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 .
Election/Restrictions
Applicant’s election of “Group II, claims 8-11, 16, and 17, drawn to a kit comprising a diallylamine/sulfur dioxide copolymer that comprises constituent compounds” is acknowledged.
Claims 1-7 and 12-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 August 11, 2026.
Claim Status/Action Summary
This action is in response to the papers filed August 11, 2026.
Claims 1-17 are currently pending in the present application. Previously presented claims 18-22 were canceled by applicant. Claims 1-7 and 12-15 were withdrawn without traverse as drawn to a nonelected invention. Claims 8-11 and 16-17 are currently under examination.
Priority/Effective Filing Date
The present application, filed on June 6, 2024, is a 371 of PCT/JP2022/044359, filed December 1, 2022, and claims foreign priority to JAPAN 2021-201175, filed on December 10, 2021.
Information Disclosure Statement
The (12) Information Disclosure Statements (IDS) dated: June 6, 2024, June 25, 2024, July 19, 2024, January 7, 2025, March 19, 2025, April 3, 2025, April 9, 2025, May 2, 2025, July 10, 2025, August 6, 2025, October 17, 2025, and August 11, 2026 have been considered (see attached 1449 documents).
Applicant is reminded that the listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
On page 3, the specification contains a list of references. If these references are not included in the information disclosure statements above, and are not cited by the examiner on form PT0-892, they have not been considered.
Drawings
The drawings filed on June 6, 2024 are acceptable.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on pages 28 and 41. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of the terms “Thermo Fisher Scientific”, “Riken Genesis”, and “Takara Bio” which are each a trade name or a mark used in commerce, has been noted in this application. Each term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Interpretation
The specification sets forth the following limiting definitions for terms recited in the claims.
“As used herein, “a standard base sequence” means a base sequence that serves as a standard when determining whether a “target base sequence” has mutations in a method for detecting mutations in the “target base sequence”, and the terms, “mutation”, “a mutation” are “mutations” mean a state in which the “target base sequence” has some difference in base sequence due to substitution, insertion, deletion, inversion, duplication, translocation, or a combination of two or more thereof, relative to the “standard base sequence” (paragraph 0020).
According to the stated definition, the “standard base sequence” has been broadly interpreted as a “reference sequence” to which the “target base sequence” is compared. The terms “mutation… mutations” have been interpreted as “target base sequences” that are not identical to a “reference sequence”.
“As used herein, the “clamp nucleic acid” is an artificial nucleic acid composed of an oligonucleotide that has a base sequence complementary to a “base sequence” which is a target for inhibiting nucleic acid amplification and contains at least one artificial nucleotide. It is to be noted that the “base sequence” as a target may be a “standard base sequence” or may be a “target base sequence”, depending on the embodiments (paragraph 0021).
According to the stated definition, the “clamp nucleic acid” has been broadly interpreted as an “artificial nucleic acid”, having a base sequence complementary to a “base sequence” which is a target for inhibiting nucleic acid amplification, wherein the “clamp nucleic acid” contains at least one “artificial nucleotide”.
Given its broadest reasonable interpretation, the claim term “artificial nucleotide” has been interpreted as a genus of nucleotides that are structurally different from nucleotides that are produced by natural processes (e.g. Adenosine phosphates, Thymidine phosphates, Cytidine phosphates, Guanosine phosphates, Uridine phosphates, and naturally occurring variants thereof such as 5-methylcytosine, 8-oxoguanosine, formamidopyrimidine phosphates, etc.). The specification further provides examples of “artificial nucleotides” encompassing peptide nucleic acids (PNA), bridged nucleic acids (BNA), peptide nucleic acids having a phosphate group (PHONA), morpholino nucleic acids, and a subset of BNAs referred to as “locked nucleic acids” (LNA).
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 8-11 and 16-17 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 8 recites the limitation "the standard base sequence" in lines 2-3. There is insufficient antecedent basis for this limitation in the claim.
Claim 16 recites, “The kit according to claim 8, wherein the kit is for inhibiting amplification of a nucleic acid having a target base sequence in a nucleic acid amplification reaction”. First, this claim appears to amount to a statement of an intended use of the claimed products, which does not further limit the claimed products. Additionally, claim 8 requires that the kit comprises “a clamp nucleic acid having a base sequence complementary to the standard base sequence”. The specification defines that: ““clamp nucleic acids” are complementary to a “base sequence” which is a target for inhibiting nucleic acid amplification” and “the “base sequence” as a target may be a “standard base sequence” or may be a “target base sequence”, depending on the embodiments (paragraph 0021)”. Because claim 8 requires that the clamp nucleic acid has a “base sequence complementary to the standard base sequence”, it appears that claim 16 encompasses broader subject matter including a clamp nucleic acid having the function “inhibiting amplification of a nucleic acid having a target base sequence”. This clamp nucleic acid necessarily comprises a sequence that is complementary to the ““base sequence” as a target” [for inhibition of amplification], which according to the special definition in the specification at paragraph 0021 (see above), encompasses sequences that are “standard base sequences” or “target base sequences”.
Therefore, while claim 16 does not positively recite any additional structural limitations to the claims, but instead is a statement of an intended use, claim 16 appears to additionally encompass contradictory subject matter that is broader than claim 8, from which claim 16 depends. It is unclear whether the applicant intends the metes and bounds of the claims to encompass these broader embodiments, whether applicant intends to somehow further limit the structures recited in claim 8 with this “intended use” or “functional” claim language, or something else entirely.
Claim 17 recites “The kit according to claim 8, wherein the kit is for detecting mutation in a target base sequence of a nucleic acid in a sample relative to a standard base sequence.” This claim appears to amount to a statement of an intended use of the claimed products recited in claim 8. Claim 17 does not positively recite any additional structural limitations that further limit claim 8. It is unclear whether the applicant intends to recite additional structural limitations to the claimed products, and if so, it is unclear what those additional structural limitations encompass from the present claim language.
Claims 9-11 and 16-17 are also indefinite because they each depend from, and thus necessarily include, the indefinite limitations of claim 8.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 16 and 17 are rejected under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 16 recites, “The kit according to claim 8, wherein the kit is for inhibiting amplification of a nucleic acid having a target base sequence in a nucleic acid amplification reaction”. This claim appears to amount to a statement of an intended use of the claimed products, which does not further limit the claimed products because the claim as presently written does not positively recite any additional structural limitations that further limit claim 8.
Claim 17 recites, “The kit according to claim 8, wherein the kit is for detecting mutation in a target base sequence of a nucleic acid in a sample relative to a standard base sequence.” This claim appears to amount to a statement of an intended use of the claimed products, which does not further limit the claimed products because the claim as presently written does not positively recite any additional structural limitations that further limit claim 8.
Applicant may cancel the claims, amend the claims to place the claims in proper dependent form, rewrite the claims in independent form, or present a sufficient showing that the dependent claims comply with the statutory requirements.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 8-11 and 16-17 are rejected under 35 U.S.C. 103 as being unpatentable over Becker et al., US 2002/0164614 A1 in view of Al-Muallem et al., “Synthesis and solution properties of a new ionic polymer and its behavior in aqueous two-phase polymer systems” Polymer 43 (2002) 1041-1050.
Regarding claim 8, Becker et al. teach kits comprising: a) polynucleotide probes which preferentially hybridize to target nucleic acids (i.e. “a standard base sequence” or “a target base sequence”) and b) a synthetic polycationic polymer in an amount sufficient to increase the association rate (i.e. stability) of the probe and the target sequence in the test sample (Becker et al., paragraph 0128). Becker et al. further teach poly(diallyldimethylammonium chloride) is one such polycationic polymer which functions to enhance the association kinetics of complementary polynucleotides which “can be easily screened for by skilled artisans following the guidance provided herein without having to engage in anything more than routine experimentation” (Becker et al., paragraph 0109). Becker et al. additionally teach that the polynucleotide probes comprise modified (i.e. artificial) nucleotides including locked nucleic acids (i.e. LNA, BNA, “bridged nucleic acid”) and peptide nucleic acids (PNA) (Becker et al., paragraph 0032). Finally, Becker et al. teach that the polynucleotide probes may be “amplification primers” which can contain a 3’ terminus which is modified to prevent or lessen the rate or amount of primer extension (i.e. “clamp” nucleic acids).
It is noted that the “poly(diallyldimethylammonium chloride)” (PDADMAC) has the following structure, where R1=R2=CH3:
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Therefore, because the present claims require a diallylamine/sulfur dioxide copolymer represented by:
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552
674
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Becker does not teach all of the structural limitations of the present claims.
However, Al-Muallem et al. teach cyclopolymerized diallylamine/sulfur dioxide copolymers (Al-Muallem et al., page 1042, column 1, “Scheme 1”, reproduced below for clarity).
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281
735
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Al-Muallem et al. further teach exemplary copolymers wherein R1=H and R2=an alkyl group added to the starting material by a simple alkyl halogenation of the tertiary amine in the monomer prior to cyclization (Al-Muallem et al., page 1042, column 2, Scheme 2, reproduced below).
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444
314
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Al-Muallem et al. teach the resulting copolymer with sulfur dioxide is a readily synthesized, water-soluble polycationic polymer that was known in the art at least as early as 2002 (the publication of Al-Muallem et al.). Furthermore, Butler et al. teach polycationic polymers which functions to enhance the association kinetics of complementary polynucleotides which “can be easily screened for by skilled artisans following the guidance provided herein without having to engage in anything more than routine experimentation” (Becker et al., paragraph 0109).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the kits comprising clamp nucleic acids and polymeric polycations taught by Becker et al. by substituting the PDADMAC polycationic polymer taught by Becker et al. with the well-known and readily-available diallylamine/sulfur dioxide copolymers taught by Al-Muallem having the claimed structures.
The ordinary artisan would have been motivated to screen additional, well-known PDADMAC-based polycationic polymers such as those taught by Becker et al. by the teachings of Becker et al. that one having skill in the art can easily screen for such compounds having the advantageous property of enhancing association kinetics of complementary polynucleotides which “following the guidance provided herein without having to engage in anything more than routine experimentation” (Becker et al., paragraph 0109).
Regarding claims 9 and 10, Al-Muallem et al. teach the diallylamine/sulfur dioxide copolymer is a diallylmethlyamine/sulfur dioxide copolymer or acid addition salt thereof (Al-Muallem et al., Scheme 1, see above).
Regarding claim 11, Becker et al. teach the artificial nucleic acid is a Locked Nucleic Acid (LNA) (i.e. a Bridged Nucleic Acid, BNA according to the definitions in the present specification) (Becker et al., paragraph 0032).
Regarding claim 16, the claim does not recite any additional structural limitations that further limit the claimed products. However, to address the intended use in the interest of compact prosecution, “for inhibiting amplification of a nucleic acid having a target base sequence…”, Becker et al. teach the clamp nucleic acid may be a “primer” comprising a 3’ terminus which is modified to prevent primer extension (Becker et al., paragraph 0058).
Regarding claim 17, the claim does not recite any additional structural limitations that further limit the claimed products. However, to address the intended use in the interest of compact prosecution, “for detecting mutation in a target base sequence… relative to a standard base sequence”, Becker et al. teach “uses… include detecting the presence of a disease-associated gene, determining the state of a disease, measuring levels of gene expression, and detecting mutations or polymorphisms in a test sample” (Becker et al., paragraph 0010).
Claims 8-11 and 16-17 are rejected under 35 U.S.C. 103 as being unpatentable over Becker et al., US 2002/0164614 A1 in view of Bouhadir et al., “Synthesis, Cyclopolymerization and Cyclo-Copolymerization of 9-(2-Diallylaminoethyl)adenine and Its Hydrochloride Salt” Molecules 2012, 17, 13290-13306.
Regarding claim 8, Becker et al. teach kits comprising: a) polynucleotide probes which preferentially hybridize to target nucleic acids (i.e. “a standard base sequence” or “a target base sequence”) and b) a synthetic polycationic polymer in an amount sufficient to increase the association rate (i.e. stability) of the probe and the target sequence in the test sample (Becker et al., paragraph 0128). Becker et al. further teach poly(diallyldimethylammonium chloride) is one such polycationic polymer which functions to enhance the association kinetics of complementary polynucleotides which “can be easily screened for by skilled artisans following the guidance provided herein without having to engage in anything more than routine experimentation” (Becker et al., paragraph 0109). Becker et al. additionally teach that the polynucleotide probes comprise modified (i.e. artificial) nucleotides including locked nucleic acids (i.e. LNA, BNA, “bridged nucleic acid”) and peptide nucleic acids (PNA) (Becher et al., paragraph 0032). Finally, Becker et al. teach that the polynucleotide probes may be “amplification primers” which can contain a 3’ terminus which is modified to prevent or lessen the rate or amount of primer extension (i.e. “clamp” nucleic acids).
It is noted that the “poly(diallyldimethylammonium chloride)” (PDADMAC) has the following structure, where R1=R2=CH3:
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Therefore, because the present claims require a diallylamine/sulfur dioxide copolymer represented by:
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552
674
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Becker does not teach all of the structural limitations of the present claims.
However, Bouhadir et al. teach diallylamine/sulfur dioxide copolymers derived from poly(diallylammonium chlorides) having the following basic structure (Bouhadir et al., scheme 2, reproduced below):
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354
707
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Furthermore, Bouhadir et al. teach copolymerization of quaternary diallylammonium salts with sulfur dioxide “typically result[s] in high molecular weight polymers in good yields… due to the introduction of a flexible sulfonyl radical into the propagating polymer chain that reduces its rigidity and increases its solubility” (Bouhadir et al., page 13294, paragraph 1). Specifically, Bouhadir et al. teach copolymers of DAAC (the base structure in scheme 2) with sulfur dioxide results in copolymers having average molecular weights less than 3,000 kDa (Bouhadir et al., Table 1, entry 5).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the products and kits comprising polycationic poly(diallylamines) taught by Becker et al. by substituting the polycationic polydiallylamines (such as PDADMAC, see above) taught by Becker et al. with the quaternary diallylammonium salts/sulfur dioxide copolymers taught by Bouhadir et al. encompassing polymers wherein R1=H and R2=alkyl (see Bouhadir et al., scheme 2 above). The ordinary artisan would have been motivated to screen for polycationic polymers having the advantageous DNA-duplex stabilizing properties taught by Becker et al. by the teachings of Becker et al. that such a screen is routine to those of skill in the art (Becker et al., paragraph 0109). Alternatively, the ordinary artisan would have been motivated to choose diallylamine sulfur dioxide copolymers as the polycationic polymer in the kits of Becker et al. because of the teaching of Bouhadir et al. that such sulfur dioxide copolymers readily form high-molecular weight polymers with good yields having the advantageous property of enhanced water solubility relative to the corresponding poly(diallylamine) (Bouhadir et al., page13294, paragraph 1).
Regarding claims 9 and 10, Bouhadir et al. teach the diallylamine/sulfur dioxide copolymer encompasses diallylmethylamine/sulfur dioxide copolymer or acid addition salt thereof (Bouhadir et al., Scheme 2, see above; R1=H, R2=alkyl, e.g. CH3)
Regarding claim 11, Becker et al. teach the artificial nucleic acid is a Locked Nucleic Acid (LNA) (i.e. a Bridged Nucleic Acid, BNA according to the definitions in the present specification) (Becker et al., paragraph 0032).
Regarding claim 16, the claim does not recite any additional structural limitations that further limit the claimed products. However, to address the intended use in the interest of compact prosecution, “for inhibiting amplification of a nucleic acid having a target base sequence…”, Becker et al. teach the clamp nucleic acid may be a “primer” comprising a 3’ terminus which is modified to prevent primer extension (Becker et al., paragraph 0058).
Regarding claim 17, the claim does not recite any additional structural limitations that further limit the claimed products. However, to address the intended use in the interest of compact prosecution, “for detecting mutation in a target base sequence… relative to a standard base sequence”, Becker et al. teach “uses… include detecting the presence of a disease-associated gene, determining the state of a disease, measuring levels of gene expression, and detecting mutations or polymorphisms in a test sample” (Becker et al., paragraph 0010).
Claims 8-11 and 16-17 are rejected under 35 U.S.C. 103 as being unpatentable over Becker et al., US 2002/0164614 A1 in view of Sato et al., WO 2011148862.
Regarding claim 8, Becker et al. teach kits comprising: a) polynucleotide probes which preferentially hybridize to target nucleic acids (i.e. “a standard base sequence” or “a target base sequence”) and b) a synthetic polycationic polymer in an amount sufficient to increase the association rate (i.e. stability) of the probe and the target sequence in the test sample (Becker et al., paragraph 0128). Becker et al. further teach poly(diallyldimethylammonium chloride) is one such polycationic polymer which functions to enhance the association kinetics of complementary polynucleotides which “can be easily screened for by skilled artisans following the guidance provided herein without having to engage in anything more than routine experimentation” (Becker et al., paragraph 0109). Becker et al. additionally teach that the polynucleotide probes comprise modified (i.e. artificial) nucleotides including locked nucleic acids (i.e. LNA, BNA, “bridged nucleic acid”) and peptide nucleic acids (PNA) (Becher et al., paragraph 0032). Finally, Becker et al. teach that the polynucleotide probes may be “amplification primers” which can contain a 3’ terminus which is modified to prevent or lessen the rate or amount of primer extension (i.e. “clamp” nucleic acids).
It is noted that the “poly(diallyldimethylammonium chloride)” (PDADMAC) has the following structure, where R1=R2=CH3:
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231
296
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Therefore, because the present claims require a diallylamine/sulfur dioxide copolymer represented by:
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552
674
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Becker does not teach all of the structural limitations of the present claims.
However, Sato et al. teach copolymers of diallylamines and sulfur dioxide represented by the following general formulas:
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689
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(Sato et al., paragraphs 0028-0031). It is noted that these structures are identical to the structures presently recited by claim 8.
Sato et al. further teach that the diallylamine/sulfur copolymers having chemical formulas according to formula (II or III) and IV with the advantageous properties of higher molecular weight and higher solubility in water relative to the diallylamine polymer without the sulfur dioxide copolymer constituent (Sato et al., paragraph 0005). Sato et al. further teaches that the process by which the diallylamine sulfur dioxide copolymer is synthesized allows for controlled polymerization and thus controlled molecular weight of the produced copolymer.
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the products and kits taught by Becker et al. by substituting the poly(diallylamine) polycationic polymers for increasing the stability of DNA duplexes with the poly(diallylamine)/sulfur dioxide copolymer taught by Sato et al.
The ordinary artisan would have been motivated to substitute the diallylamine/sulfur copolymers taught by Sato et al. into the kits taught by Becker et al. because of the teachings of Becker et al. that it is routine for those having skill in the art to screen known polycationic polymers for the DNA duplex stabilizing activity taught by Becker et al. (Becker et al., paragraph 0109) and by the teachings of Sato et al. that the diallylamine/sulfur dioxide copolymers having the structures (II or III) and IV (see above) have known advantageous properties relative to the corresponding poly(diallylamines) including: controllable polymerization, improved water solubility, and higher molecular weight.
Regarding claims 9-10, Sato et al. teach the diallylamine constituent of the diallylamine/sulfur dioxide copolymer encompasses diallylmethylamine hydrochloride (Sato et al., paragraph 0007). Sato et al. further teach the diallylamine constituent encompasses species wherein R1 and R2 independently represent a hydrogen atom or an alkyl group having 1 to 4 carbon atoms (Sato et al., paragraph 0011).
Regarding claim 11, Becker et al. teach the artificial nucleic acid is a Locked Nucleic Acid (LNA) (i.e. a Bridged Nucleic Acid, BNA according to the definitions in the present specification) (Becker et al., paragraph 0032).
Regarding claim 16, the claim does not recite any additional structural limitations that further limit the claimed products. However, to address the intended use in the interest of compact prosecution, “for inhibiting amplification of a nucleic acid having a target base sequence…”, Becker et al. teach the clamp nucleic acid may be a “primer” comprising a 3’ terminus which is modified to prevent primer extension (Becker et al., paragraph 0058).
Regarding claim 17, the claim does not recite any additional structural limitations that further limit the claimed products. However, to address the intended use in the interest of compact prosecution, “for detecting mutation in a target base sequence… relative to a standard base sequence”, Becker et al. teach “uses… include detecting the presence of a disease-associated gene, determining the state of a disease, measuring levels of gene expression, and detecting mutations or polymorphisms in a test sample” (Becker et al., paragraph 0010).
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ZACHARY MARK TURPIN whose telephone number is (703)756-5917. The examiner can normally be reached Monday-Friday 8:00 am - 5:00 pm.
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/Z.M.T./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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