DETAILED ACTION
Response to Amendment
Applicant’s response to the office action filed on December 18, 2025 has been entered. The claims pending in this application are claims 31-47 and 49 wherein claims 34, 40, 41, and 44-46 have been withdrawn due to the restriction requirement in the office action on June 18, 2025. The objections and rejections not reiterated from the previous office action are hereby withdrawn in view of applicant’s amendments filed on December 18, 2025. Claims 31-33, 35-39, 42, 43, 47, and 49 will be examined.
Claim Objections
Claim 35 or 36 or 37 is objected to because of the following informality: “said sequencing” should be “said sequencing the nucleic acid”.
Appropriate correction is required.
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.
Claims 31-33, 35, 42, 43, and 49 are rejected under 35 U.S.C. 102 (a) (1) as being anticipated by Wu (US 2016/0032370 A1, published on February 4, 2016).
Regarding claims 31-33, 35, 42, 43, and 49, Wu teaches a method of determining a nucleic acid sequence of a nucleic acid molecule, wherein the nucleic acid molecule is preserved close to its native state (ie., the nucleic acid molecule inside of a chromosome), the method comprising: a) providing a protective entity (ie., a chromosome) comprising the nucleic acid, wherein the protective entity preserves the nucleic acid closer to its native state than the case where no protective entity is provided; b) placing the protective entity in proximity of an analytical zone (ie., a surface), wherein said analytical zone comprises a surface, nanopore, nanogap or other nano-scale detection station/reading head, a nanochannel, a nanogroove, nanoslit or nanopit, a microfluidic cavity or a channel; c) releasing the nucleic acid from the protective entity (ie., a chromosome) into the analytical zone; and d) sequencing or analyzing the nucleic acid in the analytical zone as recited in claim 31 wherein the native state that is preserved is a length of the nucleic acid as claim 32, the protective entity is native to the nucleic acid and comprises a cell, a nucleus, an exosome, or chromosome as recited in claim 33, said sequencing the nucleic acid in the analytical zone is performed after elongating or stretching the nucleic acid as recited in claim 35, said releasing the nucleic acid from the protective entity into the analytical zone comprises treating the protective entity with one or more enzymes such as proteases as recited in claims 42 and 43, and using an enzyme mixture (ie., by ligation or polymerization) to repair the nucleic acid as recited in claim 49 (see paragraphs [0005] and Examples III and IV in paragraphs [0061] to [0067]).
Therefore, Wu teaches all limitations recited in claims 31-33, 35, 42, 43, and 49.
Response to Arguments
In page 11, last paragraph bridging to page 13, fifth paragraph of applicant’s remarks, applicant argues that “[A]pplicant respectfully submits that the currently amended claim 31 discloses method of determining a nucleic acid sequence, which is preserved close to its native state by a protective entity that preserves the nucleic acid closer to its native state than if no protective entity were provided (please refer to para [0194] of the present invention, reproduced
hereinbelow), followed by placing the protective entity in proximity to an analytical zone, releasing the nucleic acid into the analytical zone, and sequencing the nucleic acid therein”,
“[W]u, by contrast, is directed to removal of chromatin-associated factors from chromosomes to permit elongation of DNA, and expressly teaches disrupting native chromosomal structure through chemical and enzymatic treatments prior to analysis. A chromosome in Wu serves merely as starting material that is immobilized and dismantled (the DNA be attached to a surface at the time it is released from the protective entity and processed for analysis), not as a protective entity that preserves native-state nucleic acid for subsequent sequencing. Though, Wu relates to sequencing of DNA (please refer to as-filed claim 73 of Wu), such sequencing is limited to a specific sequencing modality, namely nanopore sequencing, and does not disclose or suggest sequencing based on transient binding of oligonucleotide probes, as disclosed in the present invention. Accordingly, Wu does not disclose preserving the nucleic acid close to its native state for the purpose of sequencing, nor does it disclose a workflow in which such preservation is functionally leveraged prior to release of the nucleic acid into an analytical zone. Accordingly, Wu does not disclose each and every limitation of Claim 31, and therefore does not anticipate Claim 31”, and “[C]laims 32-33, 35, 42, 43, and 49 are either directly or indirectly dependent on
the currently amended claim 31 and they are also novel not only by the way of dependency but
also by the novel inventive features they bring to the invention”.
The above arguments have been fully considered but they are not persuasive toward the withdrawal of the rejection. Although applicant argues that “[A] chromosome in Wu serves merely as starting material that is immobilized and dismantled (the DNA be attached to a surface at the time it is released from the protective entity and processed for analysis), not as a protective entity that preserves native-state nucleic acid for subsequent sequencing. Though, Wu relates to sequencing of DNA (please refer to as-filed claim 73 of Wu), such sequencing is limited to a specific sequencing modality, namely nanopore sequencing, and does not disclose or suggest sequencing based on transient binding of oligonucleotide probes, as disclosed in the present invention” and “[W]u does not disclose preserving the nucleic acid close to its native state for the purpose of sequencing, nor does it disclose a workflow in which such preservation is functionally leveraged prior to release of the nucleic acid into an analytical zone”, claim 31 does not require that the nucleic acid is in its native state during the process of sequencing the nucleic acid and sequencing the nucleic acid is based on transient binding of oligonucleotide probes as argued by applicant. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
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.
Claims 36 and 37 are rejected under 35 U.S.C. 103 as being unpatentable over Wu as applied to claims 31-33, 35, 42, 43, and 39 above, and further in view of Drmanac et al., (Science, 260, 1649-1652, 1993).
The teachings of Wu have been summarized previously, supra.
Wu does not disclose that said sequencing the nucleic acid in the analytical zone comprises binding a set of oligonucleotides to the nucleic acid as recited in claim 36 and said sequencing the nucleic acid in the analytical zone uses super-resolution imaging as recited in claim 37. However, Wu teaches sequencing the DNA attached to the surface (see paragraphs [0061] and [0062]).
Drmanac et al., teach DNA sequence determination by hybridization by sequentially hybridizing labeled oligonucleotides to unknown DNA samples attached to a support such as a filter and scanning the filter in a phosphor-imager after the hybridization in order to obtain hybridization image data (see page 1649, right column, page 1650, left column, first column, and page 1652, middle column, item 18 in REFERENCES AND NOTES).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have sequenced the nucleic acid in the analytical zone taught by Wu by binding a set of oligonucleotides to the nucleic acid (ie., the sequencing by hybridization method) and using super-resolution imaging (ie., using a phosphor-imager) as recited in claims 36 and 37 in view of the prior arts of Wu and Drmanac et al.. One having ordinary skill in the art would have been motivated to do so because Wu teaches sequencing the DNA attached to the surface (see paragraphs [0061] and [0062]) while Drmanac et al., teach DNA sequence determination by hybridization by sequentially hybridizing labeled oligonucleotides to unknown DNA samples attached to a support such as a filter and scanning the filter in a phosphor-imager after the hybridization in order to obtain hybridization image data (see page 1649, right column, page 1650, left column, first column, and page 1652, middle column, item 18 in REFERENCES AND NOTES) and the simple substitution of one kind of sequencing method (ie., the sequencing method taught by Wu) from another kind of sequencing method (ie., the sequencing by hybridization method taught by Drmanac et al.,) during the process of performing the method recited in claim 31, in the absence of convincing evidence to the contrary, would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made since the sequencing method taught by Wu and the sequencing by hybridization method taught by Drmanac et al., are used for the same purpose (ie., sequencing DNA). One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to perform the methods recited in claims 36 and 37 by sequencing the nucleic acid taught by Wu in the analytical zone using the sequencing by hybridization method taught by Drmanac et al., in view of the prior arts of Wu and Drmanac et al., such that sequencing the nucleic acid would be performed by binding a set of oligonucleotides to the nucleic acid and using super-resolution imaging.
Claims 38 and 39 are rejected under 35 U.S.C. 103 as being unpatentable over Wu as applied to claims 31-33, 35, 42, 43, and 39 above, and further in view of Adams et al., (US 2002/0106634 A1, published on August 8, 2002).
The teachings of Wu have been summarized previously, supra.
Wu does not disclose providing a nuclease inhibitor in the analytical zone as recited in claim 38 wherein the nuclease inhibitor comprises EDTA, EGTA, or Gallic Acid as recited in claim 39. However, Wu teaches to analyze the DNA attached to the surface by FISH (see paragraphs [0061] and [0062]).
Adams et al., teach that an in situ hybridization buffer contains 1 mM EDTA (see paragraph [0096]).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have provided a nuclease inhibitor such as EDTA in the analytical zone as recited in claims 38 and 39 in view of the prior arts of Wu and Adams et al.. One having ordinary skill in the art would have been motivated to do so because Wu teaches to analyze the DNA attached to the surface by FISH (see paragraphs [0061] and [0062]) while Adams et al., teach that an in situ hybridization buffer contains 1 mM EDTA (see paragraph [0096]). One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to perform the methods recited in claims 38 and 39 by adding a suitable concentration of a nuclease inhibitor such as EDTA to the FISH hybridization buffer taught by Wu in view of the prior arts of Wu and Adams et al., in order to prevent nucleic acids of the chromosome from cleavage by nucleases.
Response to Arguments
In page 13, sixth paragraph bridging to page 15, first paragraph of applicant’s remarks, applicant argues that “[W]ith respect to claims 38 and 39, Adams et al. merely discloses EDTA as a component of a conventional in situ hybridization buffer and does not teach or suggest providing a nuclease inhibitor in an analytical zone configured for sequencing of nucleic acids released from a protective entity. Accordingly, Adams’ EDTA disclosure is context-specific and unrelated to sequencing-configured analytical zones. For the sake of brevity, the arguments presented above with respect to novelty are not reiterated herein. Applicant respectfully submits that, for the same reasons, claims 31-33, 35, 42, 43, and 49 are not rendered obvious by Wu under 35 U.S.C. §103. Accordingly, the scope of the present invention i.e. ‘method of determining a nucleic acid sequence of a nucleic acid molecule preserved close to its native state’ is different from that of the cited references in entirety” and “applicant is of the opinion that a mere disclosure of nucleic acid sequencing would not necessarily teach, suggest or motivate a person skilled in the art to incorporate the features in the present invention or to perform the invention. The examiner's combination of references relies on impermissible hindsight. Also, Applicant submits that the invention should be considered ‘as a whole’ and a part-by-part evaluation of the invention should be prevented. Hindsight is trying to see the event as having been predictable, after the event has occurred, despite there being no objective basis for this prediction”.
The above arguments have been fully considered but they are not persuasive toward the withdrawal of the rejection. Although applicant argues that “[A]dams’ EDTA disclosure is context-specific and unrelated to sequencing-configured analytical zones”, since step d) of claim 31 is also read as “analyzing the nucleic acid in the analytical zone” (ie., analyze the DNA attached to the surface by FISH) and Adams et al., teach that an in situ hybridization buffer contains 1 mM EDTA (see paragraph [0096]), one having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to perform the methods recited in claims 38 and 39 by adding a suitable concentration of a nuclease inhibitor such as EDTA to the FISH hybridization buffer taught by Wu in view of the prior arts of Wu and Adams et al., in order to prevent nucleic acids of the chromosome from cleavage by nucleases and the limitation “sequencing the nucleic acid in the analytical zone” in step d) of claim 31argued by applicant can be either existed or not existed in claims 38 and 39. Furthermore, in response to applicant’s argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
Claim 47 is rejected under 35 U.S.C. 103 as being unpatentable over Wu as applied to claims 31-33, 35, 42, 43, and 39 above, and further in view of Rabinowitz et al., (US 2017/0166971 A1, filing date: March 1, 2017) and Pieprzyk et al., (US 2014/0186827 A1, published on July 3, 2014).
The teachings of Wu have been summarized previously, supra.
Wu does not disclose adding a distinct sequence tag to the nucleic acid when the nucleic acid is in the protective entity, thereby causing all nucleic acid species from the single protective entity to be recovered/identified when the contents of the protective entity are mixed with the contents of other protective entities as recited in claim 47.
Rabinowitz et al., teach ligating at least one adapter to chromosome segments wherein the at least one adapter comprises a universal amplification sequence (see claims 1 and 13).
Pieprzyk et al., teach useful nucleotide tags include a universal tag and a chromosome-specific nucleotide tag (see paragraphs [0049] and [0163]).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have performed the method recited in claim 47 by adding a distinct sequence tag to the nucleic acid when the nucleic acid is in the protective entity (ie., chromosome) such that all nucleic acid species from the single protective entity would be recovered/identified when the contents of the protective entity are mixed with the contents of other protective entities in view of the prior arts of Wu, Rabinowitz et al., and Pieprzyk et al.. One having ordinary skill in the art would have been motivated to do so because since Wu teaches to attach a chromosome to a surface (see paragraphs [0061] and [0062]), Rabinowitz et al., teach ligating at least one adapter to chromosome segments wherein the at least one adapter comprises a universal amplification sequence (see claims 1 and 13), and Pieprzyk et al., teach useful nucleotide tags include a universal tag and a chromosome-specific nucleotide tag (see paragraphs [0049] and [0163]). One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to perform the method recited in claim 47 by adding a chromosome-specific nucleotide tag taught by Pieprzyk et al., to the chromosome taught by Wu in view of the prior arts of Wu, Rabinowitz et al., and Pieprzyk et al., in order to recover/identify all nucleic acid species from the single protective entity when the contents of the protective entity are mixed with the contents of other protective entities.
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.
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Frank Lu, Ph. D., whose telephone number is (571)272-0746. The examiner can normally be reached Monday to Friday, 9 AM to 5 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow, Ph.D., 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.
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/FRANK W LU/
Primary Examiner, Art Unit 1683
February 11, 2026