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 .
Election/Restrictions
Applicant’s election with traverse of Group I in the reply filed April 15, 2026 is acknowledged.
In the traversal, Applicant argued that the restriction requirement never explained why the claimed inventions were said to be anticipated. Applicant argued that the Examiner did not present a prima facie case for anticipation, because the Examiner did not show how all the limitations of any claim are taught by Shin, but only asserted that Shin discloses a cell-free protein synthesis system using E. coli sigma factors. The Applicant argued that observance of similarities does not establish anticipation, and that the Office has a burden to show that each limitation for at least one Claim is taught by a single reference. The Applicant argued that the Office failed to demonstrate that the claimed inventions lack a special technical feature and that Restriction is not justified.
These arguments have been considered, but are found unpersuasive. The Examiner is not required to provide evidence of anticipation of all limitations of at least one claim by a single reference in a Requirement for Restriction for an application subject to Unity of Invention.
MPEP 1893.03(d) states: “When making a lack of unity requirement, the examiner must (1) list the different groups of claims and (2) explain why each group lacks unity with each other group (i.e., why there is no single general inventive concept) specifically describing the unique special technical feature in each group…A group of inventions is considered linked to form a single general inventive concept where there is a technical relationship among the inventions that involves at least one common or corresponding special technical feature. The expression special technical features is defined as meaning those technical features that define the contribution which each claimed invention, considered as a whole, makes over the prior art.” Additionally, MPEP 1850(II) states: “Unity of invention has to be considered in the first place only in relation to the independent claims in an international application and not the dependent claims.
In the Requirement for Restriction mailed April 15, 2026, the Examiner stated the shared technical feature between independent claims 1 and 10 (i.e. “a cell-free protein expression/synthesis system”). The Examiner demonstrated that the shared technical feature was not a special technical feature by providing a reference (i.e. ‘Shin & Noireaux…’; Abstract) which disclosed the shared technical feature before the effective filing date of the instant invention.
The Examiner has met the requirements for Requirement for Restriction in an application subject to Unity of Invention. Because the Applicant has not provided any specific arguments against the disclosure of the shared technical feature by the reference cited, the requirement is still deemed proper and is therefore made FINAL.
Status of the Claims
Claims 1-11 are currently pending.
Claim(s) 10 and 11 is/are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected subject matter, there being no allowable generic or linking claim. Election was made with traverse in the reply filed April 15, 2026.
Claims 1-9 are currently under examination.
Priority
It is acknowledged that the instant application is a 371 of international PCT Application NO. PCT/US2023/079456, filed November 13, 2023, and that it claims benefit of provisional 63/425,509, filed November 15, 2022. The effective filing date of the claims under examination is considered to be November 15, 2022.
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 3, 6, 8 and 9 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.
Claim 3 is rejected for the recitation of “sufficiently sensitive to distinguish” as being indefinite. It is not clear how the language of the claim is meant to affect the structure of the method; for example, is it required that the method actively only detect target micro RNA which is perfectly complementary to the mRNA of the expression system, or is it merely required that the methodology is capable of detecting a difference between a target micro RNA and an off-target micro RNA that differs at only one nucleotide? As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claim 6 is rejected for the recitation of “the core component of T7 RNA polymerase” as lacking antecedent basis. Although the art recognizes core T7 RNA polymerase, there are potentially several molecules which could be considered the ‘core,’ and therefore it is unclear what is required by the claim. For example, Segall-Shapiro (Segall-Shapiro et al. Mol Syst Biol. 2014 Jul 30;10(7):742) describes two core fragments (‘either core or ß core fragments’) on pg. 11, col. 2, last par. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claims 8 and 9 are rejected for the recitation of “the target RNA sequence” in step (c) of claim 8, as lacking antecedent basis. The preamble of claim 8 recites “detecting the presence or absence of a specified RNA sequence,” step (a) recites “loading RNA into Argonaute protein molecules,” and step (b) recites “any RNA bound to the RISCs.” It is not clear if or which of these recitations provides antecedent basis for “the target RNA sequence” and therefore unclear what is being detected in step (c). As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claim 9 is rejected for the recitation of “the target micro RNA” in step (a), line 5 as lacking antecedent basis. Claims 8 and 9 (before the recitation in question) provide for “the target RNA sequence” but do not explicitly discuss “a target micro RNA.” It is therefore unclear whether the target micro RNA is the same as the target RNA or if it represents a different molecule. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1 and 8 are rejected under 35 U.S.C. 103 as unpatentable over Weiss et al (effectively filed Mar 22, 2021; Patent Application Publication No. US 2022/0298509) in view of Flores-Jasso et al (published Feb 2013; Flores-Jasso et al. RNA. 2013 Feb;19(2):271-9.) and Lin et al. (published July 2021; Lin et al. Biochemical Engineering Journal, Volume 171, 2021, 108031).
Regarding claims 1 and 8, Weiss teaches a method for detecting the presence or absence of a specified target micro RNA sequence in a sample (par. 4). Weiss teaches that the method comprises the step of detecting a signal from an expression system that indicates the presence of the target micro RNA sequence in the sample, or observing the absence of such a signal as indicating the absence of the target micro RNA sequence from the sample (par. 4).
Regarding claim 1, Weiss does not teach supplying RNA-induced silencing complexes (RISCs) from the sample, under conditions that preserve the binding of any micro RNA to the RISCs; nor mixing the RISCs, along with any micro RNA that is bound to the RISCs, with an expression system for detection.
Regarding claim 8, Weiss does not teach loading RNA from the sample into Argonaute protein molecules to generate synthetic RNA-induced silencing complexes (RISCs); nor adding the synthetic RISCs, along with any RNA bound to the RISCs, to an expression system.
Regarding claim 1, Flores-Jasso teaches supplying RNA-induced silencing complexes (RISCs) from a sample, under conditions that preserve the binding of any micro RNA to the RISCs, and mixing them with an expression system for detection (pg. 275: “Purification of endogenously loaded miRNAs”).
Regarding claim 8, Flores-Jasso teaches loading RNA from the sample into Argonaute protein molecules to generate synthetic RNA-induced silencing complexes (RISCs) and adding the synthetic RISCs, along with any RNA bound to the RISCs, to an expression system (pg. 273, col. 2).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Weiss and Flores-Jasso, in order to purify freely diffusing RISC complexes for quantitative analysis of target-binding by RISC (pg. 275, col 2, Discussion). One would have reasonable expectation of success because Flores-Jasso demonstrates that active miRNA:RISC complexes may be recovered from samples (pg. 275, col. 2, 1st par.) and that RNA may be loaded into Argonaute protein molecules to create RISC complexes (pg. 273, col. 2).
Regarding claims 1 and 8, Weiss does not teach mixing the target with a cell-free protein expression system; and detecting a signal from the cell-free protein expression system.
Lin teaches mixing a target with a cell-free protein expression system; and detecting a signal from the cell-free protein expression system (Abstract; Fig. 5).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Weiss and Flores-Jasso with the teachings of Lin, in order to rationally control modular genetic circuits (pg. 4, col. 1, 1st par.). One would have had reasonable expectation of success because Lin and Weiss are both concerned with the construction of genetic circuits, and Lin demonstrates that these may be operated in cell-free systems (pg. 4: “Cell extract preparation” and “Cell-free reactions”).
Claims 2-5 and 9 are rejected under 35 U.S.C. 103 as unpatentable over Weiss et al (effectively filed Mar 22, 2021; Patent Application Publication No. US 2022/0298509) in view of Flores-Jasso et al (published Feb 2013; Flores-Jasso et al. RNA. 2013 Feb;19(2):271-9.) and Lin et al. (published July 2021; Lin et al. Biochemical Engineering Journal, Volume 171, 2021, 108031), applied to claims 1 and 8 above, and further in view of Rhodius et al. (published Oct 29, 2013; Rhodius et al. Mol Syst Biol. 2013 Oct 29;9:702. doi: 10.1038/msb.2013.58).
Weiss, Flores-Jasso, and Lin teach the limitations of claims 1 and 8, as discussed in the rejection under 35 U.S.C. 103 above.
Regarding claims 2 and 9, Weiss teaches an expression system comprises a DNA sequence that encodes an mRNA sequence complementary to the target micro RNA sequence, wherein said DNA sequence is operatively linked to a sequence encoding a repressor (par. 51-56), wherein expression of the repressor is disrupted by binding of the target micro RNA to the complementary mRNA sequence when the target micro RNA sequence is present in the sample (par. 79), and wherein the repressor sequence is expressed without disruption when the target micro RNA sequence is absent from the sample (par. 79). Weiss teaches that a reporter molecule is expressed at detectable levels when the level of repressor in the expression system is thereby down-regulated by the presence of the target micro RNA sequence; and the reporter molecule is not expressed at detectable levels when transcription of the repressor remains undisturbed in the absence of the target micro RNA sequence (par. 79).
Regarding claim 4, Lin teaches sigma proteins which are non-native to the cell-free protein expression system (pg. 1, col. 2).
Regarding claim 5, Lin teaches a step of amplifying the expression of a reporter molecule in response to the presence of a non-native sigma protein (pg. 4, col. 1, 2nd par).
It would have been obvious to a person with ordinary skill in the art before the effective filing date to use the non-native sigma + reporter construct of Lin in order to avoid cell extract endogenous interference of reporter transcription (pg. 1, col. 2). One would have had reasonable expectation of success because Lin demonstrates that native and non-native sigma factors may be used orthogonally (Fig. 3B).
Regarding claims 2, 4, and 9, Weiss, Flores-Jasso, and Lin do not teach anti-sigma proteins/sequences, wherein the anti-sigma protein is complementary to the non-native sigma protein; and wherein expression of the reporter molecule is dependent on the presence of non-native sigma protein that is unbound to complementary anti-sigma protein. Regarding claim 5, they do not explicitly teach a step of amplifying in response to the presence of non-native sigma protein which is unbound by an anti-sigma protein. However, Weiss teaches other repressors which control expression of a reporter molecule (Weiss: par. 62, 65).
Regarding claims 2 and 9, Rhodius teaches anti-sigma proteins/sequences as elements of synthetic genetic systems (pg. 1, col. 2).
Regarding claims 4 and 5, Rhodius teaches anti-sigma proteins are complementary to sigma proteins; and teaches expression of a reporter molecule which is dependent on the presence of sigma protein that is unbound to complementary anti-sigma protein (Figure 1A; Figure 5A).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to substitute the repressors of Weiss with the anti-sigma factors of Rhodius, because anti-sigma proteins and the repressors of Weiss are known for the same purpose (i.e. repression of detectable output). One would have had reasonable expectation of success because Rhodius demonstrates that systems of orthogonal sigma proteins, anti-sigma proteins, and promoters are suitable for a variety of synthetic genetic circuits (pg. 8, col. 1, par. 2-3).
Regarding claim 3, Weiss, Flores-Jasso, Lin, and Rhodius do not explicitly the property of being sufficiently sensitive to distinguish the specified target micro RNA from an off-target micro RNA that differs at only one nucleotide. However, the combination of references does provide a method which is the same as the claimed methods in structure (see the rejections for claims 1 and 2 above). Furthermore, par. 45 of the instant specification states that such specificity is granted by the use of the entire RISC-miRNA complex (vs isolated RNA). Therefore, the limitation of claim 3 flows naturally from the inclusion of the entire RISC-miRNA complex (as discussed for Flores-Jasso for claim 1), and the limitation is considered to have been met.
Claim 6 is rejected under 35 U.S.C. 103 as unpatentable over Weiss et al (effectively filed Mar 22, 2021; Patent Application Publication No. US 2022/0298509) in view of Flores-Jasso et al (published Feb 2013; Flores-Jasso et al. RNA. 2013 Feb;19(2):271-9.) and Lin et al. (published July 2021; Lin et al. Biochemical Engineering Journal, Volume 171, 2021, 108031), applied to claims 1 above, further in view of Rhodius et al. (published Oct 29, 2013; Rhodius et al. Mol Syst Biol. 2013 Oct 29;9:702. doi: 10.1038/msb.2013.58), as applied to claims 2, 4, and 5 above, and further in view of Segall-Shapiro et al. (published June 24, 2014; Segall-Shapiro et al. Mol Syst Biol. 2014 Jul 30;10(7):742).
Weiss, Flores-Jasso, and Lin teach the limitations of claim 1, as discussed above.
Weiss, Flores-Jasso, Lin, and Rhodius teach the limitations of claims 2, 4, and 5, as discussed above.
Regarding claim 6, Flores-Jasso (pg. 277, col. 1, last par.), Lin (pg. 4, col. 2, 1st par.), and Rhodius (for example, pg. 4, col. 2, 1st par.) teach expression systems comprising T7 RNA polymerase. Rhodius teaches that the association between sigma proteins and core RNA polymerases are required for function (pg. 7, col. 1, last par.).
Regarding claim 6, Weiss, Flores-Jasso, Lin, and Rhodius do not explicitly teach an expression system which comprises a core component of T7 RNA polymerase, wherein an amplifying step comprises expressing an mRNA sequence that encodes a pseudo-sigma component of T7 RNA polymerase under the control of a promoter responsive to the presence of unbound sigma protein. They do not explicitly teach that the core component and the pseudo-sigma component bind to one another when both are present in the expression system, thereby producing a functional T7 RNA polymerase; and that the functional T7 RNA polymerase in turn binds to a cognate promoter controlling expression of a reporter molecule, thereby amplifying expression of the reporter molecule.
Regarding claim 6, Segall-Shapiro teaches an expression system which comprises a core component of T7 RNA polymerase, and wherein an amplifying step comprises expressing an mRNA sequence that encodes a pseudo-sigma component of T7 RNA polymerase under the control of a promoter responsive to the presence of unbound sigma protein (pg. 7, col. 1, last par. – col. 2, par. 2; Figure 5D). Note that the core component of T7 RNA polymerase is the ‘ß (core) fragment’ and the ‘pseudo-sigma’ is the ‘α fragment.’ Segall-Shapiro teaches that the core component and the pseudo-sigma component bind to one another when both are present in the expression system, thereby producing a functional T7 RNA polymerase; and that the functional T7 RNA polymerase in turn binds to a cognate promoter controlling expression of a reporter molecule, thereby amplifying expression of the reporter molecule (see Figure 5D).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Weiss, Flores-Jasso, Lin, and Rhodius with the teachings of Segall-Shapiro, in order to modulate the fraction of the polymerase pool that is active in the genetic circuit (pg. 7, col. 2, 1st par.). One would have had reasonable expectation of success because Segall-Shapiro demonstrates that a split T7 RNA polymerase functions well in artificial genetic expression systems (Figure 5E, H).
Claims 7 is rejected under 35 U.S.C. 103 as unpatentable over Weiss et al (effectively filed Mar 22, 2021; Patent Application Publication No. US 2022/0298509) in view of Flores-Jasso et al (published Feb 2013; Flores-Jasso et al. RNA. 2013 Feb;19(2):271-9.) and Lin et al. (published July 2021; Lin et al. Biochemical Engineering Journal, Volume 171, 2021, 108031), applied to claim 1 above, further in view of Rhodius et al. (published Oct 29, 2013; Rhodius et al. Mol Syst Biol. 2013 Oct 29;9:702. doi: 10.1038/msb.2013.58), as applied to claim 2 above, and further in view of Silverman et al. (published March 2020; Silverman et al. Nat Rev Genet. 2020 Mar;21(3):151-170; provided as NPL #2 on page 2 of IDS filed 03/06/24).
Weiss, Flores-Jasso, and Lin teach the limitations of claim 1, as discussed above. Weiss, Flores-Jasso, Lin, and Rhodius teach the limitations of claim 2, as discussed above.
Regarding claim 7, Weiss, Flores-Jasso, Lin, and Rhodius do not explicitly teach that at least some of the reagents used in performing said method are first lyophilized and then rehydrated.
Silverman teaches lyophilizing and rehydrating at least some of the reagents used in cell-free expression systems (pg. 160, col. 1, 1st par.; Fig. 4).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Weiss, Flores-Jasso, Lin, and Rhodius with the teachings of Silverman, in order to preserve and distribute cell-free expression system reactions at ambient conditions (pg. 160, col. 1, 1st par.). One would have had reasonable expectation of success because Silverman demonstrates that lyophilized cell-free biosensors maintain their activity for months (pg. 160, col. 1, 1st par.).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Christine M Jones whose telephone number is (571)272-2585. The examiner can normally be reached Monday - Friday, 8AM - 4PM.
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/C.M.J./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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