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 .
The preliminary amended claims dated 3/27/2024 are under consideration.
Election/Restrictions
Applicant's election with traverse of Group II, claims 1, 2, 4, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39 and 40, in the reply filed on 7/13/2026 is acknowledged. The traversal is on the ground(s) that Morin does not teach the elements of claim 1. This is not found persuasive because even if applicant is correct regarding the Morin reference, Aksimentiev (US 2019/0062814 A1; cited on the 3/27/2024 IDS) demonstrates that the elements of claim 1 do not make a contribution over the prior art as demonstrated in the 102 rejections below.
Upon further review, claim 10 is included with the election of Group II.
The requirement is still deemed proper and is therefore made FINAL.
Claims 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31 and 32 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 7/13/2026.
Priority
The present application is a 371 national stage entry of PCT/GB2022/052466 (filed 9/29/2022) and claims benefit to UNITED KINGDOM 2113935.7 (filed 9/29/2021).
It is noted that differences are present between the foreign priority document and the present application. The present application includes more claims, a longer specification and more figures than the foreign priority document.
Drawings
The drawings are objected to because Fig. 3 includes sequences that are not identified with a SEQ ID NO.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
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 - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings. Fig. 3 does not include SEQ ID NOs for the disclosed sequences as noted above.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specification
The amendments to the specification addressing priority claims of the application are acknowledged.
Claim Objections
Claim 1 is objected to because of the following informalities: the claim recites “each linearising unit comprised a docking strand” rather than “each linearising unit comprises a docking strand”. Appropriate correction is required.
Claim 27 is objected to because of the following informalities: the claim recites “the method comprised characterizing one or more RNA transcript” rather than “the method further comprises characterizing one or more RNA transcript”. Appropriate correction is required.
Claim 34 is objected to because of the following informalities: the claim recites “the method further understood characterizing the length” rather than “the method further comprises characterizing the length”. Appropriate correction is required.
Claim Interpretation
Claims 8, 18, 21, 22, 23, 24, 25, 26, 27, 36 and 40 each include elements that are introduced as being “optionally” included as part of the claimed method. Claim scope is not limited by claim language that makes optional but does not require steps to be performed. MPEP 2111.04.
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 7, 18, 21, 27 and 34 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.
Regarding claim 7, the claim recites “the sequence of…structural color(s)”. The recitation lacks proper antecedent because no “structural color(s)” to produce a “sequence” are previously set forth in the in claim.
Regarding claim 18, the phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the optional limitations of the claim. See MPEP § 2173.05(d).
Regarding claim 21, the claim recites “structural color(s)”. The recitation lacks proper antecedent because no “structural color(s)” are previously described as being along the target nucleic acid.
Regarding claim 27, based on the use of the past tense phrase “the method comprised characterizing…”. It is unclear whether the claim requires an active method step of “characterizing…” or is setting forth a previous intended use of the claimed method.
Regarding claim 34, based on the use of the past tense phrase “the method further understood characterizing…”. It is unclear whether the claim requires an active method step of “characterizing…” or is setting forth a previous intended use of the claimed method.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1, 2, 4, 6, 7, 8, 9, 10, 18, 19, 21, 22, 27, 33, 34 and 35 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Aksimentiev (US 2019/0062814 A1; cited on the 3/27/2024 IDS).
Regarding claims 1 and 19, Aksimentiev teaches multiple approaches to “contacting” a target nucleic acid with “one or more linearizing unit(s)” in the form of nucleic acid nanoparticles or NANPs. The “contacting” of Aksimentiev results in “providing one or more structural units(s) interspaced by one or more regions of double-stranded nucleic acid”.
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One approach is depicted in Fig. 25, reproduced below with annotations provided by the Examiner in italics:
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Another set of approaches are depicted in Fig. 27, reproduced below with annotations provided by the Examiner in italics:
Aksimentiev further teaches detecting the “structural units” using a nanopore (Fig. 25; and para. 14).
Regarding claim 2, Aksimentiev teaches the “structural unit” is provided by the “linearizing unit” directly (Fig. 27, top panel or Fig. 25) or indirectly, (Fig. 27, bottom panel).
Regarding claim 4, as depicted in Fig. 25 the “linearising unit” includes a “docking strand” that hybridizes with the target nucleic acid and a “labeling region” comprised of a nucleic acid structure, such as a cube or ring.
Alternatively, as depicted in Fig. 27, the “linearising unit” includes a “docking strand” that hybridizes with the target nucleic acid and a “labeling region” that hybridizes with a strand associated with a nucleic acid structure, such as a cube or ring.
Regarding claim 6, Aksimentiev teaches the “structural units” provide a signal that is distinct from other structural units, e.g., a cube that is distinct from a ring (Fig. 4; and para. 49). Thus, Aksimentiev teaches everything sufficient to provide “one or more structural color(s)”.
Regarding claim 7, Aksimentiev teaches detecting the sequence of the structural units along the target nucleic acid using a nanopore as noted above.
Regarding claims 8 and 9, Aksimentiev teaches the “target nucleic acid” in the form of a biomarker is mRNA, i.e., an RNA transcript, or microRNA (para. 90).
Regarding claim 10, Aksimentiev teaches characterizing more than one “target nucleic acid” biomarkers as depicted in Fig. 25 above.
Regarding claim 18, Aksimentiev teaches the “labeling region” includes a “structural label”, such as a nucleic acid cube or nucleic acid ring, as noted above.
Regarding claim 21, Aksimentiev teaches the nanopore distinguishes between “structural units” based on their size and influence of the current detected by the nanopore (Fig. 4; and para. 49, 107 and 112).
Regarding claim 22, Aksimentiev teaches quantifying the concentration of a biomarker as a “target nucleic acid” (para. 102).
Regarding claim 27, the claim characterizes the method as “comprised charactering”. The claim does not positively set forth an active method step. The claim is interpreted as setting forth a previous intended use. Claim 27 is anticipated for the same reason as claim 1.
Regarding claim 33, Aksimentiev teaches the “linearising unit” minimizes unwanted secondary structure in the analyte target sequence (para. 72 and claim 10), which reshapes an RNA biomarker into a linear RNA that has “structural units” interspaced with double stranded nucleic acids as depicted in Fig. 25 and 27 reproduced above.
Regarding claims 34 and 35, the claim characterizes the method as “further understood charactering”. The claim does not positively set forth an active method step. The claim is interpreted as setting forth a previous intended use. Claim 34 is anticipated for the same reason as claim 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 23, 24, 25, 26, 36, 37, 38, 39 and 40 is/are rejected under 35 U.S.C. 103 as being unpatentable over Aksimentiev (US 2019/0062814 A1; cited on the 3/27/2024 IDS) in view of Zhang (CN 111118226 A).
Regarding claims 23, 24, 25, 26, 36, 37, 38, 39 and 40, Aksimentiev teaches multiple approaches to “contacting” a target nucleic acid with “one or more linearizing unit(s)” in the form of nucleic acid nanoparticles or NANPs. The “contacting” of Aksimentiev results in “providing one or more structural units(s) interspaced by one or more regions of double-stranded nucleic acid”.
One approach is depicted in Fig. 25, reproduced above with annotations provided by the Examiner in italics.
Another set of approaches are depicted in Fig. 27, reproduced above with annotations provided by the Examiner in italics.
Aksimentiev further teaches detecting the “structural units” using a nanopore (Fig. 25; and para. 14).
While Aksimentiev teaches the above methods, Aksimentiev does not teach the source of the RNA biomarkers.
However, Zhang teaches a number aspects related to the detection of RNA.
Regarding claims 23 and 26, Zhang teaches detecting RNA from virus pathogens was known (p. 4 of translation).
Regarding claim 24 and 26, Zhang teaches detecting RNA from coronavirus pathogens was known (p. 4 of translation).
Regarding claim 25, Zhang teaches detecting RNA from microorganisms such as fungi was known (p. 3 of translation).
Regarding claim 36 and 37, Zhang teaches bronchoalveolar lavage fluid or lung tissue biopsy specimen is known clinical samples from a subject (p. 5).
Regarding claim 38, 39 and 40, Zhang teaches extracting RNA from a sample (p. 5 of translation). It is recognized that extracting RNA involves heating and lysing of samples to release nucleic acids from cells, such as human cells in a lung biopsy, and viruses, such as coronaviruses.
It would have been prima facie obvious at the time of filing to the ordinary artisan to have modified the generic method of Aksimentiev for the detection of the known target nucleic acids of Zhang. One would have been motivated to do so in order to detect specific RNA that are relevant to human health and well-being. The modification has a reasonable expectation of success because it involves designing the generic NANPs for the detection of particular molecules. Design nucleic acid sequences that hybridize with known targets is within the skill level of the ordinary artisan.
Conclusion
No claims allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682
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