DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 7/18/2024 has been considered by the examiner.
Claim Objection
Claims 1, 4-6, and 10-13 are objected to because of the following informalities:
Claim 1: please amend “the single nanohole structure” (three places) to -- the at least one single nanohole structure--; “the dual nanohole structure” (three places) to -- the at least one dual nanohole structure--; “the nanopore” (seven places) to -- the at least one nanopore--.
Claims 4-5: please amend “measuring change in current and/or phase” to -- measuring the change in current and/or phase--; “a translocating analyte” to – [[a]] the translocating analyte--.
Claim 6: please amend “the single nanohole structure” (two places) to -- the at least one single nanohole structure--; “the dual nanohole structure” (two places) to -- the at least one dual nanohole structure--.
Claim 10: please amend “pMHC” to full name of pMHC followed by the abbreviation of pMHC in parentheses.
Claim 11: please amend “HLA-A2” to full name of HLA-A2 followed by the abbreviation of HLA-A2 in parentheses.
Claim 12: please amend “TCRm” to full name of TCRm followed by the abbreviation of TCRm in parentheses.
Claim 13: please amend “where in” to – wherein—by removing the space between “where” and “in”.
Appropriate correction is required.
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 1-19 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as failing to set forth 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 1, claim 1 recites “one or more of the analytes”, and also recites “an analyte” and “the analyte”. Thus it is unclear if there is only one analyte or plural analytes. Therefore, the scope of claim 1 is indefinite. Claims 2-19 are further rejected by virtue of their dependence upon and because they fail to cure the deficiencies of indefinite 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 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.
Claims 1-4 and 6-13 are rejected under 35 U.S.C. 103 as being unpatentable over Alexandrakis et al. (US20200393456A1), and in view of Stefureac (Stefureac R.I., Nanopore analysis of peptides and proteins, Ph.D. thesis of the University of Saskatchewan, 2012).
Regarding claim 1, Alexandrakis teaches a method of sensing (a method of sensing [abstract]; a method of sensing [claim 27]) comprising:
providing a sensor (contacting the test sample with the first layer of the sensor of claim 1 [claim 27]; a sensor [claim 1]; Figs. 1 and 4) comprising:
a first layer having at least one dual nanohole structure (a first layer having at least one dual nanohole structure [claim 1]), and
a second layer having at least one nanopore (a second layer having at least one nanopore [claim 1]),
wherein the dual nanohole structure comprises a first nanohole and a second nanohole connected by a gap (wherein the dual nanohole structure comprises a first nanohole and a second nanohole connected by a gap [claim 1]), and
wherein the gap of the first layer is aligned with the nanopore of the second layer in a direction corresponding to a translocation direction across the first and second layers (wherein the gap of the first layer is aligned with the nanopore of the second layer in a direction corresponding to a translocation direction across the first and second layers [claim 1]);
providing a test sample comprising an analyte (providing a test sample comprising complexed and/or non-complexed biomolecules [claim 27]);
contacting the test sample with the first layer of the sensor (contacting the test sample with the first layer of the sensor of claim 1 [claim 27]);
irradiating the dual nanohole structure of the first layer of the sensor with a beam of electromagnetic radiation (irradiating the dual nanohole structure of the first layer of the sensor with a beam of electromagnetic radiation [claim 27]);
optically trapping the analyte in the dual nanohole structure and/or in the gap of the first layer of the sensor (optically trapping the biomolecules in the dual nanohole structure and/or the gap of the first layer of the sensor [claim 27]);
applying a second electric field across the nanopore, wherein the second electric field comprises an alternating current (AC) electric field (applying an electric field across the nanopore of the second layer of the sensor [claim 27]; the voltage can be applied across the sensor as an AC field. For example, an AC field of frequencies up to 1 GHz can be applied to Ag/AgCl electrodes by an external function generator and detected by Axopatch electronics [para. 0073]); and
measuring change in current across the nanopore during application of the second electric field while the analyte is optically trapped and/or during one or more translocation events of the analyte through the nanopore (measuring change in current across the nanopore during one or more translocation events of the biomolecules [claim 27]; measuring change in current across the nanopore during one or more translocation events; the one or more translocation events of biomolecules includes biomolecules that were first optically trapped [para. 0076]).
Alexandrakis is silent to: (1) applying a first electric field across the nanopore to draw one or more of the analytes into the nanopore, wherein the first electric field comprises a direct current (DC) electric field; and (2) the second electric field applied across the nanopore after applying the first electric field.
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Stefureac teaches a method of sensing [Symbol font/0x61]-helica peptides through nanopores by applying a first electric field across the nanopore, wherein the first electric field comprises a direct current (DC) electric field (see “first electric field” in annotated Fig.3.7B3, which is a DC field [section 3.2.1]); and (2) the second electric field (see “second electric field” in annotated Fig.3.7B3 which is an AC field [section 3.2.1]) applied across the nanopore after applying the first electric field (see annotated Fig.3.7B3).
Alexandrakis and Stefureac are considered analogous art to the claimed invention because they are in the same field of sensing an analyte based on translocation of the analyte through a nanopore. It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method in Alexandrakis by providing a first electric field applied across the nanopore, wherein the first electric field comprises a direct current (DC) electric field; and the second electric field is applied across the nanopore after applying the first electric field, as taught by Stefureac, since it would yield a stable membrane and consistent parameters over time (the first paragraph on page 95 in Stefureac).
The limitation “to draw one or more of the analytes into the nanopore” is an intended result of a positively recited step. The court noted that a "‘whereby clause in a method claim is not given weight when it simply expresses the intended result of a process step positively recited.’" Id. (quoting Minton v. Nat’l Ass’n of Securities Dealers, Inc., 336 F.3d 1373, 1381, 67 USPQ2d 1614, 1620 (Fed. Cir. 2003)). MPEP 2111.04(I).
Regarding claim 2, modified Alexandrakis teaches the method of claim 1, and wherein the at least one kinetic parameter is measured while the analyte decelerates or comes to a stop while optically trapped (claim 1 recites “measuring one or more of:
change in current and/or phase across the nanopore during application of the second electric field while the analyte is optically trapped and/or during one or more translocation events of the analyte through the nanopore; or at least one kinetic parameter of the analyte within the nanopore after removing or turning off the second electric field”, and therefore, the limitation “wherein the at least one kinetic parameter is measured while the analyte decelerates or comes to a stop while optically trapped” of instant claim 2 is further limiting an optional step of measuring at least one kinetic parameter of claim 1, and is not further limiting the step of measuring change in current).
Regarding claim 3, modified Alexandrakis teaches the method of claim 1, wherein the at least one kinetic parameter comprises one or more of the following: equilibrium dissociation constant (Kd), binding on-rate (kon), binding off-rate (koff), and bound fraction (claim 1 recites “measuring one or more of:
change in current and/or phase across the nanopore during application of the second electric field while the analyte is optically trapped and/or during one or more translocation events of the analyte through the nanopore; or at least one kinetic parameter of the analyte within the nanopore after removing or turning off the second electric field”, and therefore, the limitation “wherein the at least one kinetic parameter comprises one or more of the following: equilibrium dissociation constant (Kd), binding on-rate (kon), binding off-rate (koff), and bound fraction” of instant claim 3 is further limiting an optional step of measuring at least one kinetic parameter of claim 1, and is not further limiting the step of measuring change in current).
Regarding claim 4, modified Alexandrakis teaches the method of claim 1, and Alexandrakis teaches wherein measuring the change in current further comprises determining a charge of the translocating analyte (the change in current provides information about the charge of the translocating biomolecule [para. 0076]).
Regarding claim 6, modified Alexandrakis teaches the method of claim 1, and Alexandrakis teaches further comprising: measuring a surface plasmon resonance of the dual nanohole structure after optically trapping the analyte in the dual nanohole structure (optically trapping the biomolecules in the dual nanohole structure of the first layer of the sensor and measuring a surface plasmon resonance of the dual nanohole structure [para. 0065]; wherein measuring the surface plasmon resonance further comprises determining the mass of an optically trapped biomolecule [para. 0184]).
Regarding claim 7, modified Alexandrakis teaches the method of claim 6, and Alexandrakis teaches wherein measuring the surface plasmon resonance further comprises determining the mass of an optically trapped analyte (wherein measuring the surface plasmon resonance further comprises determining the mass of an optically trapped biomolecule [para. 0184]).
Regarding claim 8, modified Alexandrakis teaches the method of claim 1, and Alexandrakis teaches wherein the analyte comprises complexed and/or non-complexed biomolecules (providing a test sample comprising complexed and/or non-complexed biomolecules [claim 27]).
Regarding claim 9, modified Alexandrakis teaches the method of claim 1, and Alexandrakis teaches wherein the test sample is a biological sample obtained from an animal or human subject (Analysis and quantification of these biomolecules lead to better understanding of the biological processes of the human body [para. 0094]; HLA (Human) [para. 0153]; To evaluate the sensor, several initial studies use purified MHC-peptide ligands and TCR-like antibodies. The following recombinant MHC/peptide ligands were synthesized and purified: HLA-A2/CEA, HLA-A2/p68, and HLA-A2/Her2 [para. 0151]).
Regarding claim 10, modified Alexandrakis teaches the method of claim 9, and Alexandrakis teaches wherein the analyte comprises a pMHC or pMHC component (MHC/peptide [para. 0151]).
Regarding claim 11, modified Alexandrakis teaches the method of claim 9, wherein the analyte comprises a HLA-A2 pHMC or HLA-A2 pMHC component (HLA-A2/CEA, HLA-A2/p68, and HLA-A2/Her2 [para. 0151], which are HLA-A2 peptide-major histocompatibility complex [pMHC]).
Regarding claim 12, modified Alexandrakis teaches the method of claim 9, and Alexandrakis teaches wherein the analyte comprises a TCRm antibody (TCR-like antibodies [para. 0151]).
Regarding claim 13, modified Alexandrakis teaches the method of claim 9, and Alexandrakis teaches where in the analyte comprises a TCRm antibody against a HLA-A2 pHMC or against a HLA-A2 pHMC component (The TCR-like antibodies specific for the three HLA-peptide complexes: HLA-A2/CEA, HLA-A2/p68, and HLA-A2/Her2 [para. 0151-0152]).
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Alexandrakis and Stefureac, as applied to claim 1 above, and further in view of Liu et al. (A Fourier Transform-Induced Data Process for Label-Free Selective Nanopore Analysis under Sinusoidal Voltage Excitations, Analytical Chemistry, 2020, 92, 11635-11643).
Regarding claim 14, modified Alexandrakis teaches the method of claim 1, and is silent to wherein the analyte comprises an inorganic nanoparticle.
Liu teaches sensing inorganic nanoparticles such as SiO2, Ag, and Au nanoparticles based on the measured change in current of the inorganic nanoparticle translocating through a nanopore under an AC electric field (title, abstract, Fig.2, and section of Translocation events of nanoparticles with the Fourier transform sinusoidal method).
Modified Alexandrakis and Liu are considered analogous art to the claimed invention because they are in the same field of sensing an analyte based on translocation of the analyte through a nanopore. It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the analyte in modified Alexandrakis with inorganic nanoparticles such as SiO2, Ag and Au nanoparticles, as taught by Liu, since Liu teaches the nanopore-based sensing method would allow to sense/detect solid inorganic nanoparticles in addition to soft living organisms (Conclusions).
Claims 15-19 are rejected under 35 U.S.C. 103 as being unpatentable over Alexandrakis and Stefureac, as applied to claim 1 above, and further in view of Meller et al. (US20200171489A1).
Regarding claims 15-19, modified Alexandrakis teaches the method of claim 1, and is silent to: (1) wherein the test sample is concentrated prior to contacting the test sample with the first layer of the sensor (of claim 15); wherein the test sample is concentrated using isotachophoresis (ITP) (of claim 16); and (3) wherein the test sample is concentrated using an ITP microchannel structure (of claim 17); (4) wherein the ITP microchannel structure is disposed over the first layer of the sensor (of claim 18); and (5) wherein the ITP microchannel structure forms a unitary chip with the first layer and the second layer of the sensor (of claim 19).
Meller teaches device and method for improved single-molecule detection. The method of detecting molecules of interest comprising running the molecules through the electrokinetic focusing apparatus and then detecting the focused molecules as they pass through the nanopore (title and abstract). According to a first aspect, there is provided a device for detecting a molecule of interest comprising: a. a nanopore apparatus, the nanopore apparatus comprising at least one ion-conducting nanopore; b. an electrokinetic focusing apparatus, the electrokinetic focusing apparatus comprising a microchannel, a first electrode and a second electrode, wherein the first and second electrodes are configured to produce an electric field in the microchannel; c. at least one sensor or capturing element configured for at least one of: i. detecting a position of the molecule of interest within the microchannel; and ii. capturing the molecule of interest in a region of the microchannel proximal to the nanopore; wherein the electrokinetic focusing apparatus and the nanopore apparatus are in fluidic contact via the nanopore [para. 0009; claim 1]; wherein the electrokinetic focusing apparatus is an ITP apparatus (claim 2). Figs. 1A-1C show the ITP microchannel structure for concentrating the concentration of the target analyte prior to be detected by the nanopore [para. 0085-0086], and the ITP microchannel structure is disposed over array of nanopores (see Figs. 3A-3B). Electrodes 107 and 110 are configured to generate an electrical field in the fluidics layer to induce isotachophoresis. There is a third electrode 111 for generating an electric field in the Z direction, to enable translocation through the nanopore [para. 0090]. Figs.1 and 3A-3B show that the ITP microchannel structure forms a unitary chip with the nanopore sensor.
Modified Alexandrakis and Meller are considered analogous art to the claimed invention because they are in the same field of nanopore-based detection of an analyte translocating through the nanopore. Given the teachings of Alexandrakis regarding contacting the test sample with the first layer of the sensor; and the teachings of Meller regarding concentrating the test sample prior to contacting the test sample with the nanopore-based sensor, wherein the test sample is concentrated using isotachophoresis (ITP), the test sample is concentrated using an ITP microchannel structure disposed over the nanopore-based sensor, and the ITP microchannel structure forms a unitary chip with the nanopore sensor, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method and the sensor in modified Alexandrakis by further concentrating the test sample using ITP prior to contacting the test sample with the first layer of the sensor (claims 15-16), wherein the test sample is concentrated using an ITP microchannel structure (claim 17) disposed over the first layer of the sensor (claim 18), and the ITP microchannel structure forms a unitary chip with the first layer and the second layer of the sensor (claim 19), as taught by combined Alexandrakis and Meller, since nanopore-based detection is limited in sensitivity when detecting rare/low-concentration analytes, and the modified method and sensor would improve detection of target molecules at a low concentration in a solution [para. 0003 and 0082 in Meller].
Allowable Subject Matter
Claim 5 would be allowable if they are rewritten or amended to overcome the rejection(s) under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), 2nd paragraph, set forth in this Office action.
The following is a statement of reasons for the indication of allowable subject matter.
Regarding claim 5, modified Alexandrakis teaches the method of claim 1.
Stefureac further teaches A10 peptide has a significant dipole moment while CY12(-)T2 in a liner conformation has no permanent dipole (the last paragraph in section 3.2.1). From the results present above it becomes apparent that peptide molecules possessing different dipole moments indeed have differently when in an AC environment than in an exclusive DC environment (section 3.2.3 on page 96). These results have important implication for understanding the transportation of polymers through pores and may allow the development of biosensors which can discriminate different molecules based on differences in dipole moment (the last paragraph in section 4.3 on page 167; and the 2nd paragraph in section 4.7 on page 183).
Liu (the reference for claim 14 above) teaches the measured current signals for SiO2, Au and Ag NPs are different, and Table S1 shows that their dielectric constants are different.
Wen et al. (A guide to signal processing algorithms for nanopore sensors, ACS Sensors, 2021, 6, 3536-3555) teaches simple physical models can be utilized to correlate the amplitude of spikes to the size and shape of analytes; to relate the duration to the translocation speed and nanopore-analyte interaction that in turn are connected to the physiochemical properties such as mass, charge, dipole and hydrophobicity, and to associate the frequency of spikes to the concentration of analytes at a given bias voltage (Step 4. Analyte identification in Col. 2 on page 3540). Fig. 1 shows the applied electric field is DC electric field. Thus, Wen teaches estimating dipole moment of the analyte which is related to the dielectric constant of the analyte based on the change in current across the nanopore during the application of a DC electric field instead of an AC electric field.
The prior art of the record does not teach and/or suggest wherein measuring the change in current further comprises determining a dielectric constant of the translocating analyte.
As allowable subject matter has been indicated, applicant's reply must either comply with all formal requirements or specifically traverse each requirement not complied with. See 37 CFR 1.111(b) and MPEP § 707.07(a).
Conclusion
The prior arts made of record and not relied upon are considered pertinent to applicant's disclosure: Corbera (EP3349005A1) teaches a method of sensing translocating analytes through nanopores under AC, DC or combined electric fields. Zhang et al. (US20110037486A1) teaches high frequency capacitance measurement on a single strand of DNA or RNA. Edel et al. (US20180164205A1) teaches an apparatus and associated method for concentration of polarizable molecules within a fluid medium under DC-biased AC electric field (Fig.2). Qian et al. (US 20120097539A1) teaches a nanoparticle translocation device for sensing the nanoparticle. Lathrop et al. (Monitoring the Escape of DNA from a Nanopore Using an Alternating Current Signal, J. Am. Chem Soc., 2010, 132, 1878-1885) teaches a first DC electric field followed by a second AC electric field applied across a nanopore for sensing analyte translocating through a nanopore (see Fig.1).
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/SHIZHI QIAN/Examiner, Art Unit 1795
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