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 and Formal matters
This action is in response to papers filed 12/5/2025.
Claims 1-4, 6, 10, 14-17, 19-20 and 23 are amended.
Claims 1-6, 8-10, 14-17, 19-23 are pending.
iApplicant’s election without traverse of Group 3, a solid phase flanking to a 3'-end or 5'-end nucleotide of the nucleic acid probe" from "a solid phase or an adapter or linker flanking to a 3'-end or 5'-end nucleotide of the nucleic acid probe, phosphorothioate oligo" in the reply filed on 6/25/2025 is acknowledged.
Claims 1-2, 4-5, 7-10, 16-18, 20 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as -being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 6/25/2025.
Claims 3, 6, 15, 19, 21-23 are being examined.
Priority
The instant application was filed 07/29/2022 and is a national stage entry of PCT/JP2021/003144 with an international filing date: 01/29/2021 claims foreign priority to 2020-014497, filed 01/31/2020. The priority document is not in English.
Claim Objections
Claims 23 are objected to because of the following informalities:
Claim 23 has been amended to recite, “Locked Nucleic Acid” and “Bridged Nucleic Acid.” These are not proper nouns or the first word of the claims and thus should not be capitalized.
. Appropriate correction is required.
Response to Arguments
This is a new ground of objection necessitated by amendment.
Specification
The specification is objected to as failing to provide proper antecedent basis for the claimed subject matter. See 37 CFR 1.75(d)(1) and MPEP § 608.01(o). Correction of the following is required:
Claim 3 has been amended to recite, “third base sequence,” “configured to hybridize,” and “pair of self aggregation probes.” The response asserts paragraph 0017 support the amendment, however review of 0017 did not reveal antecedent basis for these limitations. Further searching and review of the specification did not reveal antecedent basis for the limitations.
Claim 23 has been amended to recite, “Locked Nucleic Acid” and “Bridged Nucleic Acid.” The response asserts paragraph 0017 support the amendment, however review of 0017 did not reveal antecedent basis for these limitations. Further searching and review of the specification did not reveal antecedent basis for the limitations.
Claim 19has been amended to recite “configured to hybridize.” The response asserts paragraph 0017 support the amendment, however review of 0017 did not reveal antecedent basis for these limitations. Further searching and review of the specification did not reveal antecedent basis for the limitations.
Response to Arguments
This is a new ground of objection necessitated by amendment.
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.
Claims 3, 6, 15, 19, 21-23 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.
Claim 3 has been amended to recite, “A method for detecting a target nucleic acid in a sample, comprising: (i) a step of bringing a target nucleic acid in a sample, a capture probe, and an assist probe into contact with each other for hybridization such that the target nucleic acid and assist probe hybridize on the capture probe to form a hybridization complex, the capture probe containing (A) a nucleic acid probe, and (B) a solid phase or an adapter or linker flanking to a 3'-end or 5'-end nucleotide of the nucleic acid probe, the nucleic acid probe containing: a first base sequence; and a second base sequence complementary to a complete or partial sequence of the target nucleic acid, the assist probe containing (C) a third base sequence of6 to 9 nucleotides (a 6- to 9-mer) and configured to hybridize adjacent to an end of the target nucleic acid and (D_)_a complete or partial sequence one of a pair of self-aggregation probes; (ii) a step of bringing he pair of self-aggregation probes into contact with the hybridization complex to form a polymer complex consisting of the hybridization complex and an oligonucleotide polymer formed by self- aggregation of the air of self-aggregation probes; and (iii) a step of detecting the polymer complex, thereby detecting the target nucleic acid in the sample.”
Claim 19has been amended to recite “configured to hybridize.”
The response alleges paragraph 0017 provides support for the amendment. However review of 0017 did not provide support for “third base sequence,” “configured to hybridize,” and “pair of self aggregation probes.” Further searching and review of the specification did not reveal antecedent basis for the limitations. Further review and searching of the specification did not reveal specific guidance to envision the combination of elements now required of the claims as amended. Thus the claims lack written description and appear to introduce new matter.
Response to Arguments
This is a new ground of rejection necessitated by amendment.
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 3, 6, 15, 19, 21-23 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim 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.
Claim 3 is indefinite because it lacks a positive active step relating back to the preamble. The preamble recites a method for detecting a target nucleic acid in a sample; however the last positive active step is drawn to a step of detecting the polymer complex. Therefore it is unclear as to whether the method is drawn to detecting a target nucleic acid in a sample or a step of detecting the polymer complex.
Claim 3 recites,” configured to hybridize adjacent to an end of the target nucleic acid.” The metes and bounds are unclear what is required of adjacent. It is unclear if adjacent requires on the same strand, if nucleotides which are complementary are adjacent, if adjacent if adjacent requires the last nucleotide of assist probe has no nucleotides between it and the target nucleic acid, or allows nucleotides between end of assist probe and target nucleic acid. Thus the metes and bounds are unclear.
Further claim 3 provides comprising language throughout the claim. The claim in step (ii) then recites, “a step of bringing he pair of self-aggregation probes into contact with the hybridization complex to form a polymer complex consisting of the hybridization complex and an oligonucleotide polymer formed by self- aggregation of the air of self-aggregation probes.” Thus the claim is confusing and unclear how consisting limits the claim or what it excludes as the claim previously require of numerous probes including capture probe, assist probe, target nucleic acid and one of a pair self-aggregation probes. Further the recitation is unclear as to what is required of “one of a pair of self-aggregation probes.” It is unclear if this requires one self-aggregation probe or if it requires one pair (meaning two) self-aggregation probe. The claim continues the confusion by recitation of “a step of bringing the first and second oligonucleotides the pair of self-aggregation probes into contact with the hybridization product complex to form a polymer complex between consisting of the hybridization product complex and an oligonucleotide polymer formed by self- aggregation of the first and second oligonucleotides pair of self-aggregation probes.” The recitation of “the pair of self-aggregation probes” lacks antecedent basis as the claim previously recites, “one of a pair of self-aggregation probes.” Further it is unclear as (D) which recites “one of a pair of self-aggregation probes” appears to be part of the assist probe. Thus it is unclear what is required.
Further claim 6 recites, “capable of flanking to the target nucleic acid.” Capable of flanking is a relative term, which suggest some are not capable of flanking. The metes and bounds are unclear what is required. It is further unclear if flanking requires some level of complementarity, identity or something else.
Claim 15 recites, “The method according to claim 3, wherein the target nucleic acid is brought into contact with the capture probe such that the target nucleic acid hybridizes on the capture probe to form a hybridization product, and subsequently, athe is brought into contact with the assist probe such that the target nucleic acid and assist probe hybridize on the capture probe to form a hybridization complex..” The metes and bounds are unclear if this is an active step requiring the hand of man or is merely a description of the hybridization process that occurs during the mixing of the required probes. Further it is unclear how this further limits the independent claim which appears to provide the same combination of probes and target nucleic acid.
Further claim 19 recites, “wherein the assist probe isconfigured to hybridize adjacent to the end of the target nucleic acid.” Configured to hybridize is a relative term, which suggest some are not configured to hybridize. The metes and bounds are unclear what is required. It is further unclear if adjacent requires the last nucleotide of assist probe has no nucleotides between it and the target nucleic acid, or allows nucleotides between end of assist probe and target nucleic acid.
Response to Arguments
The response traverses the previous rejections in view of the amendments. This argument has been thoroughly reviewed but is not considered persuasive as the amendment has introduced new issues and/or has not addressed the issues of record.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 3, 6, 15, 19, 21 is/are rejected under 35 U.S.C. 102(a)(1)/102(a)(2) as being anticipated by Usui (US 20100256007).
It is noted the claim provides comprising and “containing” language. Both of these are being given the broadest reasonable interpretation is the claim allows for additional elements or steps. Further the claims have numerous 112 issues, which allow for the instant rejection.
Usui teaches in example 4 teaches the detection of Staph Auresus (SEQ ID NO 4) by use of a capture probe SEQ ID NO 5 with an amino linker at 3’ end and assist probe SEQ ID NO 6 to allow for detection. By a structure similar to
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Thus Usui anticipates claim 3.
With regards to claim 6, Usui teaches SEQ ID NO 6.
With regards to claim 15, the hybridization of two probes with a target nucleic acid is dependent on the interaction of the probes with the nucleic acid and thus it encompasses the hybridization of the capture to the target and the assist probe to the capture probe.
With regards to claim 19, The self-assembly or self-aggregation provided for in example 4 of Usui demonstrates the assist probe is capable of flanking the target nuclei acid by some standard.
With regards to claim 21, Usui teaches, “[0035] As a sample for measuring a target analyte in the present invention, any sample having a possibility of containing the target analyte can be applied. Examples of the sample include samples derived from living organisms such as blood, serum, urine, feces, cerebrospinal fluid, tissue fluid, sputum, and cell culture, and samples possibly containing or being infected by viruses, bacteria, molds, and the like.”
Response to Arguments
The response traverses the rejection asserting the instant by providing the following figure
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This argument has been thoroughly reviewed but is not considered persuasive as the drawing of the present invention may be encompassed by the claims, but is not required of the claims.
The response further asserts, “Usui employs only a single assist or self-assembly probe, whereas the present invention utilizes a pair of self-assembly probes that cooperatively assemble on the capture probe.” This argument has been thoroughly reviewed but is not considered persuasive as the claim recites, “(D_)_a complete or partial sequence of one of a pair of self-aggregation probes; (ii) a step of bringing he pair of self-aggregation probes into contact with the hybridization complex to form a polymer complex consisting of the hybridization complex.” Thus the argument is not commensurate in scope with the claims.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 3, 6, 15, 19, 21-23is/are rejected under 35 U.S.C. 103 as being unpatentable over Usui (US 20100256007) in view of Wei (Pharmaceutical Research, Vol. 23, No. 6, June 2006, pages 1251-1264).
It is noted the claim provides comprising and “containing” language. Both of these are being given the broadest reasonable interpretation is the claim allows for additional elements or steps. Further the claims have numerous 112 issues, which allow for the instant rejection.
Usui teaches in example 4 teaches the detection of Staph Auresus (SEQ ID NO 4) by use of a capture probe SEQ ID NO 5 with an amino linker at 3’ end and assist probe SEQ ID NO 6 to allow for detection. By a structure similar to
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Thus Usui anticipates claim 3.
Usui does not specifically teach the use modified oligonucleotides.
However, Wei teaches, “To develop and validate an ultrasensitive and specific hybridization-based enzyme-linked immunosorbent assay method for quantification of two phosphorothioate oligonucleotides (PS ODNs) (G3139 and GTI-2040) in biological fluids.” (abstract) Wei teaches, “Nucleic acid hybridization has long been known to play a vital role in biological processes, and its precise complementary association with messenger ribonucleic acid (mRNA) has recently been recognized as a potential therapeutic strategy. Specific segments of DNA-like or modified DNA known as antisense oligonucleotides (AS ODNs) capable of hybridizing with specific mRNA or regions of mRNA have now been developed to aim at disruption of the expression of genes that associate with malignancy transformation. Thus, antisense oligonucleotides inhibit processing or translation of its target mRNA to proteins. The native phosphodiester oligonucleotides suffer from low in vitro and in vivo stability and did not achieve significant therapeutic expectation. On the other hand, the first generation of antisense compounds, such as phosphorothioate oligonucleotides (PS ODNs), offer significantly improved stability and biological activities, a several are now being evaluated clinically in various molecular targets including cancer, viral diseases, and inflammatory disorders (1Y6). To date, there are over 20 ongoing clinical trials testing antisense compounds. PS ODNs possess favorable nuclease resistance and ribonuclease H (RNase H) activation properties and demonstrate clinical responses, acceptable toxicity, and thus, clinical significance (4Y6).”
Therefor it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to use phosphorothioate nucleic acids as the target nucleic acid. The artisan would be motivated to determine the level of phosphorothioate oligonucleotides in a biological sample. The artisan would be motivated to examine level of phosphorothioate oligonucleotides to examine levels of phosphorothioate oligonucleotides in sample being used to regulate gene expression. The artisan would have a reasonable expectation of success as the artisan is merely using a known type of target nucleic acid.
With regards to claim 6, Usui teaches SEQ ID NO 6.
With regards to claim 15, the hybridization of two probes with a target nucleic acid is dependent on the interaction of the probes with the nucleic acid and thus it encompasses the hybridization of the capture to the target and the assist probe to the capture probe.
The courts have haled that rearrangement of steps is obvious in the absence of unexpected results. Ex parte Rubin, 128 USPQ 440 (Bd. App. 1959) (Prior art reference disclosing a process of making a laminated sheet wherein a base sheet is first coated with a metallic film and thereafter impregnated with a thermosetting material was held to render prima facie obvious claims directed to a process of making a laminated sheet by reversing the order of the prior art process steps.). See also In re Burhans, 154 F.2d 690, 69 USPQ 330 (CCPA 1946) (selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results); In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930) (Selection of any order of mixing ingredients is prima facie obvious.).
The metes and bounds “of capable of flanking to the end of the target nucleic acid” are unclear.
With regards to claim 19, The self-assembly or self-aggregation provided for in example 4 of Usui demonstrates the assist probe is capable of flanking the target nuclei acid by some standard.
With regards to claim 21, Usui teaches, “[0035] As a sample for measuring a target analyte in the present invention, any sample having a possibility of containing the target analyte can be applied. Examples of the sample include samples derived from living organisms such as blood, serum, urine, feces, cerebrospinal fluid, tissue fluid, sputum, and cell culture, and samples possibly containing or being infected by viruses, bacteria, molds, and the like.”
Response to Arguments
The response traverses the rejection for the reasons with respect to the independent claim. This argument is not persuasive for the reasons of record.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 3, 6, 15, 19, 21-23 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-23 of copending Application No. 18/844885. Although the claims at issue are not identical, they are not patentably distinct from each other because coextensive in scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The instant claims are drawn to A method for detecting a target nucleic acid in a sample by forming a complex with a pair of probes capable of self-aggregation consisting of first and second oligonucleotides, comprising:(i) a step of bringing a target nucleic acid in a sample, a capture probe, and an assist probe into contact with each other for hybridization, the capture probe containing (A) a nucleic acid probe, and(B) a solid phase or an adapter or linker flanking to a 3'-end or 5'-end nucleotide of the nucleic acid probe, the nucleic acid probe containing: a first base sequence; and second base sequence complementary to a complete or partial sequence of the target nucleic acid, the assist probe containing a 6- to 9-mer sequence capable of flanking to the target nucleic acid and complementary to a complete or partial sequence of the first base sequence of the nucleic acid probe, and a complete or partial sequence of at least one of the first and second oligonucleotides;(ii) a step of bringing the first and second oligonucleotides into contact with the hybridization product to form a polymer complex between the hybridization product and an oligonucleotide polymer formed by self-aggregation of the first and second oligonucleotides; and(iii) a step of detecting the polymer complex.
The claims of 18/844885 require method for detecting a target oligonucleotide in a sample while distinguishing from a metabolite thereof which lacks one or more nucleotides from the 3' end or the 5' end, comprising:(i) bringing a capture probe for capturing the target oligonucleotide and an assist probe for detecting the target oligonucleotide into contact with a sample containing the target oligonucleotide or the metabolite thereof which lacks one or more nucleotides from the 3' end or the 5' end and forming a complex of the capture probe, the target oligonucleotide and the assist probe, wherein the capture probe contains a solid phase and a first nucleic acid probe immobilized on the solid phase, the assist probe contains a tag or a label and a second nucleic acid probe linked to the tag or the label, the sequence of the first nucleic acid probe is complementary to a partial sequence of the target oligonucleotide, wherein the partial sequence contains the nucleotides which are lacking in the metabolite, the sequence of the second nucleic acid probe is complementary to a sequence in the target oligonucleotide other than the partial sequence, and the solid phase is bonded to the nucleotide at an end of the first nucleic acid probe, wherein the nucleotide at the end forms a base pair with the nucleotide at the end of the target oligonucleotide which is lacking in the metabolite when the target oligonucleotide and the first nucleic acid probe hybridize; and(ii) detecting the target oligonucleotide in the sample by detecting the complex.
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims, that the claims of 885 are commensurate in scope with the instant claims. Thus the claims are at least obvious variants.
Dependent claims are rejected as they are commensurate in scope.
Response to Arguments
The response traverses the rejection asserting, “Each of these rejections is respectfully traversed. Reconsideration is respectfully requested. A complete discussion of the Examiner's rejection is set forth in the Office Action, and is not being repeated here. Reconsideration is requested in view of the present claim amendments. Otherwise, Applicant requests that these rejections be held in abeyance until allowable subject matter is found.” This argument is not persuasive for the reasons of record.
Claim 3, 6, 15, 19, 21-23 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-21 of copending Application No. 18/844787. Although the claims at issue are not identical, they are not patentably distinct from each other because coextensive in scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The instant claims are drawn to A method for detecting a target nucleic acid in a sample by forming a complex with a pair of probes capable of self-aggregation consisting of first and second oligonucleotides, comprising:(i) a step of bringing a target nucleic acid in a sample, a capture probe, and an assist probe into contact with each other for hybridization, the capture probe containing (A) a nucleic acid probe, and(B) a solid phase or an adapter or linker flanking to a 3'-end or 5'-end nucleotide of the nucleic acid probe, the nucleic acid probe containing: a first base sequence; and a second base sequence complementary to a complete or partial sequence of the target nucleic acid, the assist probe containing a 6- to 9-mer sequence capable of flanking to the target nucleic acid and complementary to a complete or partial sequence of the first base sequence of the nucleic acid probe, and a complete or partial sequence of at least one of the first and second oligonucleotides;(ii) a step of bringing the first and second oligonucleotides into contact with the hybridization product to form a polymer complex between the hybridization product and an oligonucleotide polymer formed by self-aggregation of the first and second oligonucleotides; and(iii) a step of detecting the polymer complex.
The claims of 787 require A method for detecting a target oligonucleotide in a sample, comprising:(i) bringing a capture probe for capturing the target oligonucleotide and an assist probe for detecting the target oligonucleotide into contact with a sample and forming a complex of the capture probe, the target oligonucleotide and the assist probe, wherein the capture probe contains a solid phase, a first nucleic acid probe immobilized on the solid phase and a first spacer between the solid phase and the first nucleic acid probe, the assist probe contains a tag or a label and a second nucleic acid probe linked to the tag or the label, the sequence of the first nucleic acid probe is complementary to a partial sequence of the target oligonucleotide including the nucleotide at an end of the target oligonucleotide, and the sequence of the second nucleic acid probe is complementary to a sequence in the target oligonucleotide other than the partial sequence; and (ii) detecting the target oligonucleotide in the sample by detecting the complex.
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims, that the claims of 787 are commensurate in scope with the instant claims. Thus the claims are at least obvious variants.
Dependent claims are rejected as they are commensurate in scope.
Response to Arguments
The response traverses the rejection asserting, “Each of these rejections is respectfully traversed. Reconsideration is respectfully requested. A complete discussion of the Examiner's rejection is set forth in the Office Action, and is not being repeated here. Reconsideration is requested in view of the present claim amendments. Otherwise, Applicant requests that these rejections be held in abeyance until allowable subject matter is found.” This argument is not persuasive for the reasons of record.
Claim 3, 6, 15, 19, 21-23 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-21 of copending Application No. 17776741. Although the claims at issue are not identical, they are not patentably distinct from each other because coextensive in scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The instant claims are drawn to A method for detecting a target nucleic acid in a sample, comprising: (i) a step of bringing a target nucleic acid in a sample, a capture probe, and an assist probe into contact with each other for hybridization such that the target nucleic acid and assist probe hybridize on the capture probe to form a hybridization complex, the capture probe containing (A) a nucleic acid probe, and (B) a solid phase or an adapter or linker flanking to a 3'-end or 5'-end nucleotide of the nucleic acid probe, the nucleic acid probe containing: a first base sequence; and a second base sequence complementary to a complete or partial sequence of the target nucleic acid, the assist probe containing (C) a third base sequence of6 to 9 nucleotides (a 6- to 9-mer) and configured to hybridize adjacent to an end of the target nucleic acid and (D_)_a complete or partial sequence one of a pair of self-aggregation probes; (ii) a step of bringing he pair of self-aggregation probes into contact with the hybridization complex to form a polymer complex consisting of the hybridization complex and an oligonucleotide polymer formed by self- aggregation of the air of self-aggregation probes; and (iii) a step of detecting the polymer complex, thereby detecting the target nucleic acid in the sample.
The claims of 741 require method of detecting a target oligonucleotide in a sample, in which the target oligonucleotide is an oligonucleotide or a DNA in which a nucleic acid base at a 3'-end is chemically modified, the method comprising: (i) bringing poly A polymerase into contact with the target oligonucleotide in the sample in the presence of Mn2, thereby adding poly A to the 3'-end of the target oligonucleotide; (ii) bringing the sample into contact with a capture probe for capturing the target oligonucleotide to perform hybridization; wherein the capture probe includes (A) a nucleic acid probe, and (B) a solid phase, an adapter, or a linker adjacent to a nucleotide at a 3-end or 5'-end of the nucleic acid probe, and the nucleic acid probe contains an entire sequence or a partial sequence of the target oligonucleotide; (iii) bringing a hybridization product included in the sample, into contact with a pair of self-aggregating signal amplification probes composed of first and second oligonucleotides, thereby forming a complex of the hybridization product and an oligonucleotide polymer obtained through self-aggregation of the first and second oligonucleotides; and (iv) detecting the complex..
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims, that the claims of 741 are species encompassed by the instant claims. Thus the claims are at least obvious variants.
Dependent claims are rejected as they are commensurate in scope.
Response to Arguments
The response traverses the rejection asserting, “Each of these rejections is respectfully traversed. Reconsideration is respectfully requested. A complete discussion of the Examiner's rejection is set forth in the Office Action, and is not being repeated here. Reconsideration is requested in view of the present claim amendments. Otherwise, Applicant requests that these rejections be held in abeyance until allowable subject matter is found.” This argument is not persuasive for the reasons of record.
Claim 3, 6, 15, 19, 21-23 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-21 of copending Application No. 17776741. Although the claims at issue are not identical, they are not patentably distinct from each other because coextensive in scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The instant claims are drawn to A method for detecting a target nucleic acid in a sample, comprising: (i) a step of bringing a target nucleic acid in a sample, a capture probe, and an assist probe into contact with each other for hybridization such that the target nucleic acid and assist probe hybridize on the capture probe to form a hybridization complex, the capture probe containing (A) a nucleic acid probe, and (B) a solid phase or an adapter or linker flanking to a 3'-end or 5'-end nucleotide of the nucleic acid probe, the nucleic acid probe containing: a first base sequence; and a second base sequence complementary to a complete or partial sequence of the target nucleic acid, the assist probe containing (C) a third base sequence of6 to 9 nucleotides (a 6- to 9-mer) and configured to hybridize adjacent to an end of the target nucleic acid and (D_)_a complete or partial sequence one of a pair of self-aggregation probes; (ii) a step of bringing he pair of self-aggregation probes into contact with the hybridization complex to form a polymer complex consisting of the hybridization complex and an oligonucleotide polymer formed by self- aggregation of the air of self-aggregation probes; and (iii) a step of detecting the polymer complex, thereby detecting the target nucleic acid in the sample.
The claims of 741 require method of detecting a target oligonucleotide in a sample, in which the target oligonucleotide is an oligonucleotide or a DNA in which a nucleic acid base at a 3'-end is chemically modified, the method comprising: (i) bringing poly A polymerase into contact with the target oligonucleotide in the sample in the presence of Mn2, thereby adding poly A to the 3'-end of the target oligonucleotide; (ii) bringing the sample into contact with a capture probe for capturing the target oligonucleotide to perform hybridization; wherein the capture probe includes (A) a nucleic acid probe, and (B) a solid phase, an adapter, or a linker adjacent to a nucleotide at a 3-end or 5'-end of the nucleic acid probe, and the nucleic acid probe contains an entire sequence or a partial sequence of the target oligonucleotide; (iii) bringing a hybridization product included in the sample, into contact with a pair of self-aggregating signal amplification probes composed of first and second oligonucleotides, thereby forming a complex of the hybridization product and an oligonucleotide polymer obtained through self-aggregation of the first and second oligonucleotides; and (iv) detecting the complex..
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims, that the claims of 741 are species encompassed by the instant claims. Thus the claims are at least obvious variants.
Dependent claims are rejected as they are commensurate in scope.
Response to Arguments
The response traverses the rejection asserting, “Each of these rejections is respectfully traversed. Reconsideration is respectfully requested. A complete discussion of the Examiner's rejection is set forth in the Office Action, and is not being repeated here. Reconsideration is requested in view of the present claim amendments. Otherwise, Applicant requests that these rejections be held in abeyance until allowable subject matter is found.” This argument is not persuasive for the reasons of record.
Claims 3, 6, 15, 19, 21-23 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of U.S. Patent No. 11993806. Although the claims at issue are not identical, they are not patentably distinct from each other because coextensive in scope.
The instant claims are drawn to A method for detecting a target nucleic acid in a sample, comprising: (i) a step of bringing a target nucleic acid in a sample, a capture probe, and an assist probe into contact with each other for hybridization such that the target nucleic acid and assist probe hybridize on the capture probe to form a hybridization complex, the capture probe containing (A) a nucleic acid probe, and (B) a solid phase or an adapter or linker flanking to a 3'-end or 5'-end nucleotide of the nucleic acid probe, the nucleic acid probe containing: a first base sequence; and a second base sequence complementary to a complete or partial sequence of the target nucleic acid, the assist probe containing (C) a third base sequence of6 to 9 nucleotides (a 6- to 9-mer) and configured to hybridize adjacent to an end of the target nucleic acid and (D_)_a complete or partial sequence one of a pair of self-aggregation probes; (ii) a step of bringing he pair of self-aggregation probes into contact with the hybridization complex to form a polymer complex consisting of the hybridization complex and an oligonucleotide polymer formed by self- aggregation of the air of self-aggregation probes; and (iii) a step of detecting the polymer complex, thereby detecting the target nucleic acid in the sample.
The claims of 806 are drawn to . A method of detecting a target oligonucleotide in a sample, comprising steps of: (i) bringing a capture probe for capturing the target oligonucleotide into contact with the sample, the capture probe containing (A) a nucleic acid probe, and (B) a solid phase, or an adapter or a linker, adjacent to a nucleotide at the 3′ end or 5′ end of the nucleic acid probe, the nucleic acid probe containing a sequence complementary to a complete or partial sequence of the target oligonucleotide; (ii) bringing a single-strand-specific nuclease into contact with the sample subjected to the contact step with the capture probe; (iii) making the capture probe in the sample single-stranded after the contact step with the single-strand-specific nuclease is performed; (iv) bringing a pair of probes capable of self-aggregation composed of first and second oligonucleotides into contact with the sample subjected to the step of making the capture probe single-stranded to form a complex of the capture probe and an oligonucleotide polymer generated by self-aggregation of the first and second oligonucleotides; and (v) detecting the complex, and thereby detecting the target oligonucleotide in the sample.
Thus it is prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims, the claims of 806 are a species encompassed by the instant claims. T1hus the claims are at least obvious variants.
Dependent claims are rejected as they are commensurate in scope.
Response to Arguments
The response traverses the rejection asserting, “Each of these rejections is respectfully traversed. Reconsideration is respectfully requested. A complete discussion of the Examiner's rejection is set forth in the Office Action, and is not being repeated here. Reconsideration is requested in view of the present claim amendments. Otherwise, Applicant requests that these rejections be held in abeyance until allowable subject matter is found.” This argument is not persuasive for the reasons of record.
Summary
No claims are allowed.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Usui (Biochemical and Biophysical Research Communications Volume 467, Issue 4, 27 November 2015, Pages 1012-1018)
Fujiwaka (WO2010087409)
iApplicant'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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/Steven Pohnert/Primary Examiner, Art Unit 1683
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