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 .
Claim Status/Action Summary
This action is in response to the papers filed on July 24, 2024.
Claims 1-20 are pending and under examination. No other claims are currently pending in the present application.
Priority/Effective filing date
The present application, 18/872,100, filed on July 24, 2024, claims priority to U.S. Provisional Patent Application No. 53/515,924, filed on July 27, 2023.
It is noted that the following claim terms do not appear in, and do not appear to be supported by, the provisional application: “contacting… with a third hairpin and a fourth hairpin”, “a hyperbranched chain connected to the [magnetic nanoparticle]”, and “the dye molecules comprise NIR-780”. Therefore, claims requiring these elements (claims 4-5 and 17) are determined to have the benefit of the July 24, 2024 as effective filing date.
Information Disclosure Statement
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.
It is noted that no information disclosure statement has been filed in the present application as of the mailing date of this action.
Drawings
The drawings dated July 24, 2024 are acceptable.
Specification
Applicant is reminded of the proper content of an abstract of the disclosure.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives.
Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps.
Extensive mechanical and design details of an apparatus should not be included in the abstract. The abstract should be in narrative form and generally limited to a single paragraph within the range of 50 to 150 words in length.
See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts.
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because of the presence of phrases which can be implied. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Interpretation
Claim 17 recites the claim term “NIR-780”. This dye appears to be known in the art (Zhang et al., “Mitochondria-Targeting IR-780 Dye and its Derivatives: Synthesis, Mechanisms of Action, and Theranostic Applications” Advanced Therapeutics 2018, 1, 1800069) as having the following chemical structure:
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Claim 18 requires “the method has a limit of detection (LoD) of about 10 femtomolar.” It is noted that in particular preferred embodiments and in working examples in the specification (e.g. claim 3), several different “limits of detection” are taught for cardiac Troponin I (cTnI) detection using purified cTnI. These concentrations are expressed in different units which are interconverted below for clarity of the record using the molecular weight of cTnI known in the art (24007 g/mol), Orbulescu et al., “Human Cardiac Troponin I: A Langmuir Monolayer Study” Langmuir 2010, 26(5), 3268-3274. It is further noted that the scope of claim 1 is not limited to human cardiac troponin I, but appears to encompass any “biomarker in a clinical sample”.
Claim 18: “10 femtomolar”
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i.e. 10 femtomolar cTnI is equal to 240.07 picograms per microliter cTnI.
Paragraph 0065-0072: “Femtomolar Detection of Cardiac Troponin I using Colorimetry”… “aptamer was incubated with different concentrations (5 ng/µL to 5 fg/µL) of cardiac troponin I in PBS for 30 minutes…”
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i.e. the colorimetric detection titration includes the claimed limit of detection “10 femtomolar”, which is equivalent to 240.07 pg/µL.
Paragraph 0081-0084: “Determination of the LoD of the assay using SERRS”…“the estimated detection limit, based on the IUPAC 3 sigma/m criteria, is 0.5 pg/mL”
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i.e. 0.5 picograms per milliliter is equivalent to 0.0005 picograms per microliter (alternatively expressed as 0.5 femtograms per microliter).
Paragraph 101: “Using this aptamer-based hyperbranched HCR approach for cTnI quantification using a low-cost, small form factor imaging/reader system, the limit of detection (LoD) has been calculated to be 0.117 ng/mL”
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i.e. 0.117 nanograms per milliliter is equivalent to 0.117 picograms per microliter.
Therefore, it appears that the method of claim 13 (when applied to cTnI) requires colorimetric detection, as the LoD reported for other exemplary detection methods (e.g. SERRS, hyperbranched HCR) do not have “a limit of detection of about 10 femtomolar”.
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.
Claims 10, 12, and 18 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 10 recites “the one or more reagents comprise hemin, hydrogen peroxide, 3,3’,5,5’-tetramethylbenzidine (TMB), or any combination thereof, and a substrate, wherein the hemin induces stabilization of the catalytic trimeric triplex, and wherein the stabilized catalytic trimeric triplex has horseradish peroxidase activity in the presence of the hydrogen peroxide and the substrate.” The claim language appears to require the reagents comprise: a) at least one of hemin, hydrogen peroxide, and TMB; and b) a substrate.
However, the functionally defined wherein clause appears to require the combination of at least hemin and hydrogen peroxide with the substrate because this clause requires that the stabilized catalytic trimeric triplex has [HRP] activity.
Furthermore, it is unclear to what “a substrate” refers, as this term is recited in addition to at least one of “hemin, hydrogen peroxide, TMB, or any combination thereof”.
The instant specification teaches “the amplicons from the hybridization chain reaction can be incubated with hemin to obtain a stable triplex structure that has horseradish peroxidase-like activity in the presence of hydrogen peroxide and specific substrates such as [ABTS or TMB].” (i.e. inclusion of hemin is required for HRP-like activity, and TMB is a substrate).
Therefore, the scope of “substrates” and “the one or more reagents” is indefinite because it is unclear what elements are minimally required under the broadest reasonable interpretation of the claims as presently written.
Similarly, claim 12, which depends from claim 10, requires that “the substrate comprises [ABTS] and wherein the [HRP] activity produces a color in the presence of the hydrogen peroxide and the ABTS. It is unclear whether this claim requires the combination of hemin, hydrogen peroxide, TMB, and the substrate (which is further limited to “comprises ABTS”), or is somehow intended to encompass (a) sub-combination(s) not requiring all of these elements.
Regarding claim 18, which depends from claim 1, the methods are not limited to any particular biomarker or aptamer or reagent(s) to produce a detectable signal. Claim 18 further limits the methods “wherein the method has a limit of detection (LoD) of about 10 femtomolar.” It is unclear what additional method steps or limitations upon the effectively unlimited genera “aptamer”, “biomarker”, and/or “reagents” are required to differentiate methods that do not have the recited limit of detection from those that do. Furthermore, the ordinary artisan would not be meaningfully apprised as to the breadth of these claim terms as further limited by the recited limit of detection.
Claim Rejections - 35 USC § 103
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.
Claims 1-2, 6-7, and 10-14 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al., “A label-free and signal-amplifiable assay method for colorimetric detection of carcinoembryonic antigen” Biotechnol Bioeng. 2022; 119:504-512 in view of Borsa et al., “Staphylococcus aureus detection in blood samples by silica nanoparticle-oligonucleotides conjugates” Biosensors and Bioelectronics 86 (2016) 27-32.
Regarding claim 1, Li et al. teach methods comprising detecting a biomarker in a clinical sample comprising contacting the sample with two hairpin probes (“HP1” and “HP2” with partial complementarity to each other, an aptamer locked in a double-stranded conformation with a “blocker” that comprises an “initiator” sequence for a hybridization chain reaction (HCR) between the “blocker” and the two hairpin probes (Li et al., figure 1, reproduced below). Li et al. further teach that in the presence of the aptamer ligand (e.g. CEA), the aptamer-blocker/initiator duplex is opened (i.e. the conformation of the aptamer is changed), triggering HCR between the blocker/initiator and the two hairpin probes, and the resulting trimeric triplex HCR product is a DNAzyme comprising hemin-binding G-quadruplex structures with “peroxidase-like activity” (Li et al., figure 1).
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Finally, Li et al. teach the resulting stabilized trimeric triplex DNAzymes are detected by contacting the DNAzymes with reagents comprising ABTS, which is oxidized by the DNAzyme and produces a colored product that is proportional to the amount of ligand (e.g. CEA) in the sample (Li et al., page 507, column 1, paragraph 2).
Li et al. do not teach that the aptamer-blocker/initiator complex is bound to a magnetic nanoparticle.
However, Borsa et al. teach methods for detection of analytes comprising aptamer-functionalized silica magnetic nanoparticles (Borsa et al., page 28, column 1, paragraph 5 “Synthesis of silica coated magnetic nanoparticles” – page 29, column 1, paragraph 1).
Borsa et al. further teach that the method for detection of analyte with aptamers bound to magnetic nanoparticles is advantageous because the capacity for magnetic separation and signal detection allows for easy incorporation into automated systems in portable devices (Borsa et al., page 32, column 1, paragraph 2).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods for detection of biomarkers with biomarker-specific aptamers comprising signal amplification by HCR- and peroxidase-like trimeric triplex DNAzyme, taught by Li et al. with the teachings of Borsa et al. that aptamers for specific detection of biomarkers can be easily bound to magnetic nanoparticles. The ordinary artisan would have been motivated to modify the methods of detection comprising aptamer binding specific biomarker ligands with the teachings of Borsa et al. comprising binding such aptamers to magnetic nanoparticles because of the teaching of Borsa et al. that coupling aptamers to magnetic nanoparticles predictably facilitates incorporation of such aptamer-based detection methods into automated portable devices.
Regarding claim 2, Li et al. teach the biomarker is a protein (Carcinoembryonic Antigen (CEA)). Further, Borsa et al. teach the biomarker is a bacterium (Staphylococcus aureus).
Regarding claim 6, Borsa et al. teach the magnetic nanoparticle comprises iron oxide (Fe3O4) (Borsa et al., page 29, column 2, paragraph 2).
Regarding claim 7, Borsa et al. teach the iron oxide nanoparticles are co-precipitated with amino-functionalized APTES silica (Borsa et al., page 29-30, bridging paragraph).
Regarding claim 10, Li et al. teach the detection reagents comprise hemin, hydrogen peroxide, and a substrate (ABTS), wherein the hemin stabilizes the catalytic trimeric triplex having horseradish peroxidase-like activity in the presence of hydrogen peroxide (Li et al., figure 1).
Regarding claims 11-14, Li et al. teach the detectable signal comprises a color, wherein the intensity of the color (i.e. absorbance) changes proportionally with the amount of biomarker present in the clinical sample (Li et al., figure 5, reproduced below).
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Claims 3 and 18-19 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. in view of Borsa et al. as applied to claims 1-2, 6-7, and 10-14 above, and further in view of Wong et al., “Direct immunomagnetic detection of low abundance cardiac biomarker by aptamer DNA nanocomplex” Sensors & Actuators: B. Chemical 291 (2019) 200-206.
The teachings of Li et al. in view of Borsa et al. are described above.
Regarding claim 3, Li et al. in view of Borsa et al. do not teach the biomarker is cardiac troponin I.
However, Wong et al. teach methods for detecting cardiac troponin I (cTnI) in clinical samples comprising binding an aptamer, two hairpin probes with partial complementarity to each other, and cTnI to an APTES-coated iron oxide magnetic nanoparticle (Wong et al., page 201, column 2, paragraph 2-page 202, paragraph 2), wherein the cTnI-bound aptamer initiates HCR with the two hairpin probes.
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods comprising detection of biomarkers in clinical samples comprising CEA or S. aureus using aptamers that specifically bind to said biomarkers with the teachings of Wong et al. comprising specifically detecting cTnI in clinical samples using an aptamer that binds to cTnI.
The ordinary artisan would have been motivated to utilize a cTnI aptamer in place of the CEA or S. aureus aptamers taught by Li et al. in view of Borsa et al. because of the teachings of Wong et al. that cTnI detection is the “gold standard” of myocardial infarction diagnosis relative to more expensive, slow, and less specific methods such as electrocardiography and MRI imaging (Wong et al., page 200, column 1). Furthermore, the cTnI detection using the rapid and less expensive aptamer-based methods taught by Wong et al. facilitates sequential testing of cTnI serum levels, which is advantageous because the level of these biomarkers continues to increase from the onset of myocardial infarction through about 30 hours post-infarct, and “measurement of serum cTnI level at multiple timepoints… enhances diagnostic performance” (Wong et al., page 200, column 2).
Regarding claim 18, Wong et al. teach the HCR-amplified limit of detection for cTnI (without further enzymatic enhancement of signal) using total internal reflection fluorescence microscopy has a limit of detection of 8.5 fM (i.e. about 10 fM) (Wong et al., page 201, column 1, paragraph 2).
Regarding claim 19, Wong et al. teach the method is for identifying myocardial infarction in a clinical sample from a subject, wherein the biomarker is cardiac troponin I (Wong et al., abstract).
Claims 4-5 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. in view of Borsa et al. as applied to claims 1-2, 6-7, and 10-14 above, and further in view of Ravan et al., “DNAzyme-embedded hyperbranched DNA dendrimers as signal amplifiers for colorimetric determination of nucleic acids” Microchimica Acta (2018) 185:443.
Regarding claims 4-5, Li et al. in view of Borsa et al. do not teach the method further comprises contacting the nanoparticle, aptamer, and sample with a third and fourth hairpin that forms a hyperbranched chain connected to the magnetic nanoparticle producing an increased signal intensity relative to the unbranched HCR product.
However, Ravan et al. teach methods for amplification of signal generated by HCR assembly of a trimeric triplex DNAzyme sequence having peroxidase activity in the presence of hydrogen peroxide, wherein the HCR further branches to generate chain branching growth of the DNAzyme-embedded DNA dendrimer (Ravan et al., abstract and scheme 2).
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Ravan et al. demonstrate the signal-amplification property using a biotinylated capture probe bound to a streptavidin-coated surface to detect a target DNA that hybridizes to an “adaptor” polynucleotide that initiates hyperbranching HCR, forming multiple stabilized trimeric triplexes in the presence of hemin and ABTS which results in the formation of a colored ABTS-oxidation product (Ravan et al., page 2, column 2, paragraph 2 and scheme 2).
Ravan et al. teach “the given signal amplification system offers a universal platform for the detection of other target nucleic acids by easily altering the adaptor and capturing oligonucleotides”.
Finally, Ravan et al. teach the hyperbranching HCR- and DNAzyme- amplified method for biomarker (e.g. DNA) detection has a detection limit as low as 0.8 fM (Ravan et al., page 5, column 1-2 bridging paragraph).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods taught by Li et al. in view of Borsa et al. comprising HCR- and peroxidase-like DNAzyme- signal amplification of aptamer binding to biomarker ligands with the teachings of Ravan et al. comprising a “universal signal amplification system” comprising hyperbranching HCR- and peroxidase-like DNAzyme signal amplification of polynucleotide hybridization. The ordinary artisan would have been motivated to modify the HCR signal amplification in the methods taught by Li et al. in view of Borsa et al. with the hyperbranching signal amplification taught by Ravan et al. because of the teachings of Ravan et al. that hyperbranching DNAzyme signal amplification allows for a dramatically improved limit of detection (0.8 fM) and is easily adapted to different detection systems by altering the adaptor and capturing oligonucleotides.
Claims 8-9 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. in view of Borsa et al. as applied to claims 1-2, 6-7, and 10-14 above, and further in view of Jo et al., “Electrochemical Aptasensor of Cardiac Troponin I for the Early Diagnosis of Acute Myocardial Infarction” Analytical Chemistry. 2015, 87, 9869-9875.
Regarding claims 8 and 9, Li et al. in view of Borsa et al. teach methods for biomarker detection in clinical samples comprising aptamer-linked, APTES-functionalized, silica-coated iron oxide magnetic nanoparticles (Borsa et al., page 28, column 1, paragraph 5 “Synthesis of silica coated magnetic nanoparticles” – page 29, column 1, paragraph 1).
Li et al. in view of Borsa et al. teach the aptamers are coupled to the magnetic particles by activating the APTES-amino groups with glutaraldehyde and coupling with amino-modified aptamers (Borsa et al., page 28, column 2, paragraph 3).
Li et al. in view of Borsa et al. do not teach that the nanoparticle is further coated with streptavidin and the aptamer is biotinylated and the aptamer is coupled to the nanoparticle through the streptavidin-biotin binding interaction.
However, Jo et al. teach methods for immobilizing cTnI aptamers to silica-coated iron oxide magnetic nanoparticles comprising coupling biotin-modified aptamer primers to streptavidin-coated magnetic beads.
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods taught by Li et al. in view of Borsa et al. comprising coupling aptamers to magnetic nanoparticles through the reaction between amino-modified APTES activated with glutaraldehyde (i.e. a cross-linker) and amino-modified aptamer with the teaching of Jo et al. that aptamers can conveniently be linked to magnetic nanoparticles through a biotin-streptavidin interaction, wherein the aptamer is biotinylated and the beads are coated with streptavidin. The ordinary artisan would have been motivated to modify the nanoparticle-aptamer functionalization steps taught by Li et al. in view of Borsa et al. because of the teachings of Jo et al. that biotin-modified polynucleotides (i.e. aptamers) are captured from biological sample solutions with streptavidin-modified magnetic beads under very mild chemical conditions (5mM Tris-HCl, pH 7.5, 1 M NaCl, 0.5 mM EDTA, and 0.0025% (v/v) Tween-20) at room temperature for 1 h) relative to more chemically controlled methods taught by Li et al. in view of Borsa et al. comprising treatment of amino-modified particles with an aldehyde crosslinker followed by coupling of amino-modified aptamer with the resulting aldehyde-activated particles.
Claims 15-17 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. in view of Borsa et al. as applied to claims 1-2, 6-7, and 10-14 above, and further in view of Sun et al., “A nanoscale DNA-Au dendrimer as a signal amplifier for the universal design of functional DNA-based SERS biosensors” Chem. Commun., 2011, 47, 3840-3842, and Nagy-Simon et al., “IR780-dye loaded gold nanoparticles as new near infrared activatable nanotheranostic agents for simultaneous photodynamic and photothermal therapy and intracellular tracking by surface enhanced resonant Raman scattering imaging” Journal of Colloid and Interface Science 517 (2018) 239-250.
Regarding claims 15-17, Li et al. in view of Borsa et al. do not teach the one or more reagents comprise a gold particle, the detectable signal comprises Raman scattering, and wherein the gold particle comprises a gold nanosphere or nanostar.
However, Sun et al. teach methods of detecting biomarkers using surface-bound aptamers comprising hyperbranched HCR signal amplification triggered by aptamer-biomarker binding, wherein the branch-chaining “reporter DNAs” (analogous to the hairpins taught by Li et al. in view of Borsa et al.) comprise gold nanoparticles, and the signal is detected by surface-enhanced Raman scattering (SERS) (Sun et al., page 3840, column 1 and scheme 1). Sun et al. further teach detection of adenosine using these methods and a known anti-adenosine aptamer. Sun et al. teach the SERS-enhanced signal detection resulted in a lower limit of detection than for reported fluorescent adenosine sensors or for amplified sensing methods based on a DNAzyme with peroxidase activity (Sun et al., figure 1 and page 3842, paragraph 1).
Similarly, Nagy-Simon et al. teach SERS reporters with improved properties for biomarker detection in clinical samples including successful detection and SERRS imaging of biomarker distribution in mouse models, resected tumor samples, and cultured cells (Nagy-Simon et al., page 245, column 1, paragraph 3-4). Nagy-Simon et al. teach these improved SERS reporters comprise gold nanospheres or nanostars wherein dye molecules are embedded within a silica shell surrounding a gold nanoparticle core (Nagy-Simon et al., page 245, column 1, paragraph 3-4). Finally, Nagy-Simon et al. teach the embedded dye molecules are “IR780” (i.e. “NIR-780”), which has advantageous spectral properties related to the transparency of human tissue in the near-infrared “NIR” range (Nagy-Simon et al., abstract).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods taught by Li et al. in view of Borsa et al. comprising HCR- and DNAzyme- signal amplification of detection of biomarkers using aptamers coupled to magnetic nanoparticles (i.e. a surface) with the teachings of Sun et al. and the teachings of Nagy-Simon et al. that a) inclusion of hyperbranching reporter DNAs comprising gold nanoparticles allows for Raman scattering detection of the biomarker that significantly improves the limit of detection relative to HCR- and DNAzyme- signal amplification alone (Sun et al) and b) IR780-dye loaded gold nanospheres and nanostars advantageously allow for high-resolution detection of biomarkers in a wide variety of biological samples and in living organisms (Nagy-Simon et al.). The ordinary artisan would have been motivated to modify the methods taught by Li et al. and Borsa et al. with the methods comprising gold nanoparticle hyperbranching reporters taught by Sun et al. because of the teachings of Sun et al. that detection of aptamer binding of biomarkers comprising SERS biosensors (i.e. gold nanoparticles) predictably improves the limit of detection of such assays and because of the teachings of Nagy-Simon et al. that IR780-loaded gold nanospheres and nanostars allow for live cell imaging via surface-enhanced resonance Raman scattering microscopy (SERRS).
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Li et al. in view of Borsa et al. and Wong et al. as applied to claims 3 and 18-19 above, and further in view of Mohammed et al., “Clinical Applications of Highly Sensitive Troponin Assays” Cardiology in Review 18:1, page 12-19, 2010 and Anderson et al., “Asymptomatic ST elevation myocardial infarction” Heart & Lung (2018) 363-365.
Regarding claim 20, which depends from claim 19, Li et al. in view of Borsa et al. and Wang et al. teach methods of identifying myocardial infarction in a clinical sample from a subject comprising binding a cardiac troponin I (cTnI)-specific aptamer to a magnetic nanoparticle, contacting a sample with the aptamer-nanoparticle complex and a pair of hairpin oligonucleotides that undergo hybridization chain reaction (HCR) initiated by a conformation change in the aptamer triggered by aptamer binding to cTnI, wherein the HCR generates a hemin-binding trimeric triplex DNAzyme with peroxidase-like activity in the presence of hydrogen peroxide that generates a detectable signal in the presence of a substrate (e.g. ABTS).
Li et al. in view of Borsa et al. and Wang et al. do not teach that the identified myocardial infarction is asymptomatic.
However, Anderson et al. teach that while witnessing an ongoing asymptomatic ST elevation myocardial infarction is rare, in a case report, a sub-threshold cTnI level of 8.31 ng/mL preceded a near-threshold reading 16 minutes later (without symptoms) of 35.9 ng/mL and the patient was found to have 99% stenosis of the mid left anterior descending coronary artery (Anderson et al., page 364, column 1).
Furthermore, Mohammed et al. teach cTnI is only found in cardiac muscle and not in skeletal muscle (Mohammed et al., page 12, column 2, paragraph 3) and that cTnI is released into circulation from damaged myocytes (muscle cells) (Mohammed et al., page 12, column 2, paragraph 4). Mohammed et al. teach methods for detecting cTnI at concentrations far below the 99th percentile cutoff used for definitive diagnosis of myocardial infarction that comprise identifying acute coronary syndrome, acute myocardial infarction, and identifying subjects at increased risk for inpatient mortality in the presence or absence of an acute coronary syndrome diagnosis (e.g. asymptomatic myocardial infarction) (Mohammed et al., page 17-18).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods for highly sensitive detection of cTnI for diagnosis of myocardial infarction taught by Li et al. in view of Borsa et al. and Wang et al. with the teachings of Anderson et al. and Mohammed et al. that detection of cTnI below the recognized cutoff for myocardial infarction diagnosis accompanied a case of asymptomatic ST elevation myocardial infarction and that slightly elevated cTnI levels predicted higher risk of mortality among inpatients with and without acute coronary syndrome. The ordinary artisan would have been motivated to detect asymptomatic myocardial infarction using the methods taught by Li et al. in view of Borsa et al. and Wang et al. because of the suggestion of Mohammed et al. that “These assays have enormous potential in not only identifying more patients with acute myocardial infarction, and providing superior risk prediction in those so afflicted, in addition highly sensitive troponins assays may be useful for long-term risk assessment of the patient with coronary disease.” Furthermore, the ordinary artisan would have been motivated to apply the highly sensitive cTnI assays taught by Li et al. in view of Borsa et al. and Wang et al. to asymptomatic myocardial infarction by the case study described by Anderson, wherein the asymptomatic patient’s cTnI was still below the cutoff of 40 ng/mL immediately prior to a finding of near-complete coronary artery blockage.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Asl et al., “Recent Advances in the Fabrication of Nano-aptasensors for the Detection of Troponin as a Main Biomarker of Acute Myocardial Infarction” Critical Reviews in Analytical Chemistry, published online September 2, 2021
Daubert et al., “The utility of troponin measurement to detect myocardial infarction: review of the current findings” Vascular Health and Risk Management 2010:6 691-699.
Du et al., “G-Quadruplex-based DNAzyme for colorimetric detection of cocaine: Using magnetic nanoparticles as the separation and amplification element” Analyst, 2011, 136 , 493-497.
Hao et al., “Amplified colorimetric detection of mercuric ions through autonomous assembly of G-quadruplex DNAzyme nanowires” Biosensors and Bioelectronics 52 (2014) 261-264
He et al., “Aptasensors for Biomarker Detection” Journal of Analytical Chemistry, 2022, Vol. 77, No. 12, 1481-1496.
Kamali et al., “The recent advancements in the early detection of cancer biomarkers by DNAzyme-assisted aptasensors” Journal of Nanobiotechnology (2022) 20:438.
Khan et al., “DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective” ACS Nano 2021, 15, 13943-13969.
Komarova et al., “Aptamers targeting Cardiac Biomarkers as an Analytical Tool for the Diagnostics of Cardiovascular Diseases: A Review” Biomedicines 2022, 10, 1085.
Lee et al., “Development of the Troponin Detection System Based on the Nanostructure” Micromachines 2019, 10, 203.
Lee et al., “Fabrication of electrochemical biosensor consisted of multi-functional DNA structure/porous au nanoparticle for avian influenza virus (H5N1) in chicken serum” Materials Science & Engineering C 99 (2019) 511-519.
Li et al., “A sensitive colorimetric DNA biosensor for specific detection of the HBV gene based on silver-coated glass slide and G-quadruplex-hemin DNAzyme” J Med Virol. 2018; 90:699-705.
Liu et al., “A sensitive colorimetric aptasensor based on trivalent peroxidase-mimic DNAzyme and magnetic nanoparticles” Analytica Chimica Acta 1018 (2018) 86-93.
Mi et al., “The TDs/aptamer cTnI biosensors based on HCR and Au/Ti3C2-Mxene amplification for screening serious patient in COVID-19 pandemic” Biosensors and Bioelectronics 192 (2021) 113482.
Ravan, “Isothermal RNA detection through the formation of DNA concatemers containing HRP-mimicking DNAzymes on the surface of gold nanoparticles” Biosensors and Bioelectronics 80 (2016) 67-73.
Shahbazi et al., “A facile and rapid aptasensor based on split peroxidase DNAzyme for visual detection of carcinoembryonic antigen in saliva” Sensors and Actuators B 253 (2017) 794-803.
Shatunova et al., “Aptamers for Proteins Associated with Rheumatic Diseases: Progress, Challenges, and Prospects of Diagnostic and Therapeutic Applications”. Biomedicines 2020, 8, 527.
Tang et al., “Colorimetric and Ultrasensitive Bioassay Based on a Dual-Amplification System Using Aptamer and DNAzyme” Analytical Chemistry 2012, 84, 4711-4717.
Wu et al., “Colorimetric detection of proteins based on target-induced activation of aptazyme” Analytica Chimica Acta 942 (2016) 68-73.
Zhao et al., “A label-free fluorescent aptasensor based on HCR and G-quadruplex DNAzymes for the detection of prostate-specific antigen” Analyst, 2021, 146, 1340.
Tu et al., US 20220134340 A1
Gordon et al., US 20180106791 A1
Zhao et al., US 20160231324 A1
Dirks et al., US 8105778 B2
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/Z.M.T./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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