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 .
Claims status
Applicants reply filed 6/6/2025 is acknowledged.
Claims 1-3, 5-6, 8, 11-13, 16-18, 20, 22-23, 26, 30, 32, 34 and 36 is/are currently pending with claims 30, 34, 36 is/are withdrawn. Claims 1-3, 5-6, 8, 11-13, 16-18, 20, 22-23, 26 and 32 is/are under examination.
Withdrawn Objections
The objections presented herein represent the full set of objections currently pending in this application. Any objections not specifically reiterated are hereby withdrawn.
Claim Rejections - 35 USC § 112(b) – Withdrawn
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.
Rejection of claims 2 and 20 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention is withdrawn in light of claim amendments.
Claim Rejections - 35 USC § 112(a) - Withdrawn
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Written Description
Rejection of claims 3, 17 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement is withdrawn due to persuasive arguments presented by the Applicants in the remarks filed 6/6/2025 (pages 12-13, bridging para).
Scope of Enablement
Rejection of Claims 1-3, 5, 6, 8, 11-13, 16, 17, 20, 22, 23, 26, 32 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the scope of enablement requirement is withdrawn in light of amendment to claim 1.
Claim Rejections - 35 USC § 103 – Maintained, updated to address claim amendments
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, 16-18, 20, 22, 23, 26, 32, remain rejected under 35 U.S.C. 103 as being unpatentable over Weiss et al (US 20180296702 A1, Publication date 2018-10-18; cited in IDS dated 1/22/2024; hereinafter Weiss 2018) and Weiss et al (US 20190032054 A1, Publication date 2019-01-31; cited in IDS dated 1/22/2024; hereinafter Weiss 2019) in view of Jerala et al (EP 2 898 074 B1; July 29, 2005; cited in IDS dated 1/22/2024).
Regarding claims 1, 2 and 20, Weiss 2018 teaches RNA-based synthetic circuits with on/off toggle switch functionality based on reciprocal repressive relationship between the two constructs that comprise the circuit (Figure 3A, 8E, 37D, 63A, 63B, 64). In some embodiments, the constructs comprise from 5’ to 3’ a promoter, a RNA motif that binds a first RNA-binding protein, a sequence that encodes a orthogonal second RNA-binding protein and siRNA recognition sites for degradation. See for example, in Figure 3A, the top construct comprises from 5’ to 3’ SGP promoter, L7Ae RNA-binding motif, MS2 RNA-binding proteins sequence and siRNA-FF5 recognition sites for degradation. Herein the toggle-switch circuit of Figure 3A, the bottom construct comprises from 5’ to 3’ SGP promoter, L7Ae RNA-binding proteins sequence, MS2 RNA-binding motif and siRNA-FF5 recognition sites for degradation (note that in this orthogonal construct the MS2 RNA-binding motif is positioned 3’ due the functional nature of MS2 RNA-binding protein). In another circuit taught in Figure 64, the two orthogonal constructs are housed on the same vector wherein both constructs comprise from 5’ to 3’ SGP promoter, Csy4 or L7Ae RNA-binding motif, Csy4 or L7Ae RNA-binding protein and siRNA-FF4 recognition sites for degradation. Weiss 2018 teaches the use of both RNA-binding translation-repressor proteins such as L7Ae and MS2 and their recognition motifs as well as endoribonuclease as Csy4 endoribonucleases and their cleavage sites in their toggle-switch circuits. Each of the toggle-switch circuits of Weiss 2018 are shown to stably express each state as is evident from the data shown in associated truth tables (see for example the truth table for Figure 63B that shows mVenus expression in state 1 with OHT with no mKate expression and vice versa in state 2 without OHT). Taken together, Weiss teaches engineered bi-stable toggle switch circuits comprising two constructs in reciprocal repressive relationship due to the presence of orthogonal RNA-binding proteins in each construct and their respective RNA motifs present on the other construct.
Weiss 2018 does not teach circuits wherein the RNA-binding proteins in both constructs are endoribonucleases. Furthermore, Weiss 2018 does not teach circuits wherein the constructs comprise a second RNA-binding motif recognized by the RNA-binding protein encoded by the same construct; specifically wherein the second RNA-binding motif is a second RNA-cleavage site recognized by the RNA-binding cleavage protein encoded by the same construct and wherein a transcript stabilization sequence, such as optionally recited MALAT1, a triplex RNA stabilization sequence, is directly downstream of the RNA-binding cleavage proteins but before the degradation motifs (as recited in claims 2 and 20).
Regarding toggle-switch circuits wherein the RNA-binding proteins in both constructs are endoribonuclease: Weiss 2018 teaches that toggle-switch circuits could be generated by using two constructs that are in a reciprocal repressive relationship. Weiss 2018 teaches several designs for such circuits using different RNA-binding proteins (both repressors and endoribonucleases) and their associated recognition motifs. Specifically, Weiss 2018 teaches that such circuits could comprise at least one endoribonuclease such as Csy4 and their RNA cleavage site (Figure 63, 64). Although Weiss 2018 does not teach circuits wherein both constructs comprised endoribonuclease, an ordinary artisan recognizes the modularity of Weiss 2018 toggle-switch circuit and would substitute one or both the RNA-binding repressor protein(s) (for example in circuit of Figure 3 or 64) with one or both endoribonuclease which would result in a circuit functionally identical to the claimed circuit. To this end, several endoribonucleases from the Cas endoribonuclease family were known in the art. Weiss 2019 teaches Cse3, Cas6, CasE and Csy4 as endoribonucleases and also teach their respective recognition sites (Table 1).
Regarding toggle-switch circuits wherein the constructs comprise a second RNA-cleavage site upstream of the RNA degradation motifs wherein the second RNA-cleavage site is recognized by the endoribonuclease encoded by the same construct: This configuration allows for the construct to remove the degradation signal from its own RNA transcript allowing for its translation and thus further activation. Although Weiss 2018 teaches circuits wherein the constructs repress each other’s activity/expression, Weiss 2018 does not teach circuit wherein each construct is further capable of activating/enhancing self-activity itself. However utility of toggle-switch circuits comprising both constructs that reciprocally repress and enhance their own activity was taught by Jerala. The toggle-switch circuits taught by Jerala comprise constructs wherein in each construct comprises a repressor and an activator (Figure 1). Jerala teaches that this additional self-activator functionality enhances the stability of the switch when compared to circuits that only comprise repressors and also increases the expression of the output molecule associated with the selected state i.e. improved signal to noise ([0011]). Although Jerala exemplifies their circuit using DNA-based components, Weiss 2019 teaches RNA-based constructs that allow for the construct to remove the degradation signal from its own RNA transcript allowing for its translation and thus further activation. Weiss 2019 teaches constructs wherein a RNA cleavage site is placed between an output molecule and degradation signals and that the output molecule can be a RNA-binding cleavage proteins (such as Cas endoribonucleases) (Figure 1A, B; [0013], Table 1). As required for claims 2 and 20, Weiss 2019 additionally teaches inclusion of MALAT1, a triplex RNA stabilization sequence directly downstream of the RNA-binding cleavage proteins but before the degradation motifs (Figure 1A, B, [0013-0013]).
The combination of prior art cited above under 35 U.S.C. 103 satisfies the factual inquiries as set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966). Once this has been accomplished the holdings in KSR can be applied (KSR International Co. v. Teleflex Inc. (KSR), 550 U.S., 82 USPQ2d 1385 (2007). MPEP 2143 (I) provides exemplary rationales. In the present situation, rationale A is applicable. MPEP 2143 guides that for rationale A “Office personnel must articulate the following: (1) a finding that the prior art included each element claimed, although not necessarily in a single prior art reference, with the only difference between the claimed invention and the prior art being the lack of actual combination of the elements in a single prior art reference; (2) a finding that one of ordinary skill in the art could have combined the elements as claimed by known methods, and that in combination, each element merely performs the same function as it does separately; (3) a finding that one of ordinary skill in the art would have recognized that the results of the combination were predictable; and (4) whatever additional findings based on the Graham factual inquiries may be necessary, in view of the facts of the case under consideration, to explain a conclusion of obviousness.”
(1) The prior art of Weiss 2018 teaches bi-stable toggle switch circuits comprising two constructs wherein at least one construct comprises a promoter, a RNA cleavage site, a RNA-binding protein and RNA degradation motifs. The prior art of Weiss 2019 teaches several endoribonucleases and their associated cleavage sites. The prior art of Weiss 2019 also teaches constructs comprising a RNA cleavage site placed after the RNA-binding cleavage protein and before RNA degradation motifs. (2) An ordinary artisan would combine the elements of Weiss 2018 and Weiss 2019 which would predictably result in a bi-stable toggle switch circuit comprising two endoribonucleases and their associated RNA cleavage sites such that each endoribonuclease would continue function as expected i.e. recognize its respective cleavage site. For reciprocal repression purposes, an ordinary artisan would place RNA cleavage site of one of the endoribonucleases in the reciprocal construct 5’ of sequence encoding the orthogonal (i.e. other) RNA-binding cleavage proteins. Use of endoribonuclease was taught by Weiss 2018 and Weiss 2019. Herein again, an ordinary artisan would predict endoribonucleases to would continue function as expected i.e. recognize its respective cleavage site and repress the expression of the other construct. For self-activation purposes, an ordinary artisan would place RNA cleavage site of one of the endoribonuclease 3’ of sequence encoding the same RNA-binding cleavage proteins but 5’ of the attached RNA degradation motif, as taught by Weiss 2019. Herein again, an ordinary artisan would predict the endoribonuclease to would continue function as expected i.e. recognize its respective cleavage site and remove the RNA degradation motif. (3) As established above, an ordinary artisan would recognize that the combination of the elements of Weiss 2018 and Weiss 2019 would yield predictable results since each of the elements is expected to perform its respective function and these elements are highly modular with their use exemplified by both Weiss 2018 and 2019.
Therefore, the teachings of the cited prior art in the obviousness rejection above provide the requisite teachings with a clear, reasonable expectation. The cited prior art meets the criteria set forth in both Graham and KSR. Therefore, it would be obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the elements of Weiss 2018 and Weiss 2019 to yield a predictable result of a toggle-switch circuit comprising two constructs that reciprocally repress each other and additionally self-activate. Furthermore, an ordinary artisan would be motivated to combine the teachings of Weiss 2018 and Weiss 2019 to further expand the toolkit for genetic circuits to include the various endoribonucleases and their respective recognition sites. Due to teachings of Jerala, an ordinary artisan would also recognize that combination of the circuit elements taught by Weiss 2018 and Weiss 2019 would result in an improved toggle-switch circuit since it would not comprise a reciprocal repressor component but also a self-activator component.
Regarding claim 3, Weiss 2018 teaches several genetic circuits in which the RNA cleavers/inhibitors are operably joined with an output molecule on the same expression cassette (Figure 5A, 37F, 37G, 63B). Weiss 2018’s embodiments do not teach a spacer such as IRES or 2A between the output molecule and the RNA cleavers/inhibitors since their embodiments are RNA replicons and thus use SGP promoters as amplification initiation sites. Its noteworthy that the instant specification do not include any examples in which the output molecule and the RNA effectors are separated by a spacer. Regardless, use of IRES and 2A spacer sequences for allowing expression of multiple non-fused proteins from the same nucleotide sequence is well known in the art. To this end, Weiss 2018 also suggests use of spacers, such as the optionally recited IRES, when polycistronic expression is desired [0020].
Regarding claim 16, Weiss 2018 teaches use of several promoters. They primarily rely on different sub-genomic promoters for their RNA replicons which are constitutively active resulting in a self-replicating RNA sequence. In some embodiments, they also use pCMV promoter to drive expression (Figure 11, 13).
Regarding claim 17, Weiss 2018 teaches embodiments in which output molecules are proteins that include therapeutic and detectable proteins [0010].
Regarding claim 18, Weiss 2018 teaches use of Cys4 in their genetic circuit. Weiss 2019 discloses use several Cas endoribonucleases (Table 1, [0006]).
Regarding claim 22, Weiss 2018 teaches siRNA and miRNA target sequences as degradation motifs (Figure 1A, 3A, 8E, 37D). Weiss 2019 discloses the 8-nt sequence that is capable of recruiting deadenylating complexes to result in RNA degradation [0037].
Regarding claim 23, Weiss 2018 teaches an RNA replicon as a vector in most of its examples however also notes that the RNA molecules may be encoded on one or more plasmids [0017]. Weiss 2019 discloses using plasmids and viral vectors as a vector for their genetic circuits [0096].
Regarding claims 26, Weiss 2018 teaches delivering their genetic circuits to cells (Figure 11, 12, 13, 15) and animals (mice) (Figure 44, 45, 46) in several examples. Thus, Weiss 2018 teaches cells that comprise their genetic circuit. An ordinary artisan would use such routine methods as used by Weiss 2018 to deliver expression cassettes to various cells and thus generate the optionally claimed cell types.
Regarding claim 32, Weiss 2018 teaches compositions comprising the toggle switch circuit and lipid nanoparticles, a pharmaceutically acceptable carrier ([0339], [0486],[0488]). Weiss 2019 also teaches using pharmaceutically acceptable carriers to deliver genetic circuits [0107] and lists them in [0108].
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the effective time of filing of the invention, especially in the absence of evidence to the contrary.
Claims 5, 6, 8 remain rejected under 35 U.S.C. 103 as being unpatentable over Weiss et al (US 20180296702 A1, Publication date 2018-10-18; cited in IDS dated 1/22/2024; hereinafter Weiss 2018) and Weiss et al (US 20190032054 A1, Publication date 2019-01-31; cited in IDS dated 1/22/2024; hereinafter Weiss 2019) in view of Jerala et al (EP 2 898 074 B1; July 29, 2005; cited in IDS dated 1/22/2024) as applied to claim 1 above, and further in view of Cervera et al (Extended Gene Expression by Medium Exchange and Repeated Transient Transfection for Recombinant Protein Production Enhancement. Biotechnology and Bioengineering, Volume 112, May 2015; cited in IDS dated 1/22/2024).
Regarding claims 5, 6 and 8, Weiss 2018 teaches several cascade design circuits in which additional expression constructs (such as the third and fourth expression cassettes of instant claim 5) comprise elements that alter the structure/function of the elements within the base constructs of the circuit (such as the first and second expression cassettes of instant claim 1) (Figure 2A, 2C, 8A, 18A). They also teach several designs showing the use of small-molecule controlled degradation domains connected directly to the N-terminus of the RNA cleavage/inhibitor within these circuits (Figure 5A, 37G, 38A-C, 46A, 61A, 63B; as required by claims 6 and 8). Specifically, the embodiment described in [0049] may further include “a sequence encoding Csy4 protein and a Csy4 recognition site” and “the Csy4 protein is a fusion of a destabilization domain and Csy4” wherein “the destabilization domain is regulated by trimethoprim (TMP) or 4-hydroxytamoxifin (4-OHT)” [0058]. The promoter for this embodiment is a SGP promoter. In the gene circuit shown in Figure 63B, Weiss 2018 demonstrates the use of two different small-molecule controlled destabilization/degradation domains connected to the N-terminus of the RNA binding proteins (repressor or cleavage) to achieve small-molecule controlled switch within a genetic circuit. Therefore, Weiss 2018 discloses each of the elements of claims 5 (additional cassettes and different small molecule controlled degradation domains), 6 (direct fusion) and 8 (N-terminus fusion) and, demonstrate the use of these elements in various circuit designs.
Weiss 2018 does not teach a specific circuit design with two additional constructs that encode the same RNA binding proteins (repressor or cleavage) as the base constructs. Cervera teaches a method of multiple transfection in which the same plasmid was repeatedly transfected to achieve prolonged expression of the plasmid with a 4-12 fold increase in the expression of the plasmid (abstract, last line) thus indicating that transfection with the same plasmids/additional elements allow for the prolonged overexpression of those plasmids/additional elements. Therefore, it will be obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to include additional constructs that encode the same RNA binding proteins (repressor or cleavage) as the base constructs of Weiss 2018 and Weiss 2019 to result in their overexpression as taught by Cervera. An ordinary artisan would be motivated to include additional constructs that encode the same RNA binding proteins (repressor or cleavage) as the base constructs of Weiss 2018 and Weiss 2019 because it would be expected to prolong and increased the expression of the RNA binding proteins (repressor or cleavage).
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the effective time of filing of the invention, especially in the absence of evidence to the contrary.
Claim 11 remains rejected under 35 U.S.C. 103 as being unpatentable over Weiss et al (US 20180296702 A1, Publication date 2018-10-18; cited in IDS dated 1/22/2024; hereinafter Weiss 2018) and Weiss et al (US 20190032054 A1, Publication date 2019-01-31; cited in IDS dated 1/22/2024; hereinafter Weiss 2019) in view of Jerala et al (EP 2 898 074 B1; July 29, 2005; cited in IDS dated 1/22/2024) as applied to claim 1 above, and further in view of Kundert et al (Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nature Communications, Volume 10, May 2019; cited in IDS dated 1/22/2024).
Regarding claim 11, Weiss 2018 and Weiss 2019 do not teach a RNA cleavage site comprising a small-molecule controlled aptamer sequence. Kundert discloses sgRNA (endonuclease RNA cleavage site) designed with aptamer sequences inserted within the sgRNA sequence so as it either allows or inhibits sgRNA binding with Cas endonucleases (Figure 1A). They disclose such aptamer including sgRNAs that can respond to different small molecules such as theophylline (Figure 2, 3a) or trimethoprim (Figure 3c). It is important to note that similar to the small-molecule controlled degradation domains of claim 5 (taught by Weiss 2018), the RNA cleavage sites comprising small-molecule controlled aptamer sequences recited in claim 11 perform the same function of a switch between the two RNA binding proteins. Degradation domains, ribozymes, aptazymes, small-molecule responsive aptamers are alternate elements that perform the same function within the toggle-switch circuit of the instant claims and could be substituted for each other. Therefore, it will be obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to substitute the degradation domains of Weiss 2018 with endonuclease RNA cleavage site comprising an aptamer from Kundert to yield the predictable result of a switchable genetic circuit. An ordinary artisan would be motivated to generate circuits comprising endonuclease RNA cleavage site comprising an aptamer from Kundert to further expand the toolkit for genetic circuits to include additional means of regulatory control using small-molecules. An ordinary artisan would reasonably expect endonuclease RNA cleavage site comprising an aptamer from Kundert would function as taught by Kundert in Weiss 2018 and Weiss2019’s circuit because Kundert teaches their use in constructs blocks interaction between the cleavage site and endonuclease in the presence of small molecules.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in
the art at the effective time of filing of the invention, especially in the absence of evidence to the
contrary.
Claims 12 and 13 remain rejected under 35 U.S.C. 103 as being unpatentable over Weiss et al (US 20180296702 A1, Publication date 2018-10-18; cited in IDS dated 1/22/2024; hereinafter Weiss 2018) and Weiss et al (US 20190032054 A1, Publication date 2019-01-31; cited in IDS dated 1/22/2024; hereinafter Weiss 2019) in view of Jerala et al (EP 2 898 074 B1; July 29, 2005; cited in IDS dated 1/22/2024) as applied to claim 1 above, and further in view of Win et al (A modular and extensible RNA-based gene-regulatory platform for engineering cellular function, PNAS, Volume 104, September 2007; cited in IDS dated 1/22/2024).
Regarding claims 12 and 13, Weiss 2018 and Weiss 2019 do not teach the use of self-cleavage sites such as ribozymes or small-molecule controlled ribozymes (i.e. aptazymes) in their genetic circuit. Win teaches aptazymes that can respond to different small molecules (Figure 5) and provide a basic example demonstrating their function in a gene circuit (Figure 6). It is important to note that similar to the small-molecule controlled degradation domains of claim 5 (taught by Weiss 2018), these elements of claim 12 and 13 (ribozymes or aptazymes) perform the same function of a switch between the two RNA effectors. Degradation domains, ribozymes, aptazymes, small-molecule responsive aptamers are alternate elements that perform the same function within the toggle-switch circuit of the instant claims and can easily be substituted for each other. Therefore, it will be obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to substitute the degradation domains of Weiss 2018 with aptazymes from Win to yield the predictable result of a switchable genetic circuit. An ordinary artisan would be motivated to generate circuits comprising aptazymes from Win to further expand the toolkit for genetic circuits to include additional means of regulatory control using small-molecules. An ordinary artisan would reasonably expect aptazymes from Win would function as taught by Win in Weiss 2018 and Weiss2019’s circuit because Win teaches their use in constructs to cleave RNA motifs in the presence of small molecules.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in
the art at the effective time of filing of the invention, especially in the absence of evidence to the
contrary.
Response to Arguments
Applicant's arguments filed 6/6/2025 regarding the U.S.C. 103 rejection of claims 1-3, 16-18, 20, 22, 23, 26 and 32 as being unpatentable over Weiss 2018 and Weiss 2019 in view of Jerala have been fully considered but they are not persuasive.
Applicant argue that “one of ordinary skill in the art would not be motivated to modify the constructs of Weiss 2018 according to Weiss 2019 or Jerala, as suggested by the Examiner, because doing so would render the constructs of Weiss 2018 inoperable for their intended purpose” (emphasis added; page 15, para 2). Applicant allege that the intended purpose “according to Weiss 2018, is to sense miRNA to regulate expression of output molecules in different cellular environments that express (or do not express) different miRNAs” (emphasis added; page 15, para 2). Applicant describe the functioning of the circuit shown in Figure 3A of Weiss 2018 (page 15, para 3) and they allege that it “operates to sense the presence of miRNA” (page 15, para 4). Furthermore, Applicant argue that since the circuits taught by Weiss 2018, such as in Figure 3A, do not comprise elements that activate or enhance self-activity (as was noted in OA), “altering the constructs of FIG. 3A of Weiss 2018 to do so would render them inoperable for the detecting of miRNA and consequent regulation of output molecule expression” (page 16, para 1). Taken together, Applicant allege that “one of ordinary skill in the art would recognize that the generic circuit of Weiss 2018's FIG. 3A operates to increase sensitivity of output molecule expression to low levels of miRNA” and that replacements of elements of the circuit in Figure 3A “would render this construct inoperable for detecting any extrinsic molecule, as both constructs would become subject to degradation by non-miRNA factors even in the absence of siRNA” (page 16, para 2).
In response, Applicant did not provide any evidence for the allegation regarding Weiss 2018’s intended purpose. Weiss 2018 does not state or suggest that the purpose of their constructs, including the constructs illustrated in Figure 3A, is merely to sense intracellular miRNAs. Weiss 2018 is broadly interested in solving the problem of synthetic circuits being primarily DNA-centered [0004-0005] while they intended to provide RNA-based circuits that could be regulated at the translational level [0003]. They note that devices based on RNA-binding proteins can be easily wired together to create constructs of various complexities (emphasis added; [0007]). In the introduction to Example 1, that figure 3A is part of, Weiss 2018 state “Towards the goal of creating a platform for future applications through a plug-and-play post-transcriptional regulation framework we engineered a set of diverse regulatory circuits including a multi-input cell type classifier, a cascade and a two-state switch. Additional capabilities, or further tuning of the synthetic regulatory pathways can be achieved with the use of small molecule dependent aptamers or degradation domains” (emphasis added; [215]). In describing Figure 3A, Weiss 2018 state “The state of the system can be set with the use of a synthetic siRNA, synthetic or endogenous miRNA, or other endogenous repressors” [219]. Furthermore, the modularity of RNA circuits taught by Weiss 2018 allow for more than one ‘toggle’ type. Weiss 2018 teaches siRNAs, both endogenous and exogenously delivered, as well as other ‘toggles’ such as small molecules that modulate degradation domains or aptamers or aptazymes ([220-223], see at least Figure 5, 6, 38). Thus, Weiss 2018 does not intend to limit their modular RNA circuits comprising various RNA regulatory elements to be limited in use for only sensing “cellular environments that express (or do not express) different miRNAs”.
Applicant does not provide evidence that modification of constructs of Figure 3A to substitute RBPs and their target sites with endonucleases with their cleavage sites would render the construct inoperable for the detecting of miRNA. Indeed, in circuit shown in Figure 3A, they use siRNAs to ‘toggle’ the switch between the two constructs i.e. use the presence of siRNA to ‘turn on’ a construct which orthogonally turns off the other construct. This does not imply that the circuits are limited to siRNA-based toggle i.e. intend to only detect miRNA/siRNA; especially considering teachings in Weiss 2018 regarding other toggles ([220-223], see at least Figure 5, 6, 38). Critically, this does not imply that an siRNA-based toggle could not be used in combination with a circuit wherein the RBPs are replaced with endonucleases. In fact, instant claim 22 limits the RNA degradation motif in the claimed circuit to miRNA target site. This is the configuration that would result from combination of Weiss 2018 and Weiss 2019 in view of Jerala wherein Weiss 2018’s RBP are substituted with endonucleases, as taught by Weiss 2018 and Weiss 2019, and cleavage sites are placed such that they can support orthogonal repression and self-enhancement, as taught by Weiss 2019 in view of Jerala. Thus, allegations that the circuit of Figure 3A could not modified in the way noted in OA are unfounded.
Applicant argue similarly regarding the circuits of Figure 63 and 64 in Weiss 2018. Applicant allege that the circuit of Figure 64 is “described as functioning as a “microRNA (miRNA) high sensor” (page 16, last para) and in this construct, “the RNA cleavage effector acts to stabilize the first construct against miR-FF4-mediated degradation of the second construct, but that this cleavage does not repress the second construct; indeed, to provide an accurate read out of miRNA abundance, the second construct must by degraded solely by the miRNA. Thus, one of ordinary skill in the art would understand that in no circumstances does Csy4 act as a repressor of the second construct of Weiss 2018's FIG. 64, and, that altering the construct to do so would eliminate its intended function as a sensor of an miRNA for regulating expression of output molecules.” (page 17, para 2).
In response, indeed, Csy4 in Figure 64 is used to split the replicon while the RBP in the second half of the replicon (L7Ae) acts as an orthogonal repressor. However, the relevance of this fact as pertinent to the instant rejection is unclear. The teachings from Figure 64 show that Weiss 2018 teaches the use of endoribonucleases and their cleavage sites. Weiss 2018 provides detailed description for elements such as RBPs, degradation domains, endoribonucleases; their functioning and some means to use them in RNA circuits [378-381]. Thus, Weiss 2018 provides requisite teaching to an artisan regarding endoribonucleases and their functioning as a nucleic acid cleavage effector. Applicant did not provide any evidence that circuit of Figure 64 which functions as a miRNA high sensor would be inoperable because it would be unable to detect the miRNA if the RBP is substituted by an endoribonuclease. The construct would continue to ‘sense’ miRNA via the miRNA-recognition sites. Furthermore, due to the teachings in Weiss 2018 regarding other toggles, an artisan recognizes that a construct in Weiss 2018 is not limited to only using siRNAs as toggles ([220-223], see at least Figure 5, 6, 38). The teachings of Weiss 2018 and Weiss 2019 provide several RNA-based elements, their function and various configurations to exemplify the use of such elements. An artisan recognizes the ‘plug-and-play’ nature of these elements.
Applicant's arguments filed 6/6/2025 regarding the U.S.C. 103 rejection of claims 5, 6, 8, 36 as being unpatentable over Weiss 2018 and Weiss 2019 in view of Jerala; further in view of Cervera have been fully considered but they are not persuasive
Applicant argue that “The deficiencies of Weiss 2018, Weiss 2019, and Jerala have been described hereinabove; Cervera does not remedy these deficiencies” (page 18, para 2). In response, arguments pertaining to alleged deficiencies of Weiss 2018, Weiss 2019, and Jerala were unpersuasive.
Applicant's arguments filed 6/6/2025 regarding the U.S.C. 103 rejection of claim 11 as being unpatentable over Weiss 2018 and Weiss 2019 in view of Jerala; further in view of Kundert have been fully considered but they are not persuasive.
Applicant argue that “The deficiencies of Weiss 2018, Weiss 2019, and Jerala have been described hereinabove; Kundert does not remedy these deficiencies” (page 18, para 5). In response, arguments pertaining to alleged deficiencies of Weiss 2018, Weiss 2019, and Jerala were unpersuasive.
Applicant's arguments filed 6/6/2025 regarding the U.S.C. 103 rejection of claims 12 and 13 as being unpatentable over Weiss 2018 and Weiss 2019 in view of Jerala; further in view of Win have been fully considered but they are not persuasive.
Applicant argue that “The deficiencies of Weiss 2018, Weiss 2019, and Jerala have been described hereinabove; Win does not remedy these deficiencies” (page 19, para 3). In response, arguments pertaining to alleged deficiencies of Weiss 2018, Weiss 2019, and Jerala were unpersuasive.
Conclusion
No claim is allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MATASHA DHAR whose telephone number is (571)272-1680. The examiner can normally be reached M-F 8am-4pm (EST).
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/MATASHA DHAR/Examiner, Art Unit 1632
/EMILY A CORDAS/Primary Examiner, Art Unit 1632