper, specifically for claim 1 see Fig. 1b and legend). The circuit comprises: an (i) Input sensing: miRNA-responsive mRNAs detect specific intracellular miRNAs (a sensor circuit) comprising:(a) a nucleic acid sequence encoding a repressor, the RNA-binding protein (RBP) - L7Ae, that inhibits translation of a constitutively expressed RNA; and(b) one or more target sequences for a first set of one or more miRNAs; and (ii) Output control: wherein the repressors can then regulate output mRNAs, e.g., output represented in Figs. by green “Output”, turning output genes on or off (a signal circuit) comprising a nucleic acid sequence encoding:(a) a repressor recognition sequence, 1x Kt, binding of repressor to this sequence modulates output; and(b) a nucleic acid sequence encoding an output molecule; and wherein reduction or absence of the repressor results in increased expression of the output molecule. See this in Matsuura’s Fig 3 below represented with Examiners annotations. Further, Matsuura teaches a DNA molecule that encodes the above. See Methods section on pg. 6, Preparation of DNA template for in vitro transcription (IVT). The DNA molecule is driven by the T7 promoter.
The T7 promoter is a constitutive promoter, as evidenced by Registry of Standard Biological Parts.
Thus, when the all-RNA circuit and the DNA encoding the same is put together, Matsuura’s circuit reads on instant claim 1, a sensor circuit comprising a first constitutive promoter and a signal circuit comprising a second constitutive promoter, and all categories of components therein except for the repressor being an endoribonuclease or ribozyme.
Regarding claim 2, Matsuura further teach wherein the one or more target sequences for the first set of one or more miRNAs of (i)(b) are downstream from the nucleic acid sequence encoding the repressor (Fig. 3).
Regarding claim 3, Matsuura further teach wherein the repressor recognition sequence of (ii)(a) is upstream from the nucleic acid sequence encoding the repressor (Fig. 3).
Regarding claim 4, Matsuura further teach wherein the nucleic acid sequence encoded by the signal circuit of (ii) further comprises one or more target sequences for a second set of one or more miRNAs and wherein these sequences are downstream from the nucleic acid sequence encoding the output molecule (Fig. 3).
Regarding claim 6, Matsuura further teach various embodiments of their circuits. Matsuura Fig. 3 shows two output modules (signal circuit) comprising EGFP with the repressor sequences 1x Kt and sc2x MS2box (XOR, Fig. 3).
Regarding claim 8, Matsuura further teach wherein the sequestron system comprises a plurality of the sensor circuit (Fig. 3). Thus, a sequestron comprising two sensor circuits, comprising two repressors, wherein the repressors are MS2CP and L7Ae, that cumulatively exert repressing and/or inhibitory effect(s) on a (ii) a (plurality of) signal circuits, described for claim 6.
Regarding claim 11, Matsuura teach that their system can be further expanded by using new RBP-mediated repressors, such as CRISPR-Cas effector Cas13 (pg. 6, first para, L col).
Regarding claim 17, 18, 20, 23, 25, 29, and 37, Matsuura further teach treating a mammalian cell with their RNA circuits (To investigate whether the T21-L7-4xT21 circuit can detect endogenous miRNAs, we transfected it into HeLa cells, which express endogenous miR-21 9,30, pg. 2, 2nd to the last para, R col.). As evidenced by Matsuura diseased cells are characterized by at least one set of miRNAs (miRNA expression profile is related to important biological processes, including development, cancer, pg. 2, 2nd para, L col.).
Regarding claim 35, Matsuura further teach target sequences for the second set of one or more miRNAs are downstream from the nucleic acid sequence encoding the output molecule (Fig. 3).
Regarding claim 35, Matsuura further teach the method comprising:(ii) detecting the output molecule; and(iii) classifying the cell (detection, Fig. 1; and thus can be used to classify the cell state 5,19–21, pg. 2, 2nd para, L col.).
See Fig. 3 of Matsuura with Examiner annotations indicating concordance of instant claim terms with Matsuura’s figure:
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Matsuura does not teach wherein the repressor is an endoribonuclease, or a ribozyme (claim 1) or the CRISPR endoribonuclease is as recited in claim 36.
However, before the effective filing date, Liang and Loque had taught a system for translation control of a sequence of interest making use of the ability of CRISPR endoribonuclease Csy4 to control the mRNA stability and translation of a coding gene (abstract, Fig. 1). Liang and Loque taught, in Fig. 1D, a nucleic acid with p35S promoter driving expression of Csy4 gene and pC4H promoter with a cognition sequence of Csy4 protein with coding sequence of interest (COI) all on a single nucleic acid.
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date to encode the RNA circuitry of Matsuura in DNA to arrive at DNA-based circuitry of instant sequestron. A person of ordinary skill in the art would have been motivated to combine the teachings for the advantage of a DNA-based sequestron’s therapeutic applications in regenerative medicine since therapeutic applications would require more than an RNA-circuit since RNA is short-lived. Permanent expression is preferred for gene editing or cell reprogramming. One of skill would further be motivated to use an endoribonuclease as a repressor as taught by Liang and Loque in place of L7Ae in Matsuura’s RNA circuit creating a sequestron capable of increased control of translational expression of intended targets, because Matsuura specifically say, their system can be expanded with a repressor from the CRISPR system. It would be a simple substitution for one of ordinary skill in the art to replace one RNA binding repressor with another RNA binding repressor i.e., L7Ae in the RNA circuit of Matsuura with the CRISPR endoribonuclease Csy4 taught by Liang and Loque and make such a substitution with reasonable expectation of success because Liang and Loque have tested a system of translational control with the latter endoribonuclease and proved its efficacy. See MPEP 2143 I.(B) and 2144 II.
Thus, Matsuura in view of Liang and Loque make obvious instant claims 1-4,6,8,11, 17-18,20,23,25, 29 and 35-38.
Claims 13 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Matsuura (Matsuura, S., Ono, H., Kawasaki, S. et al. Nat Commun 9, 4847, 2018) in view of Liang and Loque (US 20200332304, pub. 10/22/2020) where claim 1 is evidenced by Registry of Standard Biological Parts (<https://parts.igem.org/Promoters/T7/Constitutive/Overview> accessed 07/02/2026, 1 pg.) as applied to claims 1-4,6,8,11, 17-18,20,23,25, 29 and 35-38 above and further in view of Molina (US 20200199619A1, published 2020-06-25).
Regarding claim 13, the sequestron of claim 1 is taught above. Neither Matsuura nor Liang and Loque teach hEF1 promoter.
However, before the effective filing date of instant invention, Molina had taught hEF1-alpha promoter in a system for transgene expression to improve gene therapy wherein the system comprised two regulatory control elements and two coding sequences, where one coding sequence encodes a repressor of the other (abstract). Molina had taught hEF1-alpha promoter maintained repressor expression and reduced promoter silencing in stem cells (Detailed Description; Example 4; Claim 30).
Regarding claim 15, Molina had taught their system for transgene expression may be comprised in a pharmaceutical composition and delivered to cells [0066].
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date to have substituted the T7 promoter of Matsuura with hEF-1 promoter into the sequestron, to arrive at the limitations in the claimed invention. A person of ordinary skill in the art would be motivated to do so for the advantage of not using a viral promoter so that the construct may be used in therapy and see modest but consistent gene expression. One would have had a reasonable expectation of success in doing so because Molina had tested hEF-1 and demonstrated its efficacy and such a substitution would be within the scope of one of ordinary skill. See MPEP 2143 I. B and 2144 II.
Thus, Matsuura and Liang and Loque in view of Molina make obvious instant claims 13 and 15.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Matsuura (Matsuura, S., Ono, H., Kawasaki, S. et al. Nat Commun 9, 4847, 2018) in view of Liang and Loque (US 20200332304, pub. 10/22/2020) where claim 1 is evidenced by Registry of Standard Biological Parts (<https://parts.igem.org/Promoters/T7/Constitutive/Overview> accessed 07/02/2026, 1 pg.) as applied to claims 1-4,6,8,11, 17-18,20,23,25, 29 and 35-38 above and further in view of Kerr (CA 3127799A1, published 2020-07-30).
The sequestron system of claim 1 is taught above. Matsuura contemplate a plurality of sequestron systems of claim 1 (to perform more complexed logic computation in cells, we need to scale-up the RNA-based circuits by using a set of orthogonal RBPs., pg. 6 second para).
Matsuura’s teachings for:
i. claim 8 discussed wherein (A) the sensor circuit encodes a combination of different repressors (Fig. 3),
ii. claim 6 discussed (B) the signal circuit encodes a combination of different repressor recognition sequences,
iii. claim 1 discussed (C) and (D) each repressor encoded by the sensor circuit specifically recognizes its distinct repressor recognition sequence on the signal circuit of the same sequestron.
Regarding claim 14, Matsuura does not teach a plurality of sequestrons.
However, before the effective filing date of instant invention, Kerr had taught a constructs comprising transgenes and delivery of the same to cells. Kerr’s constructs (ceDNA vector) comprise repressors, the expression of which would inhibit translation of a target mRNA [001176]. Kerr had taught that multiple constructs can be utilized simultaneously, wherein each construct is operatively linked to different promoters and expresses different repressors. Kerr had taught that such a strategy allows for separate regulation and thus an additional level of control of expression. See pertinent recitation from Kerr below:
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It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date to have separated the various embodiments of Matsuura and obvious variations of the same into a plurality of sequestrons, to arrive at the limitations in the claimed invention. A person of ordinary skill in the art would be motivated by looking at various embodiments of Matsuura to make separate each of the combination of different repressors with their cognate recognition sequences in to separate sequestrons because Kerr had taught the advantage in doing so. One would have had a reasonable expectation of success in doing so because Kerr had demonstrated that a plurality of constructs, where in each construct had a distinct repressor could be simultaneously utilized as a means to modulate gene expression and such a separation would be within the scope of one of ordinary skill. See MPEP 2143 I. G and 2144 II.
Thus, Matsuura and Liang and Loque in view of Molina make obvious instant claim 14.
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 4/21/2026 to obviousness rejection of claims under 35 USC § 103 have been fully considered but are not found persuasive. Applicant's arguments begin with a summary of the video interview held on 3/19/2026. Next Applicants argue by:
stating the claims have been amended as discussed in the interview.
discussing the primary reference of Benenson. Applicants state, Benenson’s circuit works by inhibiting transcription of a gene encoding an output molecule and instant application inhibits translation of constitutively expressed transcripts encoding an output molecule (Remarks, pg. 8).
Modifying the circuit of Benenson would change principle operation of Benenson's circuits beyond a simple rearrangement of parts.
Applicants arguments have been fully considered and are persuasive. The presence of a recombinase module in Benenson's circuits indicate a transcription-repression system and indeed requiring a translation inhibition system as in instant application, would require substantial reengineering of Benenson’s circuit.
Thus, Examiner agrees that the rejections raised in the prior Action should be withdrawn. However, a new § 103 rejection, not necessitated by amendment is made in this office action.
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 1-4,6,8,11,13-15,17-18,20,23,25, 29 and 35-38 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of U.S. Patent No. US 11351271 B2 in view of Matsuura (Matsuura, S., Ono, H., Kawasaki, S. et al. Nat Commun 9, 4847, 2018) in view of Liang and Loque (US 20200332304, pub. 10/22/2020) where claim 1 is evidenced by Registry of Standard Biological Parts (<https://parts.igem.org/Promoters/T7/Constitutive/Overview> accessed 07/02/2026, 1 pg.).
Although the claims at issue are not identical, they are not patentably distinct from each other because both the ‘271 application and the instant application claim microRNA sensitive expression of a repressor molecule such that reduction or absence of the repressor results in increased expression of the output molecule. Both the ‘271 patent and the instant application claim two RNA molecules wherein the first RNA molecule comprises the repressor and the second RNA molecule comprises the cognate recognition sequence of the repressor. Further, both the ‘271 patent and the instant application claim a repressor that binds to an RNA molecule. See comparison of independent claims below:
The independent claims have the following patentably indistinct recitations:
Instant claim 1
Reference claim 1
A sequestron comprising:(i) a sensor circuit comprising a first constitutive promoter operably linked to a nucleic acid sequence encoding:
(a) a nucleic acid sequence encoding a repressor, wherein the repressor is an endoribonuclease, an RNAi molecule, or a ribozyme that inhibits translation of a constitutively expressed RNA; and
(b) one or more target sequences for a first set of one or more miRNAs; and
(ii) a signal circuit comprising a second constitutive promoter operably linked to a nucleic acid sequence encoding:(a) a repressor recognition sequence that is capable of being cleaved by the repressor of (i)(a); and(b) a nucleic acid sequence encoding an output molecule; and wherein reduction or absence of the repressor results in increased expression of the output molecule.
A synthetic RNA circuit comprising (a) a first RNA molecule comprising a 5′ cap, at least one target site specific for a first microRNA molecule,
a sequence encoding an RNA binding protein, and a poly(A) tail; and
(b) a second RNA molecule comprising a 5′ cap, at least one target site specific for a second microRNA molecule, at least one RNA motif that is capable of being bound by the RNA binding protein in (a), a sequence encoding an output molecule, and a poly(A) tail, wherein the first microRNA molecule and the second microRNA molecule are different, wherein the first microRNA molecule is a microRNA that is present in a first cell type such that it reduces expression of the first RNA molecule in the first cell type and the second microRNA molecule is a microRNA that is present in a second cell type such that it reduces expression of the second RNA molecule in the second cell type but does not reduce expression of the second RNA molecule in the first cell type or reduces expression of the second RNA molecule less in the first cell type compared to the second cell type, wherein the first cell type and the second cell type are different, wherein the RNA binding protein inhibits production of the output molecule when bound to the at least one RNA motif, and wherein the synthetic RNA circuit is capable of being expressed in a eukaryotic cell.
Reference patent does not claim constitutive promoters or that the repressor is specifically an endoribonuclease or ribozyme that cleaves the second molecule.
However, teachings of Matsuura and Liang and Loque as discussed in the §103 rejection above apply.
It would have been obvious to one with ordinary skill in the art at the time the invention was made to modify ref ‘271 patent’s RNA circuit with the teachings of Matsuura and Liang and Loque to arrive at instant claims for the advantage of effectively using the construct arrived at in gene therapy. It would be a simple substitution to replace the RNA binding protein of the reference claim with an endoribonuclease, as taught by Liang and Loque, because Liang and Loque have experimentally validated the efficacy of Cys4 as an endoribonuclease in a translational repression system. One of ordinary skill in the art would be motivated to express the RNA circuit of the reference claim in a system driven by a constitutive promoter, as taught by Matsuura, for the advantage of obtaining a stable and consistent expression of and RNA repressor that would effectuate a translational repression system and thus effectively be used in gene therapy. An RNA circuit would not be used in gene therapy in view of its short life.
Therefore, the claims of the ‘271 patent and the instant application are deemed to be patentably indistinct in view of Matsuura and Liang and Loque.
Conclusion
No claim is allowed.
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.
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/SHABANA S MEYERING/Examiner, Art Unit 1635
/SHABANA S MEYERING/Examiner, Art Unit 1635
/CATHERINE KONOPKA/Primary Examiner, Art Unit 1635
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