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 .
Response to Amendment
Applicant’s amendment and remark filed on 07/02/26 has been entered. Claims 1-20 remain pending and examined herein. Applicant’s amendment and remark have overcome each and every rejection under 112(b) set forth in Office Action mailed on 04/08/26.
Status of Rejection
The double patenting rejection of claims 1-7, 13, and 20 is withdrawn in view of Applicant’s Amendment.
The 112(b) rejection of claims 13 and 20 is withdrawn in view of Applicant’s Amendment.
The double patenting rejection of claims 12 and 14-19 is maintained.
The 102 and 103 rejections of claim 12-19 in view of Goto 3 (US 2018/0074006 A1) are maintained.
The amendment necessitates new ground of rejection for claims 1-11 and 20.
Double Patenting
Claims 12 and 14-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 15, 16, 17, 17, and 19-21 of U.S. Patent No. 12429449 B2 (Akahori). Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding claim 12, Claim 15 of Akahori discloses a biomolecule analyzing reagent for use in analyzing a biomolecule by allowing the biomolecule to pass through a nanopore with a diameter in a range of ±20% of a diameter of the biomolecule, wherein the biomolecule analyzing reagent contains ammonium ions and sulfate ions (claim 15).
Regarding claim 14, Akahori discloses the claimed invention as discussed above in claim 12. Claim 16 of Akahori discloses the biomolecule analyzing reagent is an ammonium sulfate solution, and the ammonium sulfate has a concentration of 0.01 M or more and a saturation concentration or less (identical wording).
Regarding claims 15-16, Akahori discloses the claimed invention as discussed above in claim 14. Claim 17 of Akahori discloses the ammonium sulfate has a concentration of 0.1 M or more and a saturation concentration or less and a concentration of 1 M or more and a saturation concentration or less (wherein an ammonium sulfate concentration of the ammonium sulfate solution is 0.01 M or more and 1 M or less, claim 17).
Regarding claims 17-19, Akahori discloses the claimed invention as discussed above in claim 12. Claims 19-21 of AKahori disclose the biomolecule analyzing reagent contains ammonium sulfate and another salt as salts, and a ratio of a concentration of the ammonium sulfate to a total concentration of the salts is 5/25/50% or more and less than 100% (identical wording).
Claim Rejections - 35 USC § 102
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.
Claim(s) 12 and 13 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Goto 3 (US 2018/0074006 A1).
Regarding claim 12, Goto 3 discloses a biomolecule analyzing reagent contains ammonium ions and sulfate ions (para. [0034]).
Regarding claim 13, Goto 3 discloses the claimed invention as discussed above in claim 1. The limitation of the biomolecule analyzing reagent is further used in degrading the biopolymer into the biomolecules is a recitation of intended use. Manner of operating an apparatus does not differentiate apparatus claim from the prior art. A claim containing a “recitation with respect to the manner in which a claimed apparatus is intended to be employed does not differentiate the claimed apparatus from a prior art apparatus” if the prior art apparatus teaches all the structural limitations of the claim (MPEP 2114, II). A recitation of intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 13 is/are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claim recites the “biomolecule analyzing reagent further degrades the biopolymer into the biomolecule”, which implies a function/reaction. However, upon examination of the specification, there is no support of the biomolecule analyzing reagent materially participates in the degradation reaction. At best, the degradation happens within the electrolyte solution, but specification provides no indication the degradation involves reaction between the biopolymer and the biomolecule analyzing reagent.
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.
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.
Claim(s) 1--11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Goto 1 (Silicon nitride nanopore created by dielectric breakdown with a divalent cation: deceleration of translocation speed and identification of single nucleotides, 2019) in view of Goto 2 (Solid-state nanopores towards single-molecule DNA sequencing, 2020) and Goto 3 (US 2018/0074006 A1) as cited in previous Office Action and Schurmann (Decomposition of DNA Nucleobases by Laser Irradiation of Gold Nanoparticles Monitored by Surface-Enhanced Raman Scattering, 2016).
Regarding claim 1, Goto 1 discloses a biomolecule analysis method (Abstract; Nanopore DNA sequencing with a solid-state nanopore…) comprising:
preparing a biomolecule analysis device (nanopore devices, Experimental, Nanopore fabrication with dielectric breakdown, Page 14427, right col.) that includes a thin film having a nanopore (Si3N4 film; We used substrates with a 5 nm-thick Si3N4 membrane for the nanopore devices shown in Fig. S1. Experimental, Nanopore fabrication with dielectric breakdown, Page 14427, left col.; Fig. S1, Supplementary Information, SI-1. Device structure for silicon nitride nanopore fabrication, page S2) with a diameter in a range of +-20% of a diameter of a biomolecule (1 nm; This means that three different nanopores have the almost the same 1.0 nm size. Fig. 2 caption, Page 14429), a first liquid tank and a second liquid tank separated by the thin film (The cleaned and hydrophilized substrates were assembled into a custom-made flow cell with two chambers… Experimental, Nanopore fabrication with dielectric breakdown, Page 14427, left col.; Supplementary Information, Fig. S1, page S2; the 5 nm Si3N4 film in between the two chambers), a first electrode disposed in the first liquid tank, a second electrode disposed in the second liquid tank (Both chambers were filled with various electrolyte solutions for CBD…Two Ag/AgCl electrodes (cis and trans electrodes) were immersed in the solutions… Experimental, Nanopore fabrication with dielectric breakdown, Page 14427, right col., para. 1), and
applying a voltage between the first electrode and the second electrode in a state where a measurement solution (a 1 M or 4 M CsCl solution buffered with 10 mM Tris-HCl at pH 7.5) is enclosed in the first liquid tank and the second liquid tank, and measuring a current flowing between the first electrode and the second electrode (The solutions in both chambers were replaced with a 1 M or 4 M CsCl solution buffered with 10 mM Tris-HCl at pH 7.5 containing 50 nM ssDNA or 1 μM dNMPs. Ionic currents were measured with a patch-clamp amplifier (Axopatch 200B, Axon Instruments, Union City, CA) at applied voltages ranging from 0.1 to 0.5 V. Experimental, ssDNA translocation measurements, page 14428).
Though Goto 1 discloses the method is applicable to both DNA (interpreted as claimed biopolymer) and nucleotide monomers (dNMPs) (interpreted as claimed biomolecule; Nucleotide monomers (dNMPs) were similarly measured as described above in the same setup. Experimental, ssDNA translocation measurements, page 14428), Goto 1 does not specify a biopolymer degradation mechanism. Furthermore, Goto does not disclose the measuring solution containing ammonium ions and sulfate ions.
In an analogous art, Goto 2 discloses a single molecule DNA sequencing method using solid-state nanopores in the same manner as Goto 1 (Abstract and Fig. 3(b), Goto 2). Goto 2 describes an alternative method of measuring different dNMPs producing different signals. The method involves having the DNA strand decomposed from one end by an exonuclease to generate individual dNMPs, as another promising sequencing method ( Bayley’s group have demonstrated exonuclease-assisted nanopore sequencing, as shown in Fig. 5a [75]. The concept is that different 2-deoxyribonucleoside 5′-monophosphates (dNMPs) become distinct electrical signals when individual dNMPs are cleaved from one end of a DNA strand by an exonuclease. Other promising sequencing techniques, p. 73, right column, from the bottom, p. 74, left column, line 6, fig.5(a)).
In another analogous art, Schurmann discloses a process of fragmentation of DNA target molecules by laser irradiation in a solution (Abstract; Experimental Section, Preparation of Gold and Silver Nanoparticles).
It would have been obvious to one of ordinary skills in the art before the effective filing date to have introduced laser degradation of Schurmann as a degradation mechanism for DNA target molecule for Goto 1. Degrading/decomposing target molecules into smaller fragment/ssDNA prevents clogging by allowing the fragment to go through the nanopore (Goto 2, Principle of nanopore sequencing, para. 1-2).
The combination of Goto 1 and Goto 2 and Schurmann does not disclose the measurement solutions contain ammonium ions and sulfate ions. Goto 1 discloses the measurement solution comprises cesium and chloride ions (Experimental, ssDNA translocation measurements, page 14428).
In another art by Goto, Goto 3 discloses a biomolecule analysis method (Abstract) comprising:
preparing a biomolecule analysis device (Fig. 1) that includes a thin film (thin membrane 103, Fig. 1) having a nanopore (nanopore 104, Fig. 1) with a diameter in a range of +-20% of a diameter of a biomolecule (0.9 nm to 10 nm, para. [0029]), a first liquid tank (first tank 102a, Fig. 1) and a second liquid tank (second tank 102b, Fig. 1) separated by the thin film (See Fig. 1), a first electrode disposed in the first liquid tank (first electrode 105, Fig. 1) a second electrode disposed in the second liquid tank (second electrode 106, Fig. 1), and
applying a voltage between the first electrode and the second electrode in a state where a measurement solution (solution 101, Fig. 1) is enclosed in the first liquid tank and the second liquid tank (A voltage is applied on at least either one of the electrodes 105 and 106 to cause a difference in potential, para. [0037]), and measuring a current flowing between the first electrode and the second electrode (whereby an ion current is induced to detect the measurement object. para. [0037]),
wherein the electrolytes in the measurement solution can contain cesium, chloride, ammonium, and sulfate ions (para. [0034]).
As all the arts cited by Goto share same lead researcher and feature of performing sequencing of polynucleotides and measurement using nanopores, it would have been obvious to one of ordinary skill in the art before the effective filing date to have substituted the CsCl measurement solution of the method of Goto 1 in view of 2 with ammonium and sulfate ions as taught by Goto 3 to yield a predictable results of measuring the current the nucleotides as Goto 3 discloses the electrolytes in the measurement solution are not limited to cesium and chloride ions, and ions like ammonium and sulfate can serve as alternatives (Goto 3, para. [0034]).
Regarding claim 2, Modified Goto discloses the claimed invention as discussed above in claim 1. Gotos discloses the biomolecule analysis method further comprising, applying, before preparing the biomolecule analysis device, a voltage between the first electrode and the second electrode, in a state where a nanopore forming solution is enclosed in the first liquid tank and the second liquid tank (Both chambers were filled with various electrolyte solutions for CBD (controlled dielectric breakdown. For divalent cation solutions, 1 M CaCl2, MgCl2, BaCl2, and SrCl2 aqueous solutions buffered with 10 mM Tris-HCl at pH 7.5 were used Goto 1, Experimental, Nanopore fabrication with dielectric breakdown, p. 14427), to form the nanopore in thin film (The dielectric breakdown procedure was controlled by a program written using Excel Visual Basic for Applications. The applied voltage and pulse duration were optimized to fabricate a nanopore with the desired diameter. Goto 1, Experimental, Nanopore fabrication with dielectric breakdown, p. 14427; Fig. 2(b) and Fabrication of an ultrasmall solid-state nanopore, para. 3 in Goto 2; In this case, examples of a method for forming a pore in the thin membrane include a method by electron beam irradiation by transmission electron microscope and the like and a method by dielectric breakdown by voltage application. Para. [0029], Goto 3); and
Wherein the nanopore forming solution contains ammonium ions and sulfate ions (Goto 3 after incorporation into the method of Goto 1 and 2; para. [0034]).
Regarding claim 3, Modified Goto discloses the claimed invention as discussed above in claim 1. Goto 1 discloses wherein the biopolymer is a nucleic acid (ssDNA, Experimental, ssDNA translocation measurements, page 14428), the biomolecule is a nucleotide (dNMPs, Experimental, ssDNA translocation measurements, page 14428), and the diameter of the nanopore is 1 nm or less (1 nm; This means that three different nanopores have the almost the same 1.0 nm size. Fig. 2 caption, Page 14429).
Regarding claim 4, Modified Goto discloses the claimed invention as discussed above in claim 1. Goto 1 the diameter of the nanopore is 1 nm or less (1 nm; This means that three different nanopores have the almost the same 1.0 nm size. Fig. 2 caption, Page 14429) (Note: Goto 3 also discloses when a fine particle is mentioned as the measurement object, a nanopore having a diameter that is 10% or more larger than the diameter of the fine particle similar to the diameter of the fine particle is preferred. Para. [0029]).
Regarding claim 5-10, Modified Goto 1 discloses the claimed invention as discussed above in claim 1. Goto 1 does not teach the specific concentrations as claimed in claims 5-10. Goto 1 discloses the need to control/slow the speed of DNA during signal detection (This speed is usually faster than 1 μs per base,18,19 which cannot be recorded with commercially available amplifiers.20 … For instance, the features of a solution, such as viscosity,21 temperature,22 species of electrolyte23,24 and gradient concentration of electrolyte,25 have been adjusted to slow the speed of DNA movement. Introduction). It would have been obvious to one of ordinary skill in the art before the effective filing date to have routinely experimented the concentration of the electrolyte solution of ammonium and sulfate of Goto 3 in Modified Goto (after incorporation with Goto 1 and 2) to derive the claimed ranges. Deriving an optimum concentration as claimed allows for deceleration of the DNA molecules movement for detection (This slowing effect was similarly observed using other ssDNA sequences (Fig. S4†), and a highly concentrated electrolyte solution was preferred because it not only increases the ionic current but also decelerates the ssDNA movement speed more than a low-concentration electrolyte solution when using an ultrasmall nanopore. Deceleration of ssDNA translocation speed with divalent-cation nanopore, para. 2). Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." See MPEP 2144.05 and In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).
Regarding claim 11, Modified Goto discloses the claimed invention as discussed above in claim 1. Goto discloses the thin film contains silicon nitride (Goto 1, Abstract; Goto 3, para. [0003]).
Claim(s) 14-19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Goto 3 in view of Goto 1.
Regarding claims 14-19, Goto 3 discloses the claimed invention as discussed above in claim 12. Goto 3 teaches the electrolyte may contain a sulfate ion and an ammonium ion, among other possible ions/salts ([0034]).
Goto 3 does not teach specific concentrations.
In an analogous art, Goto 1 discloses a biomolecule analysis device/method (Abstract; Nanopore DNA sequencing with a solid-state nanopore…) comprising:
preparing a biomolecule analysis device (nanopore devices, Experimental, Nanopore fabrication with dielectric breakdown, Page 14427, right col.) that includes a thin film having a nanopore (Si3N4 film; We used substrates with a 5 nm-thick Si3N4 membrane for the nanopore devices shown in Fig. S1. Experimental, Nanopore fabrication with dielectric breakdown, Page 14427, left col.; Fig. S1, Supplementary Information, SI-1. Device structure for silicon nitride nanopore fabrication, page S2) with a diameter in a range of +-20% of a diameter of a biomolecule (1 nm; This means that three different nanopores have the almost the same 1.0 nm size. Fig. 2 caption, Page 14429), a first liquid tank and a second liquid tank separated by the thin film (The cleaned and hydrophilized substrates were assembled into a custom-made flow cell with two chambers… Experimental, Nanopore fabrication with dielectric breakdown, Page 14427, left col.; Supplementary Information, Fig. S1, page S2; the 5 nm Si3N4 film in between the two chambers), a first electrode disposed in the first liquid tank, a second electrode disposed in the second liquid tank (Both chambers were filled with various electrolyte solutions for CBD…Two Ag/AgCl electrodes (cis and trans electrodes) were immersed in the solutions… Experimental, Nanopore fabrication with dielectric breakdown, Page 14427, right col., para. 1).
Goto 1 discloses the need to control/slow the speed of DNA during signal detection (This speed is usually faster than 1 μs per base,18,19 which cannot be recorded with commercially available amplifiers.20 … For instance, the features of a solution, such as viscosity,21 temperature,22 species of electrolyte23,24 and gradient concentration of electrolyte,25 have been adjusted to slow the speed of DNA movement. Introduction).
Both Goto 1 and 3 share same lead researcher and feature of performing sequencing of polynucleotides and measurement using nanopores. It would have been obvious to one of ordinary skill in the art before the effective filing date to have routinely experimented the concentration of the electrolyte solution of ammonium and sulfate of Goto 3 in Modified Goto (after incorporation with Goto 1 and 2) to derive the claimed ranges. Deriving an optimum concentration as claimed allows for deceleration of the DNA molecules movement for detection (This slowing effect was similarly observed using other ssDNA sequences (Fig. S4†), and a highly concentrated electrolyte solution was preferred because it not only increases the ionic current but also decelerates the ssDNA movement speed more than a low-concentration electrolyte solution when using an ultrasmall nanopore. Deceleration of ssDNA translocation speed with divalent-cation nanopore, para. 2).
Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05 II A).
Claim(s) 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Goto 3 (US 2018/0074006 A1) in view of Goto 2 (Solid-state nanopores towards single-molecule DNA sequencing, 2020) and Schurmann.
Regarding claim 20, Goto 3 discloses a biomolecule analysis device (Fig. 1) comprising:
a thin film (thin membrane 103, Fig. 1) in which a nanopore (nanopore 104, Fig. 1) with a diameter in a range of +-20% of a diameter of a biomolecule (0.9 nm to 10 nm, para. [0029]) is to be formed,
a first liquid tank (first tank 102a, Fig. 1) and a second liquid tank (second tank 102b, Fig. 1) separated by the thin film (See Fig. 1) and contain an electrolyte solution (solution 101, Fig. 1),
a first electrode disposed in the first liquid tank (first electrode 105, Fig. 1), and
a second electrode disposed in the second liquid tank (second electrode 106, Fig. 1),
wherein the measurement solution contains ammonium ions and sulfate ions (para. [0034]).
Goto 3 does not disclose specify a biopolymer degradation mechanism as claimed.
In an analogous art, Goto 2 discloses a single molecule DNA sequencing method using solid-state nanopores in the same manner as Goto 3 (Abstract and Fig. 3(b), Goto 2). Goto 2 describes an alternative method of measuring different dNMPs producing different signals. The method involves having the DNA strand decomposed from one end by an exonuclease to generate individual dNMPs, as another promising sequencing method (Bayley’s group have demonstrated exonuclease-assisted nanopore sequencing, as shown in Fig. 5a [75]. The concept is that different 2-deoxyribonucleoside 5′-monophosphates (dNMPs) become distinct electrical signals when individual dNMPs are cleaved from one end of a DNA strand by an exonuclease. Other promising sequencing techniques, p. 73, right column, from the bottom, p. 74, left column, line 6, fig.5(a)).
In another analogous art, Schurmann discloses a process of fragmentation of DNA target molecules by laser irradiation in a solution (Abstract; Experimental Section, Preparation of Gold and Silver Nanoparticles).
It would have been obvious to one of ordinary skills in the art before the effective filing date to have introduced laser degradation of Schurmann as a degradation mechanism for DNA target molecule for Goto 3. Degrading/decomposing target molecules into smaller fragment/ssDNA prevents clogging by allowing the fragment to go through the nanopore (Goto 2, Principle of nanopore sequencing, para. 1-2).
Response to Arguments
Applicant’s arguments, see Page 8, filed 07/02/26, with respect to the double patenting rejection of claims 1-7 and 20 have been fully considered and are persuasive. The double patenting rejection of claims 1-7 and 20 has been withdrawn.
Applicant's arguments filed 07/02/2026 have been fully considered but they are not persuasive. In the remark, the applicant argues that the arts of record do not teach the newly amended limitation for claims 12-19. The limitation recites the degradation mechanism being hydrochloric, pyrophosphoric acid, and laser in the preamble. Applicant’s arguments rely on language solely recited in preamble recitations in claim(s) 12. When reading the preamble in the context of the entire claim, the recitation is not limiting because the body of the claim describes a complete invention and the language recited solely in the preamble does not provide any distinct definition of any of the claimed invention’s limitations. Thus, the preamble of the claim(s) is not considered a limitation and is of no significance to claim construction. See Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See MPEP § 2111.02. Essentially, despite the preamble, the claim solely requires a composition comprising ammonium and sulfate ions.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/M.H./Examiner, Art Unit 1758
/REBECCA M FRITCHMAN/Primary Examiner, Art Unit 1758
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