DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. 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
2. Applicant’s election without traverse of Group I (claims 1-9) in the reply filed on July 1, 2026 is acknowledged.
The response does not state whether the requirement to elect an invention for examination is traversed, but the response does not include anything that would constitute a traversal. In other words, since Applicant did not distinctly and specifically point out any errors in the restriction requirement, the election has been treated as an election without traverse per MPEP § 818.01(a).
It is also noted that Applicant’s response of July 1, 2026 does not include an election of species of solid-state pore structure material for examination. Upon further consideration, though, the election of species requirement set forth in the Office action mailed on May 19, 2026 has been withdrawn in its entirety. The full scope of the elected invention set forth in claims 1-9 has been examined on the merits herein.
Claims 10-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on July 1, 2026.
Priority
3. 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. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Provisional Application No. 63/246,851, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. In particular, the ‘851 application does not provide support for the instant claims 1-9 because it lacks support for the following ranges for the diameter of the solid-state pore structure: (i) greater than 10 nm (claim 1); (ii) smaller than 5 micrometers (claim 2); (iii) between 100 and 500 nm or between 200 and 300 nm (claim 3); and (iv) 250 nm (claim 4). The ‘851 application only discloses a nanopore diameter (400 nm) (see, e.g., page 4). This is insufficient to support the broader ranges recited in claims 1, 2, and line 1 of claim 3. It is also insufficient to support the different range of 200-300 nm in claim 3 or the smaller diameter of 250 nm recited in claim 4. Accordingly, the instant claims have an effective filing date of September 20, 2022 (i.e., the filing date of PCT/US2022/044089).
Information Disclosure Statement
4. All references cited on the Information Disclosure Statement filed on March 19, 2024 have been considered.
Drawings
5. The drawings filed on March 19, 2024 are acceptable.
Substitute Specification
6. The substitute specification filed on March 19, 2024 has been entered.
The substitute specification is objected to because there is insufficient antecedent basis for “a solid-state pore structure with a diameter greater than 10 nm” as recited in claim 1. The disclosure only provides support for pores with a diameter of “a few 100s nanometers to a few micrometers,” “10 nm to 5 micrometers,” “100-500 nm,” “200-300 nm,” or “250 nm” (page 3, para. 13). It is noted that this is not a new matter issue since the original claims provide support for the range of diameters recited in claim 1. As noted in MPEP 2163.06 III, the specification can be amended to provide support for the subject matter of original claims without introducing new matter.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
7. 37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.831-1.834 because it does not contain a “Sequence Listing XML” as a separate part of the disclosure. A “Sequence Listing XML” is required because Figure 2 contains oligonucleotide sequences that fall within the definition set forth in 37 CFR 1.831(b)(2). These oligonucleotides are identified with Sequence Identifiers, but a “Sequence Listing XML” has not been filed.
Required response - Applicant must provide:
• A “Sequence Listing XML” part of the disclosure, as described above in item 1. or 2.; together with
o A statement that indicates the basis for the amendment, with specific references to particular parts of the application as originally filed, as required by 37 CFR 1.835(a)(3);
o A statement that the “Sequence Listing XML” includes no new matter as required by 37 CFR 1.835(a)(4)
AND
• A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph as required by 37 CFR 1.835(a)(2), consisting of:
o A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
o A copy of the amended specification without markings (clean version); and
o A statement that the substitute specification contains no new matter.
Claim Objections
8. Claim 1 is objected to because the word “padlock” should be inserted before “probe” in line 3 and also before “probes” in line 6 to maintain consistency with the language in line 2. As well, “target miRNAs” should be used throughout the body of the claim to maintain consistency with the preamble and line 2. Further, the “ligating” and “elongating” steps should be amended to account for the fact that more than one hybridized complex may be formed in preceding “binding” step.
Claim 2 is objected to because “5um” in line 2 should be replaced with either “5 micrometers” or “5 mM”.
Claims 3 and 4 are objected to because a space should be inserted before each instance of “nm” in each claim.
Claim 5 is objected to because “70 k nucleotides” should be replaced with “70k nucleotides”.
Claim 6 is objected to because the “2” in each of “SiO2,” “ZrO2,” “HfO2,” and “TiO2” should be a subscript.
Claims 7 and 8 are objected to because “the miRNAs” in line 1 of each claim should be replaced with “the target miRNAs” to maintain consistency with claim 1.
Claim 8 is also objected to because of the following additional informality. Replacing “are” in line 1 with “include” is suggested to improve the claim language and better agree with the language in claim 1.
Claim Rejections - 35 USC § 112
9. 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.
Claim 6 is 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 6 depends from claim 1 and requires the pore structure to be selected from a list of particular materials. The list includes the recitation “TiO2 (oxide dielectric material)” in line 2. This recitation causes the claim to be indefinite because the use of parenthesis suggests that titanium dioxide is synonymous with “oxide dielectric material,” which is not the case since “oxide dielectric material encompasses oxides other than titanium dioxide (e.g., SiO2 or HfO2). As a result, it is not clear whether the claim contains an error and “oxide dielectric material” was intended to be a separate option or if Applicant intends the two terms to be synonymous. Clarification is required if the latter interpretation is correct.
Claim Rejections - 35 USC § 102
10. 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.
11. Claims 1-3 and 5-9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Dong et al. (Analytical Chemistry 2022; 94: 3865-3871).1
The instant claims are drawn to a method for counting target miRNAs in a sample comprising rolling circle amplification and the use of a solid-state nanopore with a diameter greater than 10 nm.
Regarding claim 1, Dong discloses a method containing the following steps:
hybridizing a target-specific padlock probe to a target miRNA in a sample to form a hybridized complex (Fig. 1a; see also page 3866, “Materials and Chemicals” section and “Rolling Circle Amplification Assay” sections);
ligating the hybridized complex to form a closed circular structure (Fig. 1a; see also page 3866, “Materials and Chemicals” section and “Rolling Circle Amplification Assay” sections);
elongating the hybridized complex using the closed padlock probe as a template to produce an elongated ssDNA product via rolling circle amplification (RCA) (Fig. 1a; see also page 3866, “Materials and Chemicals” section and “Rolling Circle Amplification Assay” sections);
providing a counting platform including a solid-state pore structure with a diameter greater than 10 nm (page 3867, “Glass Nanopore Fabrication” section);
measuring a concentration of the elongated ssDNA RCA product through a translocation event rate through the pore structure of the counting platform (page 3867, “Nanopore Sensing and Data Analysis” section; see also Fig. 1); and
determining the initial concentration of the target miRNA based on a quantity of the initial miRNA molecules, the quantity of initial miRNA molecules being linear with the concentration of elongated ssDNA RCA products (see Fig. 1; page 3867, “Nanopore Sensing and Data Analysis” section; and page 3867, “Principle Validation” section).
Regarding claims 2 and 3, the nanopore used by Dong has a diameter of 217 ± 9 nm (page 3867, “Glass Nanopore Fabrication” section). This value lies within the claimed ranges.
Regarding claim 5, Dong teaches that the elongated ssDNA RCA product is greater than 70,000 nucleotides in length (see, e.g., page 3867, column 2).
Regarding claim 6, the solid-state nanopore used by Dong is made of glass (page 3867, “Glass Nanopore Fabrication” section).
Regarding claims 7-9, Dong used the method to detect salivary miRNAs related to mild traumatic brain injury (mTBI) (see, e.g., the abstract and pages 3866-3867). The tested salivary miRNAs included let-7a, miR-30e, and miR-21 (Fig. 1; see also pages 3866-3867). Dong further teaches that the target miRNAs could include multiple miRNAs present in a mixture (see, e.g., the abstract and pages 3867-3870, the “Principle Validation” and “Quantification of miRNAs with and without Salivary RNA Background,” and “Profiling mTBI-Related miRNAs from a Mixture” sections).
Claim Rejections - 35 USC § 103
12. 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.
13. 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.
14. Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Dong et al. (Analytical Chemistry 2022; 94: 3865-3871).2
As discussed above, the teachings of Dong anticipate the methods of claims 1-3 and 5-9.
Regarding claim 4, Dong teaches that the nanopore used by Dong has a diameter of 217 ± 9 nm (page 3867, “Glass Nanopore Fabrication” section). This value lies close to the required diameter of 250 nm and no evidence of unexpected results has been presented with respect to the claimed diameter. Accordingly, a prima facie case of obviousness exists per MPEP 2144.05 I. As well, the ordinary artisan would have recognized that the pore size was a results-effective variable based on the teachings of Dong at pages 3867 and 3870, and accordingly, would have been motivated to conduct routine experimentation to optimize the size of the nanopore. As discussed in MPEP 2144.05 II, such experimentation is prima facie obvious in the absence of unexpected results. Thus, the method of claim 4 is prima facie obvious over Dong.
15. Claims 1-6 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Sekedat et al. (WO 2020/206170 A1) in view of Tang et al. (Nano Letters 2019; 19: 7927-7934) and further in view of Howorka & Siwy (Chemical Society Reviews 2009; 38: 2360-2384).
The instant claims are drawn to a method for counting target miRNAs in a sample comprising rolling circle amplification and the use of a solid-state nanopore with a diameter greater than 10 nm.
Regarding claim 1, Sekedat discloses methods for counting biomolecules of interest, wherein the biomolecules may be miRNAs (abstract and page 3, lines 23-27). The method may comprise counting products generated by rolling circle amplification (RCA) from circularized padlock probes used as template when bound specifically to a target nucleic acid (page 5, lines 5-13; page 5, line 19 – page 6, line 6). Sekedat further teaches that the counting of RCA products may include nanopore sensing (page 11, lines 3-5) and additionally discloses the use of a solid-state nanopore (page 70, last para. and page and 79, last para.).
Sekedat is not anticipatory because the reference fails to teach the concentration measurement and determination steps recited in claim 1.
Tang, though, discloses a method for counting loop-mediated isothermal amplification (LAMP) products that comprises the use of a solid-state nanopore (abstract; Fig. 1; and pages 7928-7929). Regarding claims 1 and 6, the method of Tang uses a glass solid-state nanopore with a pore size “around 10 nm” (Fig. 1; page 7928, and page 7932, col. 2). This range in Tang overlaps with the range of “greater than 10 nm” recited in claim 1 as well as the range “smaller than 5 micrometers” recited in claim 2. Further regarding claim 1, the method of Tang comprises measuring a concentration of an elongated ssDNA product (i.e., the LAMP product) through a translocation event rate through the solid-state nanopore and correlating the measured concentration with the initial concentration of the target nucleic acid used to generate the LAMP product, wherein said initial concentration of the target nucleic acid used to generate the LAMP product is linear with the concentration of the elongated ssDNA product passed through the solid-state nanopore (Figs. 1-2 and 7; pages 7928-7929, esp. the “Working Principle” and “Concept Validation” sections; page 7931, the “Quantitative Testing” section).
As well, further regarding claim 1 and also regarding claims 2-4, Howorka & Siwy review solid-state nanopores and teach that said nanopores may have a pore size ranging from a few nanometers to “several hundreds of nanometers” (page 2364, col. 1). Howorka & Siwy also review methods for making various solid-state nanopores, including nanopores with a larger pore size (pages 2364-2366).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for the ordinary artisan practicing the counting method of Sekedat to use a solid-state nanopore as described in Tang for the counting step. As discussed above, Sekedat teaches that a nanopore can be used to detect target nucleic acids, and Tang taught a method for using a nanopore to determine the concentration of a desired nucleic acid product. Therefore, the ordinary artisan would have recognized that a solid-state nanopore as described in Tang could be used to conduct the counting step in the method of Sekedat, and accordingly, would have been motivated to select this known method with a reasonable expectation of success. See also MPEP 2144.07, which notes that in the absence of unexpected results, it is prima facie obvious to select a known material or method based on its suitability for the intended purpose. In this case, the ordinary artisan would have expected a solid-state nanopore as taught in Tang to be capable of counting ssDNA products of rolling circle amplification (RCA) since Tang successfully used the disclosed solid-state nanopore to count the products of a loop-mediated amplification reaction (LAMP), which like RCA, generates long single-stranded nucleic acid products.
Lastly, further regarding the pore size of the solid-state nanopore, as noted above, Tang teaches a pore size range that overlaps with the pore size ranges recited in claims 1 and 2. This is sufficient to establish a prima facie case of obviousness per MPEP 2144.05 I since no evidence of unexpected results has been presented with respect to the claimed ranges. And, further regarding claims 1 and 2 and also regarding claims 3 and 4, it also would have been prima facie obvious to use solid-state nanopores with larger diameters when practicing the method suggested by Sekedat in view of Tang. The ordinary would have recognized that the pore size of the solid-state nanopore used in the method was a results-effective variable based on the teachings of Tang at page 7929, and accordingly, would have been motivated to conduct routine experimentation to optimize the size of the nanopore. As discussed in MPEP 2144.05 II, such experimentation is prima facie obvious in the absence of unexpected results, and the ordinary artisan would have had a reasonable expectation of success in producing larger solid-state pores in view of the guidance in Howorka & Siwy. Thus, the methods of claims 1-4 and 6 are prima facie obvious.
Further regarding claim 5, Sekedat does not specify the length of the ssDNA product generated by rolling circle amplification. The reference does teach, though, that rolling circle amplification “results in a long concatemer of single stranded DNA that contains tens to hundreds to thousands of tandem repeats” (page 49, lines 16-19). This teaching in combination with the general knowledge of RCA possessed by the ordinary artisan would render obvious the requirement in claim 5 for the ssDNA product to be more than 70,000 nucleotides in length. In other words, the ordinary artisan would have recognized that RCA typically generates very long ssDNA products and would have been motivated to use routine experimentation to modify the reaction conditions to arrive at any desired length for the ssDNA product of RCA (e.g., the claimed length) with a reasonable expectation of success. Thus, the method of claim 5 is also prima facie obvious.
Further regarding claim 9, it also would have been prima facie obvious to practice the method suggested by Sekedat in view of Tang and further in view of Howorka & Siwy to detect multiple target miRNAs present in a mixture. Sekedat provides motivation to do so by teaching the desirability of multiplexed detection in general (see, e.g., page 46, last para.). The ordinary artisan also would have had a reasonable expectation of success since solid-state nanopores could be provided fabricated in parallel on an array and Tang also suggested the use of multiple parallel nanopores (page 7932, col. 1). Thus, the method of claim 9 is also prima facie obvious.
16. Claims 7 and 8 is rejected under 35 U.S.C. 103 as being unpatentable over Sekedat et al. (WO 2020/206170 A1) in view of Tang et al. (Nano Letters 2019; 19: 7927-7934) and further in view of Howorka & Siwy (Chemical Society Reviews 2009; 38: 2360-2384) and further in view of Di Pietro et al. (Frontiers in Neurology 2018; 9: Article 429; doi:10.3389/fneur.2018.00429).
As discussed above, the teachings of Sekedat in view of Tang and further in view of Howorka & Siwy render obvious the methods of claims 1-6 and 9.
Regarding claim 7, as noted above, Sekedat teaches that the method may be used to detect microRNAs (page 3, lines 23-27). Sekedat also teaches that the method may be used to detect nucleic acids present in a saliva sample (page 27, lines 16-18), but the reference does not clearly teach detecting microRNAs present in a salivary sample. For this reason, the reference also does not teach detecting salivary miRNAs related to mild traumatic brain injury (mTBI).
Regarding claim 8, Sekedat does not disclose any specific miRNAs for detection. Accordingly, the reference fails to teach detecting one or more of let-7a, miR-30e, or miR-21.
Neither Tang nor Howorka & Siwy remedies these deficiencies in Sekedat.
Prior to the effective filing date of the claimed invention, though, it would have been prima facie obvious to use the method suggested by Sekedat in view of Tang and further in view of Howorka & Siwy to detect salivary miRNAs related to mTBI (e.g., miR-21, let-7a, and/or miR-30e). The ordinary artisan would have been motivated to use the method suggested by Sekedat in view of Tang and further in view of Howorka & Siwy to detect any miRNA known to be clinically relevant, recognizing that doing so would increase the number of useful applications of the method. Then, since Di Pietro disclosed a number of clinically relevant miRNAs, including those recited in claim 8 in addition to disclosing clinically relevant mTBI-related salivary miRNAs (pages 4-5 and Table 2), the ordinary artisan would have had motivation and a reasonable expectation of success in applying the method suggested by Sekedat in view of Tang and further in view of Howorka & Siwy to the detection of these miRNA targets. Thus, the methods of claims 7 and 8 are prima facie obvious.
Conclusion
17. No claims are currently allowable.
Dong et al. (NSF Public Access Repository; October 10, 2021) is also cited as a prior art reference of interest. This reference also discloses miRNA counting via rolling circle amplification and nanopore sensing, but the diameter of the nanopore is not disclosed.
Wu et al. (Analytical Chemistry 2021; 93: 16043-16050) is also cited as a prior art reference of interest for its teaching of the use rolling circle amplification and a nanochannel to detect an miRNA target (abstract and Fig. 1). The RCA step and also the detection step differ from those recited in the instant claim 1, however.
Kim et al. (Advanced Materials 2006; 18: 3149-3153) is also cited as a prior art reference of interest for its teachings throughout the reference related to the fabrication of arrays of solid-state nanopores.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Angela Bertagna whose telephone number is (571)272-8291. The examiner can normally be reached 8-5, M-F.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1681
1 As noted above, the effective filing date of the instant claims is September 20, 2022. Accordingly, Dong et al. qualifies as prior art.
2 As noted above, the effective filing date of the instant claims is September 20, 2022. Accordingly, Dong et al. qualifies as prior art.
Prosecution Insights