DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant's election with traverse of group 1, Applicants elect the capture oligonucleotide probe directly immobilized to the solid phase, non- covalent binding to the solid, electrospray ionization (ESI), streptavidin, at least 5 nucleotides, phosphatase, alkaline phosphatase, ammonium bicarbonate, late wherein the surface is selected from polystyrene, AMP, the product ion which is assayed by SIM at 268 m/z,, disuccinimidyl suberate (DSS), in the reply filed on 2/5/2026 is acknowledged. The traversal is on the ground(s) that Applicant respectfully submits that and Group II (claims 46-48) which are directed to a method of quantitating a nucleic acid molecule, rely on claim 1 and include only an additional step to the method of claim 1, namely a step of quantifying the amount of target based on the ionizable targets detected in the multistep method of claim 1. Applicant submits Group I and Group II should be examined together and that it would not impose serious burden on the Examiner to do so. Group III claims have been cancelled. This is not found persuasive because the instant application is a national stage entry of PCT. Thus lack of unity practices not search burden is the determinate of restriction.
Claim 46-49 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention/species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 2/5/2026.
Priority
The instant application was filed 04/26/2023 and is a national stage entry of PCT/CA2021/051510 , International Filing Date: 10/26/2021 PCT/CA2021/051510 and claims priority from provisional application 63105554 , filed 10/26/2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4/29/2024, 10/2/2024, 1/31/2025 are being considered by the examiner.
The IDS of 12/11/2025 cites a Japanese application, but provides WO2010/020750. Thus it is marked through as it does not provide the Japanese application.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Drawings
The drawings are objected to because the figures are not labeled consistent with 37 CFR 1.84 (u) (1) which requires, “The different views must be numbered in consecutive Arabic numerals, starting with 1,independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s). Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter. View numbers must be preceded by the abbreviation “FIG. ” Where only a single view is used in an application to illustrate the claimed invention, it must not be numbered and the abbreviation “FIG. ” must not appear.. 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
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," 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 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) 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") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) 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 of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, 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.
Claim Objections
Claims 1, 3, 8, 16-20, 24, 27, 35, 39, 44, 45 are objected to because of the following informalities:
Claim 1 recites, “a.”, “i.”, “ii.”, “b.”, “c.”, “d.”, “e.”, “f.”, MPEP 608.01(m) states: Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations. See Fressola v.Manbeck, 36 USPQ2d 1211 (D.D.C. 1995).
Appropriate correction is required.
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.
Claim(s) 1, 3, 8, 16-20, 24, 27, 35, 39 is/are rejected under 35 U.S.C. 103 as being unpatentable over Marshall (WO2014186874 A1)
With regards to claim 1, Marshall teaches a method of detecting a target substance comprising immobilizing the target substance to a solid phase, either directly or indirectly via a capture molecule; incubating the immobilized target substance with a reporter enzyme detection probe in solution to form a complex; washing to remove unbound probe; incubating the complex with a substrate for the reporter enzyme to generate ionizable products, and detecting one or more of the ionizable products using mass spectrometry. Marshall teaches the ionizable products may be separated, such as by liquid chromatography, prior to detection. The immobilized target may be incubated with a primary detection agent specific for the target, prior to incubation with the reporter enzyme detection probe to form the complex. The target substance identified in the method of Marshall may be a nucleic acid, and the detection agent or capture molecule may be oligonucleotides. Marshall teaches the target can be nucleic acid. Marshall teaches paragraph [00197] to an enzyme-linked oligosorbent assay in the prior art wherein a nucleic acid target is hybridized to an immobilized capture probe and a horseradish peroxidase- labelled oligonucleotide detection probe. In this prior art assay, capture and detection probes of 18-27 nucleotides, including those with non- overlapping binding regions within the target, are disclosed.
Marshall teaches that nonspecific binding can be reduced by washing with a blocking agent, such as BSA. The wash buffers or binding solutions for the capture molecule, detection probe, and reporter enzyme substrate may be the same, may be salt free, and may include a Tris buffer, depending on the probe and reporter enzyme components selected (see paragraphs [0177]-[0184], [253]).
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to detect nucleic acids by immobilizing the target substance to a solid phase, either directly or indirectly via a capture molecule; incubating the immobilized target substance with a reporter enzyme detection probe in solution to form a complex; washing to remove unbound probe; incubating the complex with a substrate for the reporter enzyme to generate ionizable products, and detecting one or more of the ionizable products using mass spectrometry. Thea artisan would be motivated as Marshall suggests the method. The artisan would have a reasonable expectation of success as the artisan is merely following the teachings of Marshall.
With regards to claim 3, Marshall teaches the target is immobilized to a solid support (00170, 00172, claim 2) Marshall teaches use of streptavidin to bind avidin which is a non-covalent attachment.
With regards to claim 8, Marshall claims, “the step of detecting the one or more
ionizable products using MS comprises ionizing the one or more ionizable products, optionally by electrospray ionization (ESI), MALDI, chemical ionization, electron impact, laser desorption, electrical ionization, or heat ionization to produce one or more product ions with a selected signal to noise ratio and subjecting the one or more product ions to MS optionally tandem MS (MS/MS).” (claim 9).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to have capture oligonucleotide and detection oligonucleotide bound to different regions of the target nucleic acid. The artisan would be motivated to provide have capture oligonucleotide and detection oligonucleotide which do not compete for the sequence and thus maximize the ability to hybridize.
With regards to claim 17, 19-20, Marshall teaches, “[0015] In another embodiment, the reporter enzyme comprises lyase, hydrolase, synthase, synthetase, oxidoreductase, dehydrogenase, oxidase, transferease, isomerase, ligase, protease, such as trypsin, proteinase, peroxidase, glucose oxidase, myeloperoxidase, oxidase, monooxygenase, cytochrome, alkaline phosphatase, decarboxylase, lipase, caspase, amylase, peptidase, transaminase, and/or kinase activity. In another embodiment, the reporter enzyme is selected from DNA or RNA polymerase, TAO, restriction enzymes, klenow fragment and DNA ligase.”
With regards to claim 18, Marshall teaches streptavidin (0016).
With regards to claim 35, Marchall teaches, “[00183] The solid phase can be any reaction vessel, optionally a bead, rod or plate, such as a microtitre plate, for example having a polystyrene surface.”
With regards toc alim 39, Marshall teaches, “[00252] [00209] In an embodiment, the substrate is AMP the product ion of which is assayed 15 by SIM at 268 m/z and/or by SRM of the major intense fragment at 268-136 m/z in the positive ionization mode and by SIM at 266 m/z and/or by SRM of the major intense fragment at 266-134 m/z in the negative ionization mode.”
Claim(s) 44-45 is/are rejected under 35 U.S.C. 103 as being unpatentable over Marshall (WO2014186874 A1) as applied to claims 1, 3, 8, 16-20, 24, 27, 35, 39 above, and further in view of Tinnefeld ( Eur. J. Mass Spectrom. 20, 99–116 (2014)
The teachings of Marshall are set forth above.
While Marshall teaches detection of nucleic acids with alkaline phosphatase by mass spectrometry.
Marshall does not specifically teach crosslinking the nucleic acid to a protein.
However, Tinnefeld provides a review of crosslinking for mass spectroscopy. Tinnefeld teaches “This group of coupling agents mediates the amide/phosphoramidate linkage of primaryamines with carboxylates (e.g., aspartic acid, glutamatic acid,C-terminus) or phosphates and is therefore not limited to protein–protein cross-linking (e.g., oligonucleotide–proteincross-links).” Tinnefeld teaches, “Common NHS esters are not water soluble, but byadding sulfo-groups this problem can be solved.54 Prominentexamples are disuccinimidyl suberate (DSS) and its water-soluble analog bis(sulfosuccinimidyl) suberate (BS3).” (page 103, 2nd column, bottom)
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to cross link the enzyme reporter complex to oligonucleotide. The artisan would be motivated to stabilize the reporter oligonucleotide complex. The artisan would have a reasonable expectation of success as the artisan is merely using known reagents to cross link for mass spectrometry.
Claim(s) 24 and 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Marshall (WO2014186874 A1) as applied to claims 1, 3, 8, 16-20, 24, 27, 35, 39 above, and further in view of Pugia (US2018/0284108)
The teachings of Marshall are set forth above.
While Marshall teaches detection of nucleic acids with alkaline phosphatase by mass spectrometry.
Marshall does not specifically teach the use of ammonium bicarbonate in the buffers.
However, Pugia teaches, “[0149] The spray solvent can be any spray solvent employed in electrospray mass spectroscopy. In some examples, solvents for electrospray ionization include, but are not limited to, polar organic compounds such as, e.g., alcohols (e.g., methanol, ethanol and propanol), acetonitrile, dichloromethane, dichloroethane, tetrahydrofuran, dimethylformamide, dimethylsulphoxide, and nitromethane; non-polar organic compounds such as, e.g., hexane, toluene, cyclohexane; and water, for example, or combinations of two or more thereof. Optionally, the solvents may contain one or more of an acid or a base as a modifier (such as, volatile salts and buffer, e.g., ammonium acetate, ammonium bicarbonate, volatile acids such as formic acid, acetic acid, trifluoroacetic acid, heptafluorobutyric acid, sodium dodecyl sulphate, ethylenediamine tetraacetic acid, and non-volatile salts or buffers such as, e.g., chlorides and phosphates of sodium and potassium, for example.”
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to use ammonium bicarbonate in the buffers. The artisan would have been motivated as Pugia teaches ammonium bicarbonate is a volatile salt that is used as a spray solvent buffer for mass spectroscopy. The artisan would have a reasonable expectation of success as the artisan is merely using known buffers.
Summary
No claims are allowed.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEVEN C POHNERT PhD whose telephone number is (571)272-3803. The examiner can normally be reached Monday- Friday about 6:00 AM-5:00 PM, every second Friday off.
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, Anne Gussow can be reached at (571)272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Steven Pohnert/ Primary Examiner, Art Unit 1683
Prosecution Insights