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 .
DETAILED ACTION
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Status of Claims
Claims 1-3 and 5-20 are currently pending. Claims 1-3, 5-9 and 12-20 have been amended by Applicants’ amendment filed 06-30-2026. Claim 4 has been canceled by Applicants’ amendment filed 06-30-2026. No claims have been added by Applicants’ amendment filed 06-30-2026.
Claims 10, 11 and 12 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim.
Claims 3, 6-8 and 13-20 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on April 6, 2026.
The restriction requirement was deemed proper and was made FINAL.
The claims will be examined insofar as they read on the elected species.
A complete reply to the final rejection must include cancellation of nonelected claims or other appropriate action (37 CFR 1.144) See MPEP § 821.01.
Therefore, claims 1, 2, 5 and 9 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed November 22, 2022 is a CON of PCT/JP2021/042250, filed November 17, 2021, which claims the benefit Japanese Patent Application JP2020-191550, filed November 18, 2020.
Acknowledgment is made of Applicant's claim for foreign priority based on an application filed in the Japan on November 18, 2020; and of Applicant’s filing of the certified copy of Japanese Patent Application JP2020-191550 on November 8, 2023 as required by 37 CFR 1.55.
Should applicant desire to obtain the benefit of foreign priority under 35 U.S.C. 119(a)-(d) prior to declaration of an interference, a certified English translation of the foreign application must be submitted in reply to this action. 37 CFR 41.154(b) and 41.202(e).
Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed June 30, 2026 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection not specifically addressed below are herein withdrawn.
“Claim Objection”
As noted in the Office Action Summary (PTO-326) there was no objection to the claims in the Office Action mailed April 9, 20206. The term “Claim Objections/Rejections” is a heading, whereas the term referred to by Applicant is the Examiner’s interpretation of a term (e.g., Claim Interpretation: “barcode sequences has…”).
Specification Objection
The objection to the disclosure is withdrawn because it contains an embedded hyperlink and/or other form of browser-executable code, due to Applicant’s filing of the Specification on June 30, 2026.
Maintained Objections/Rejections
Claim Rejections – 35 USC § 112(b)
The rejection of claims 1, 2, 5 and 9 is maintained under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards
as the invention.
Claim 1 is indefinite for the recitation of the term “the RNA modification reagent selective modifies…and the barcode sequences” such as recited in claim 1, lines 11-12 because claim 1, lines 6-7 already recites that the RNA modification reagent “modifies one or more nucleotides in the one or the plurality of RNA probes.” Thus, it is completely unclear whether the RNA modification reagent modifies one or more nucleotides in RNA probes, or whether it selectively modifies a single chain region of RNA probes. Moreover, it is unclear what the limitation refers to and/or what is selectively modified in a “single chain region” and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “a single chain region” as recited in claim 1, line 11 because the as-filed Specification and/or the original claims do not teach “a single chain region” and/or that a “single chain region” is selectively modified by an RNA modification reagent, such that it is completely unclear what “single chain region” is present in the one or the plurality of RNA probes is being referred to and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “the barcode sequences” such as recited in claim 1, line 12. There is insufficient antecedent basis for the term “the barcode sequences” in the claim because claim 1, line 4 recites the term “a barcode sequence”.
Claim 1 is indefinite for the recitation of the term “barcode sequences forms a structure comprising from a plurality of base pairs” such as recited in claim 1, line 12 because it is unclear what is being claimed. It is unclear whether the barcode sequence recited in line 4 are single-stranded or whether they already comprise base pairs, such that modification of the RNA probes causes a single-stranded barcode sequence to form a double-stranded structure; whether the step of “detecting a position and a frequency” causes the barcode sequence to form base pairs; and/or whether the term refers to something else and, thus, the metes and bounds of the claim cannot be determined.
Claims 2, 5 and 9 are indefinite insofar as they ultimately depend from instant claim 1.
Claim Rejections - 35 USC § 102
The rejection of claims 1, 2, 5 and 9 is maintained under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Smola et al. (hereinafter “Smola”) (Nature Protocols, 2015, 10(11), 1643-1669).
Regarding claims 1, 2, 5 and 9, Smola teaches the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit small electrophilic reagents that react with 2′-hydroxyl groups to interrogate RNA structure at single-nucleotide resolution; and mutational profiling (MaP) identifies modified residues by using reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing, such that the SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as can be done for simple model RNAs (interpreted 2’-hydroxyl acylation as encompassing RNA modification reagents; and synthesizing cDNA, claims 1 and 2) (Abstract, lines 1-5). Smola teaches in Figure 2, an overview of SHAPE-MaP and ShapeMapper, the method comprising: (a) RNA is treated with a SHAPE reagent that reacts at conformationally dynamic nucleotides; (b) Specialized reverse transcription conditions—the MaP strategy—allow the polymerase to read through chemical adducts in the RNA and to record the site as a nucleotide noncomplementary to the original sequence in the cDNA; (c) the resulting cDNA is processed through one of three workflows including barcoding (Figure 4) and subjected to massively parallel sequencing; (d–f) ShapeMapper then aligns sequenced reads back to the target sequence (d), calculates mutation rates; (e) and generates SHAPE reactivity profiles (f), wherein SHAPE reactivities can be used to model secondary structures, visualize competing and alternative structures and quantify any process that modulates local nucleotide RNA dynamics (interpreting (a) as contacting RNA probes and an RNA modification agent in claim 1b, and showing that the RNA has at least one structural motif of claim 9; (b) as synthesizing cDNA using RNA as a template, and reverse transcription in claim 2c1; (c) sequencing as a workflow that includes barcoding the probes as recited in claim 1a, determining nucleotide sequences in claim 2c2, barcodes forming base pairs during PCR and sequencing in claim 4; (d) as alignment and mutation counting in claim 2c2; (e) and (f) are interpreted to provide mutation rates for detecting a position and frequency of mutations in claim 2c3; and interpreting SHAPE reagents to selectively modify unbound nucleotides in single-stranded regions, claims 1, 2, 5 and 9) (pg. 1645, Figure 2; and pg. 1647, Figure 4). Figure 2 is shown below:
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Smola teaches that SHAPE electrophiles are added to the folded RNA (or virus or cell) and then incubated until the reagent has either reacted with RNA or degraded via hydroly-sis with water (five hydrolysis half-lives, Fig. 1b,c), wherein two con-trol reactions are performed in parallel: a no-reagent control and a denaturing control (interpreted as contacting the RNA probe and an RNA modification reagent, claim 1b) (pg. 1645, col 1, last partial paragraph). Smola teaches that Figure 4 is an overview of workflows useful for converting RNAs modified with SHAPE reagents into libraries compatible with massively parallel sequencing, wherein RNAs are modified with a SHAPE reagent and subjected to reverse transcription under MaP conditions, during which adduct-induced mutations are recorded in the cDNA strand, such that one of three workflows is then used to construct high-quality libraries for sequencing and recovery of the SHAPE chemical probing information (interpreted as synthesizing cDNA, sequencing to determine nucleotide sequences comprising mutations; barcoding probes; and forming base pairs during PCR and sequencing, claims 1, 2 and 5) (pg. 1647, Figure 4). Figure 4 is shown below:
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Smola teaches in Figure 1 that SHAPE reagents include 1M7, 1M6 and NMIA, wherein 1M6 and NMIA are selective for nucleobases that have one face available for stacking and that achieve a reaction- competent conformation on a slow time scale, respectively (interpreting SHAPE reagents 1M6 and NMIA selectively modify unbound nucleotides in single-stranded regions) (Figure 1). Smola teaches that low SHAPE reactivity across a region of RNA is indicative of stable base pairing (interpreted as barcodes having reduced reactivity with the RNA modification reagent, claim 1) (pg. 1645, col 1, first partial paragraph, lines 1-2). Smola teaches that cellular or viral RNAs that were obtained by gentle extraction to maintain secondary structure should be DNase-treated following SHAPE modifica-tion, before reverse transcription (interpreted as RNA to be analyzed; and interpreting a secondary structure as an RNA comprising a structural motif, claims 1a and 9) (pg. 1645, col 2, last partial paragraph, lines 7-10).
Smola meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Response to Arguments
Applicants’ arguments filed June 30, 2026 have been fully considered but they are not persuasive. Applicants essentially asserts: (a) Smola does not disclose "preparing one or a plurality of RNA probes, each comprising an RNA to be analyzed attached to a barcode sequence," as recited in amended claim 1, wherein the claimed barcode sequence is attached to each RNA probe before the modification reaction (Applicant Remarks, pg. 8, last full paragraph through pg. 9, first partial paragraph); (b) Smola does not teach that "the barcode sequences form a structure comprising a plurality of base pairs as recited in amended claim 1 (pg. 9, second and third full paragraphs); and (c) Saito does not teach that the barcode that the barcode sequence itself forms the claimed structure (Applicant Remarks, pg. 9, third and fourth full paragraphs).
Regarding (a), although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26USPQ2d 1057 (Fed. Cir. 1993). MPEP 2112.01(I) states:
where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990) (underline added).
Applicants’ assertion that Smola does not disclose that the claimed barcode sequence is attached to each RNA probe before the modification reaction, is not found persuasive. The Examiner respectfully notes that instant claim 1 does not recite what Applicant asserts. Instant claim 1 does not recite that the steps of the method are carried out in any particular order (e.g., “carried out in the order as recited”). For example, because step (b) does not recite that the plurality of RNA probes each comprises a barcode sequence, the steps of instant claim 1 could clearly be carried out in the order of: step (b), step (a) and step (c) (e.g., modifying, barcoding, and detecting). Smola teaches that RNA is treated with SHAPE, reverse transcription (induced mutation), then processed through a workflow as illustrated in Figure 4 including PCR with barcoded primers (pg. 1645, Figure 2; pg. 1647, Figure 4; and pg. 1653, Table 3). Smola teaches all of the limitations of the claims. Thus, the claims remain rejected.
Regarding (b) and (c), as an initial matter, please see the 35 USC 112(b) rejection supra regarding that the initial structure of the barcodes is unclear. Applicants’ assertion that Smola does not teach that "the barcode sequences form a structure comprising a plurality of base pairs”; or that the barcode sequence itself forms the base-paired structured as recited in amended claim 1, is not found persuasive. Smola teaches RT-PCR using primers comprising barcodes (See; Tables 3 and 4). It is noted that RT-PCR of an RNA probe comprising a single-stranded barcode forms a barcode sequences comprising a plurality of base pairs, as shown in Figure 4 below:
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and as shown during RT-PCR and PCR as evidenced by Omega (pg. 2) as shown below:
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Smola teaches all of the limitations of the claims. Thus, the claims remain rejected.
Claim Rejections - 35 USC § 103
The rejection of claims 1, 2, 5 and 9 is maintained under 35 U.S.C. 103 as being unpatentable over Smola et al. (hereinafter “Smola”) (Nature Protocols, 2015, 10(11), 1643-1669) in view of Saito et. al. (hereinafter “Saito”) (US Patent No. 12091775, issued September 17, 2024; and International Application WO2018/003809, published January 4, 2018).
The teachings of Smola as applied to claims 1, 2, 5 and 9 are described supra.
Smola does not specifically exemplify additional instances of a barcode forming base pairs (claim 4, in part).
Regarding claim 1 (in part), Saito teaches an RNA probe containing RNA functional structural units is prepared by the following steps: (1) recognizing one or more stem structures contained in the RNA based on RNA sequence information; (2) extracting a motif region with reference to the one or more recognized stem structures; (3) adding an assistive stem region to the extracted motif region; and (4) adding a barcode region, which represents a complementary sequence to a DNA barcode sequence, to the assistive stem region; and a method for detecting a protein-binding RNA by using an RNA probe containing RNA functional structural units (interpreted as preparing RNA probes; attaching a barcode sequence comprising base pairs; and inherently having a structure with reduced reactivity with RNA modification reagents, claim 1) (Abstract). Saito teaches the analysis of the functions of large RNA structural units containing a plurality of loop structures, which have been heretofore difficult to analyze; and since the RNA functional structural units can be extracted based only on RNA sequence information, it is possible to analyze the functional structural units extracted from a wide variety of RNAs (col 3, lines 56-62). Saito teaches adding a first assistive stem portion sequence (interpreted as a ssRNA barcode) and a second assistive stem portion sequence (interpreted as a ssRNA barcode) to the extracted motif region, wherein the second assistive stem portion sequence is complementary to the first assistive stem portion sequence and hybridizes to the first assistive stem portion sequence to form a double-stranded assistive stem (interpreting the hybridized assistive stem base-pairs as forming barcode base-pairs, claim 1) (col 2, lines 49-55). Saito teaches an RNA microarray prepared by hybridizing a microarray having DNA barcode sequences immobilized on a support with the RNA probe library (interpreting the hybridized DNA barcode sequence to the RNA probe as forming barcode base-pairs, claim 1) (col 3, lines 32-34). Saito teaches that the barcode region which represents a complementary sequence to a DNA barcode sequence is added to the assistive stem (Figures 2b and 2c), wherein the DNA barcode sequence of the present invention, it is possible to use tags (JP 1998-507357 A and JP 2002-518060 A), zip codes (JP 2001-519648 A) or normalized orthogonal sequences (JP 2012-181813 A), barcode sequences (Xu, Q. et al., Proc. Natl. Acad. Sci., Vol. 106, pp. 2289-2294, 2009), or the like, such that the term "motif region" refers to a functional structural unit for an RNA to interact with a target substance, wherein the DNA barcode sequence desirably has less cross-reactivity (cross-hybridization); and preferably has a sequence of 20 to 30 bases, and particularly preferably 25 bases (interpreted as a double-stranded structure; a forming a plurality of base pairs; and reduced reactivity, claim 1) (col 6, lines 28-41). Figure 2C is shown below:
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Base pairs
Saito teaches that the extracted RNA probe is contacted with a microarray having DNA barcode
sequences immobilized on a support, and the RNA probe hybridized with the DNA barcode sequences is identified (interpreting the barcode to comprise base pairs, claim 1) (col 9, lines 43-46). Saito teaches that RNA structure data of the HIV-1 genome used data analyzed by SHAPE-MaP (col 13, lines 1-4).
“It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose.... [T]he idea of combining them flows logically from there having been individually taught in the prior art.” In re Kerkhoven, 626 F.2d 846, 850, 205 USPQ 1069, 1072 (CCPA 1980). Moreover, it is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of producing RNA probes containing RNA functional structural units as exemplified by Saito, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of mutational profiling using SHAPE chemistries and mutational profiling as disclosed by Smola to include the RNA probes comprising a motif region, an assistive stem region, a barcode region, and a DNA barcode sequence as taught by Saito with a reasonable expectation of success in identifying modified residues; in producing a thorough and robust strategy for higher order RNA structure probing at multiple scales; and/or in identifying specific RNA probes hybridized to the DNA barcode sequence. Moreover, it would have been prima facie obvious for one of ordinary skill in the art to analyze the RNA structure data obtained by the methods of Saito using the SHAPE-MaP method disclosed by Smola with a reasonable expectation of success in converting the RNA structure information into secondary structure information.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly
rejected under 35 USC §103(a) as obvious over the art.
Response to Arguments
Applicants’ arguments filed June 30, 2026 have been fully considered but they are not persuasive. Applicants essentially asserts: (a) Saito does not teach that the barcode sequences form a structure comprising a plurality of base pairs as recited in claim 1, where the barcode sequence of the claimed embodiment forms a structure in itself comprising a plurality of base pairs as shown in Figures 3A and 3B (Applicant Remarks, pg. 10, last full paragraph; and pg. 11, first and second full paragraphs).
Regarding (a), please see the discussion supra regarding the 35 USC 112(b) rejection; and the teachings of Smola, wherein PCR of RNA probes generates barcode sequences that form a structure comprising a plurality of base pairs (e.g., a complementary sequence). Applicants’ assertion that Saito does not teach that the barcode sequences form a structure comprising a plurality of base pairs as recited in claim 1 as shown in Figures 3A and 3B, is not found persuasive. It is noted that although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26USPQ2d 1057 (Fed. Cir. 1993). As an initial matter, instant claim 1 does not recite:
“the barcode sequence of the claimed embodiment forms a structure in itself comprising a plurality of base pairs”.
Instead, instant claim 1 recites:
“the barcode sequences form a structure comprising a plurality of base pairs”
Additionally, the Examiner contends that Saito also teaches that the barcode sequences forms a structure comprising a plurality of base pairs. To that end –
Smola teaches:
RT-PCR using primers comprising barcodes (See; Tables 3 and 4), wherein RT-PCR of an RNA probe comprising a single-stranded barcode forms a barcode sequences comprising a plurality of base pairs (pg. 1654, col 2, Modified RT-PCR primers for small RNA workflow).
Saito teaches:
The single-stranded template DNA is amplified by PCR.
The second assistive stem portion sequence is complementary to the first assistive stem portion sequence and hybridizes to the first assistive stem portion sequence to form a double-stranded assistive stem (interpreted as a structure comprising a plurality of base pairs) (col 2, lines 49-55).
Figure 2C shows the barcode structure comprising a plurality of base pairs, as shown below:
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DNA template amplification by PCR (interpreted as a structure comprising a plurality of base pairs (col 11, lines 65-67).
The combined references of Smola and Saito teach all of the limitations of the claims. Thus, the claims remain rejected.
New Objections/Rejections
Claim Objections
Claim 9 is objected to because of the following informalities: Claim 9 recites “selected from a stem, stem-loop, pseudoknot, or multi-junction” in lines 2-3, wherein the term “selected from the group consisting of a stem, stem-loop, pseudoknot, and multi-junction” might be more appropriate.
Appropriate correction is required.
Conclusion
Claims 1, 2, 5 and 9 remain rejected.
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 AMY M BUNKER whose telephone number is (313) 446-4833. The examiner can normally be reached on Monday-Friday (6am-2:30pm).
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/AMY M BUNKER/Primary Examiner, Art Unit 1684
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