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 .
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 05/29/2024; 03/10/2025; 03/28/2025; 08/20/2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of Claims
This office action is in response to Applicant's Response to Election / Restriction filed on August 5, 2026. No claims amendment is made in the response filed on August 5, 2026.
Claims 1-7 are pending and under examination. This is the first action on the merits.
Election/Restrictions
Applicant's election without traverse of the following species in the reply filed Aug 05, 2026 is acknowledged:
Species of detection target: A) Protein (claim 7);
Species of detection phenomenon:
G) generation of hydrogen ions associated with incorporation of a nucleotide through the amplification of the single-stranded nucleic acid preparation, the phenomenon is detected using a pH meter (claim 2, 3, 6; [0063] in spec);
Species of Isothermal Amplification:
I) rolling circle amplification method (RCA) (claim 4, 5, 6; [0058] in spec).
Examination on the merits commences on claims 1-7.
Priority
The effective filling date of the instant claims 1-7 is 05/29/2024, the filling date of the instant U.S. nonprovisional application.
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Specifically, Applicant's claim to domestic priority is acknowledged as a 371 national stage entry of PCT/JP2022/044042. Applicant's claim to foreign priority to JAPAN Application 2021-196184 is also acknowledged. However, neither of the submitted document is in English, and English translations have not been submitted.
The domestic benefit date may be the effective filing date of the claimed invention if:
• the earlier application to which domestic benefit is claimed supports the claimed invention under 35 U.S.C. 112(a).
The foreign priority date may be the effective filing date of the claimed invention if:
• the foreign application supports the claimed invention under 35 U.S.C. 112(a), AND
• the applicant has perfected the right of priority by providing a certified copy of the priority application, and a translation of the certified copy (if not in English) along with a statement that the translation of the certified copy is accurate.
See MPEP 213.04 and 216; See also MPEP 2304.01(c)
In this instant case, the priority documents submitted are not in English, without a translation; without an English translation, the examiner is unable to verify whether the earlier applications provide written description support for the claimed invention under 35 U.S.C. 112(a). Thus, since an English translation of the priority application has not been filed, the effective filing date (EFD) of the claimed invention is the filing date of the application.
However, if applicant perfects the right of priority by providing a certified English translation of the priority application that supports the claimed invention under 35 U.S.C. 112(a), the effective filing date will be the filing date of the foreign application.
Objection to Specification -- Title of Invention Is Not Descriptive
The title of the invention is not descriptive. A new title is required that is clearly indicative of the invention to which the claims are directed.
The following title is suggested: “Methods for detecting target-dependent single-stranded nucleic acid amplification.”
Claim Objections
Claim 5 is objected to because of the following informalities:
In claim 5, lines 3-4, to properly reference "a 3' terminal region of the single-stranded nucleic acid preparation," recited in base claim 1, it should read:
"the 3’ terminal region [[and]]of the single-stranded nucleic acid preparation."
Claim Interpretation
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
For the purpose of applying prior art, claim 1 recites "a single-stranded nucleic acid preparation having activity to bind to the target substance."
The specification does not expressly define the term "single-stranded nucleic acid preparation" with any structural features that distinguishes it from single-stranded nucleic acids known in the art. Accordingly, the recited "single-stranded nucleic acid preparation having activity to bind to the target substance" is interpreted to encompass any single-stranded nucleic acid capable of binding to a target. An example of the single-stranded nucleic acid preparation, provided in the specification, is a nucleic acid aptamer. ([0028])
For the purpose of applying prior art, claim 1 recites a step of "amplifying the single-stranded nucleic acid preparation in a solution."
In light of the specification, this amplifying step is interpreted as not being limited to generating copies of the single-stranded nucleic acid preparation. Rather, the step broadly encompasses any step of using the single-stranded nucleic acid preparation in an amplification reaction.
This interpretation is consistent with the specification, which in Fig. 7 describes rolling circle amplification of single-stranded nucleic acid preparation:
"Next, as shown in STEP 5 of FIG. 7 , a process of amplifying the single-stranded nucleic acid preparation 3 is performed. The single-stranded nucleic acid preparation 3 included in the first binding substance 1A bound to the target substance 7 is amplified to generate an amplified nucleic acid 27. When a first binding substance 1A that is not bound to the target substance 7 is present in the reaction solution 23 for nucleic acid amplification, the single-stranded nucleic acid preparation 3 contained in the first binding substance 1A forms the base pair 35 with the complementary nucleic acid 5 and becomes difficult to amplify." (specification, [0056])
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Here, the specification explicitly describes STEP 5 of FIG. 7 as "a process of amplifying the single-stranded nucleic acid preparation 3." However, in that process, the single-stranded nucleic acid preparation is used to initiate nucleotide polymerization. The sequence being copied or amplified is not the sequence of the single-stranded nucleic acid preparation itself, but rather the circular DNA template.
For the purpose of applying prior art, claim 6 recites a reaction solution that "contains a Tris buffer solution at a final concentration of 0 mM or more and 10 mM or less," this concentration limitation is interpreted as reciting a range from 0 mM to 10mM. Because the range includes 0mM, under BRI, it is interpreted that the limitation also encompasses reaction solutions that do not contain Tris.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-5 and 7 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by
Cheng (Cheng et al., A facile scanometric strategy for ultrasensitive detection of protein using aptamer-initiated rolling circle amplification. Chem Commun (Camb). 2010 Sep 28;46(36):6720-2. doi: 10.1039/c002078h. Epub 2010 Aug 23. PMID: 20730209; cited as NPL Document #1 in IDS filed 03/10/2025).
Cheng teaches a strategy for ultrasensitive detection of protein, with aptamer-initiated rolling circle amplification (Abstract; Scheme 1).
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Regarding claim 1, Cheng teaches an analysis method for detecting a target substance using a binding substance,
the binding substance comprising:
a single-stranded nucleic acid preparation having activity to bind to the target substance (Scheme 1, Aptamer); and
a complementary nucleic acid that forms a base pair with a 3' terminal region of the single-stranded nucleic acid preparation when the single-stranded nucleic acid preparation is not bound to the target substance, and that dissociates from the 3' terminal region when the single-stranded nucleic acid preparation is bound to the target substance (Scheme 1, the portion of circular DNA template that is complementary to the 3’ region of Aptamer, a skilled artisan would readily understand the depiction in scheme 1 shows Aptamers are hybridized to circular DNA on its 3’end, because that end is subsequently extended to initiate rolling circle amplification. In other words, the Aptamer functions as a primer for the circular DNA, and primer extension necessarily occurs from the 3’end ; p. 6720, right-hand col, para 1, “the amino-modified aptamer for human vascular endothelial growth factor 165 (VEGF) was immobilized on an epoxy-coated glass slide. The resulting aptamer chip was then hybridized with a complementary circular DNA template to form a duplex structure (see ESI†). In presence of target protein, the bound circular DNA could be substituted by a target-induced strand release process due to the higher affinity of the selected aptamer to its protein than to the complementary DNA strand”).
the analysis method comprising:
mixing the binding substance and a sample containing the target substance (Scheme 1, target protein is mixed with aptamer-circular DNA duplex structure);
amplifying the single-stranded nucleic acid preparation in a solution (Scheme 1, RCA amplification is carried out in solution; see also S3, “Protein detection protocol”)
where the binding substance not bound to the target substance is present (Scheme 1 ; p. 6720, right-hand col, para 1, “The remaining aptamer–circular DNA duplex, whose amount depended on the quantity of target protein, could initiate RCA catalyzed by phi29 DNA polymerase”); and
detecting a phenomenon caused by the amplifying of the single-stranded nucleic acid preparation (Scheme 1).
Regarding claim 2, Cheng teaches phenomenon is coloration obtained by using a detection reagent that binds to the amplified single-stranded nucleic acid preparation (Scheme 1; Fig. 1).
Regarding claim 3, Cheng teaches detecting phenomenon using a light-receiving device ( p. 6720, left-hand col, para 2, lines 18-20, “The scanometric readout could be conveniently performed with a computer-controlled scanner after a silver enhanced step on an aptamer chip”; Fig. 1; ).
Regarding claim 4, Cheng teaches the single-stranded nucleic acid preparation is amplified by an isothermal nucleic acid amplification method not requiring a temperature cycle (scheme 1, amplifying aptamer using RCA, which is isothermal amplification; p. 6720, left-hand col, para 3),
Regarding claim 5, Cheng teaches forming a complex by using a single-stranded cyclic nucleic acid including
a sequence complementary to the 3’ terminal region of the single-stranded nucleic acid preparation, and
amplifying the single-stranded nucleic acid preparation with the complex serving as a starting point by a rolling circle amplification method using a reaction solution for nucleic acid amplification (Scheme 1).
Regarding claim 7, Cheng teaches the target substance is a protein (Scheme 1).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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 6 is rejected under 35 U.S.C. 103 as being unpatentable over Cheng (Cheng et al., A facile scanometric strategy for ultrasensitive detection of protein using aptamer-initiated rolling circle amplification. Chem Commun (Camb). 2010 Sep 28;46(36):6720-2. doi: 10.1039/c002078h. Epub 2010 Aug 23. PMID: 20730209; cited as NPL Document #1 in IDS filed 03/10/2025), in view of
Ducani (WO2020161187A1 - Method and products for producing functionalised single stranded oligonucleotides; Published 2020-08-13) and
Tang (Tang et al. Metal-ion-induced DNAzyme on magnetic beads for detection of lead(II) by using rolling circle amplification, glucose oxidase, and readout of pH changes. Microchim Acta 186, 318 (2019).
The teachings of Cheng are recited above and applied as for base claim 1.
Regarding claim 6, Cheng teaches single-stranded nucleic acid preparation is amplified by a rolling circle amplification method (Scheme 1), in an amplification reaction solution containing 50mM pH 7.5 Tris-HCl buffer (S3, lines 19-21).
Although Cheng does not explicitly teach a concentration of Tris buffer that falls within the claimed range of 0mM to 10mM, the use of Tris as a buffering agent in RCA reaction is well-known, and adjusting its concentration to achieve optimal reaction conditions would have been an obvious, routine optimization process for a skilled artisan, see MPEP 2143.
This is supported by Ducani, which discloses that buffering agents for RCA reaction include Tris, and other alternatives such as Tricine, HEPES, and MOPS, where the concentration of buffering agent will typically range from about 5 to 150 mM. (page 14, lines 7-9).
Furthermore, as set forth at MPEP 2144.05 II. A: “Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical.”
One having ordinary skill in the art would have a reasonable expectation of success because determining the optimum and/or workable conditions is well within the skill level of the ordinary artisan.
Regarding the limitation “the phenomenon is detected using a pH meter,” Cheng teaches detecting a phenomenon caused by the amplifying of the single-stranded nucleic acid preparation (Scheme 1), specifically, detection of rolling circle amplification product by using a DNA probe modified with Au nanoparticle (AuNP) with scanometric readout.
The long DNA strand generated by the RCA step contains hundreds of tandem-repeat complementary sequences of the circular DNA and could be hybridized with complementary AuNP probes. After silver enhancement, a scanometric readout is performed with a scanner for detection of target protein. (p. 6720, right-hand col, para 1).
Although Cheng does not explicitly teach using a pH meter, a skilled artisan would have found this feature obvious because it is an alternative way to detect RCA products, this is supported by Tang.
Tang teaches a method of detecting target molecule via target-dependent rolling circle amplification, hybridization of glucose oxidase-labeled ssDNA probes to rolling circle amplification product, with the glucose oxidase oxidizes glucose into gluconic acid and hydrogen peroxide. The produced gluconic acid changes the pH value of detection solution which is detected on a portable pH meter (scheme 1; p. 2, right-hand col., para. 1).
Accordingly, a skilled artisan would have readily understood that the DNA probes modified with Au nanoparticle (AuNP) with scanometric readout, as disclosed by Cheng, and the DNA probes modified with glucose oxidase with pH meter readout, taught in Tang, are alternative means for detecting RCA products.
Therefore, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to substitute a known detection approach for another.
This rationale aligns with the principle of KSR for a simple substitution of one known element for another to obtain predictable results, see MPEP 2141.
The use of Tang’s DNA probes modified with glucose oxidase with pH meter readout in place of the AuNP DNA probes with scanometric readout, in Voelkerding et al., is a predictable use of prior art elements according to their established functions, leading to the predictable result of detection of RCA products.
The person of ordinary skill would have had a reasonable expectation of success because the alternative detection methods serve the same function of detecting RCA products.
Prior Art
Below are relevant prior art not used in rejection but pertinent to the claims or disclosure.
The combined use of target-binding aptamers and rolling circle amplification (RCA) is well-known in the art.
See Sharma (Sharma et al., ABCs of DNA aptamer and related assay development. Biotechnol Adv. 2017 Mar-Apr;35(2):275-301. doi: 10.1016/j.biotechadv.2017.01.003. Epub 2017 Jan 18. PMID: 28108354.); page 286-287;
See Zhou (Zhou et al. Aptamer-based rolling circle amplification: a platform for electrochemical detection of protein. Anal Chem. 2007 Oct 1;79(19):7492-500. doi: 10.1021/ac071059s. Epub 2007 Aug 28. PMID: 17722881.); Figure 1;
See Song (Song et al., Target-catalyzed hairpin structure-mediated padlock cyclization for ultrasensitive rolling circle amplification. Talanta. 2019 Nov 1;204:29-35. doi: 10.1016/j.talanta.2019.05.057. Epub 2019 May 15. PMID: 31357296.).
The references below also teach nucleic acid duplex, wherein upon target binding, a strand of the duplex dissociates.
Kim (Kim et al. Molecular assembly for high-performance bivalent nucleic acid inhibitor. Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5664-9. doi: 10.1073/pnas.0711803105. Epub 2008 Apr 8. PMID: 18398007; PMCID: PMC2311377.) ;
Elskens (Elskens et al. Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects. Int J Mol Sci. 2020 Jun 25;21(12):4522. doi: 10.3390/ijms21124522. PMID: 32630547; PMCID: PMC7350236.) ; see Fig. 16;
Li (Li et al., A graphene oxide-based strand displacement amplification platform for ricin detection using aptamer as recognition element. Biosens Bioelectron. 2017 May 15;91:149-154. doi: 10.1016/j.bios.2016.12.010. Epub 2016 Dec 6. PMID: 28006682.).
Conclusion
Claim 5 is objected to; claims 1-7 are rejected. No claims are allowed.
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/TIAN NMN YU/Examiner , Art Unit 1681
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