DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 07/26/2023 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of Claims
This office action is in response to Applicant's Amendment filed on February 03, 2026.
Claims 1-14, 29-32 and 34-35 were previously pending. Applicant amended claims 11-12, 32, 34; cancelled claims 1-10 and 29; claims 36-43 are newly added.
Claims 11-14, 30-32 and 34-43 are currently pending, with claims 12, 14, 30-32 and 43 withdrawn.
Claims 11, 13, 34-42 are under examination. This is the first action on the merits.
Election/Restrictions
Applicant’s election without traverse of Group III (claims 11-14, 30-32 and 34-35) in the reply filed on February 03, 2026 is acknowledged.
Applicant’s election without traverse of the following species in the reply filed on February 03, 2026 is acknowledged:
Species of step (e) in amplification methods: Species A (claim 11) 1;
Species of applications for the method of claim 11: Species A-2 (claim 34) 2.
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 12, 14, 30-32 and 43 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention.
Examination on the merits commences on claims 11, 13 and 34-42.
Specification
The disclosure is objected to because page 24, lines 15, 22, 33 of the specification contains embedded hyperlinks and/or other form of browser-executable code. 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.
Claim Objections
Claims 11, 34 and 37-38 are objected to because of the following informalities:
In claim 11, lines 8-9, "wherein the selector polynucleotide comprises at least a single residue a selector nucleotide" should read "wherein the selector polynucleotide comprises at least a single residue selector nucleotide."
In claim 11, part (d), line 1, "contacting the duplex" should read "contacting the nucleic acid duplex."
In claim 34, lines 2-3, "a method of claim 11" should read "the method of claim 11," to properly reference base claim 11.
Claims 37 and 38 are objected to for not ending the claims with a period.
See MPEP 608.01(m) "Each claim begins with a capital letter and ends with a period."
Priority
The priority date of the instant claims 11, 13 and 34-42 is 02/02/2021, filling date of the US provisional application NO. 63/144,723.
Claim Interpretation
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
For the purpose of applying prior art, claim 11 recites "selector polynucleotide" comprising "at least a single residue selector nucleotide." The application's disclosure does not expressly define the terms "selector polynucleotide" and "single residue selector nucleotide." The specification broadly describes "single residue selector nucleotide" as a single residue (see in specification, page 3, lines 20-22 for example).
The recitation "…located at the first (ultimate), second (penultimate), third (antepenultimate), fourth (preantepenultimate), fifth (propreantepenultimate), or sixth (one residue to the 5' side of the propreantepenultimate) position in reference to a 3' end, or is at a position that is even more distal to the 3' end, " encompasses any nucleotide location on the "selector polynucleotide" from the 3' end to the 5' end. Because a position that is even more distal to the 3’ end than the sixth position encompasses any and all nucleotide positions further from the 3’ end than the sixth position on a polynucleotide.
Thus, a "single residue selector nucleotide" is interpreted under BRI as a single residue located anywhere in within the "selector polynucleotide," which is construed as encompassing any polynucleotide comprising a "single residue selector nucleotide."
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 11, 13 and 34-42 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 (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claim 11, it recites in part (a):
"wherein the at least single residue selector nucleotide is structurally or chemically unlike any other residue within the region or section of the selector polynucleotide necessary for binding of the selector polynucleotide to a target nucleic acid"
This claim language is indefinite for several reasons.
First, the metes and bounds of a "selector nucleotide" that is "structurally or chemically unlike any other residue" are unclear. The disclosure only discloses a single species for “selector nucleotide" ꟷ a single ribonucleotide residue. However, neither the claim nor the specification clearly defines what other nucleotide qualifies as a nucleotide that is "structurally or chemically unlike" another residue ꟷ there is no objective criteria for making such a determination. For example, it is unclear whether naturally occurring nucleotides such as G (deoxyguanosine) and T (deoxythymidine) would be considered "structurally or chemically unlike" one another, or whether the limitation requires a modified nucleotide. Without clear definition, the scope of this limitation cannot be determined with reasonably certainty.
Second, the claim recites "region or section" of the selector polynucleotide as alternatives, but the application's disclosure does not define either term with structural features. It is unclear whether "region" and "section" are intended to have distinct scope or not, as the application provides no structural distinction between the two. Thus, it is unclear whether the scope of the claim differs depending on which term is applied.
Third, the phrase "necessary for binding of the selector polynucleotide to a target nucleic acid" further renders the claim indefinite. The claim does not define what structural features makes a region of section "necessary for binding." It is unclear whether this requires complementary sequence to the target, a particular sequence length, specific melting temperature, or some other characteristic.
Regarding claim 11, part (d) recites "the synthetic DNA polynucleotide (or selector polynucleotide)," which is definite.
First, "the synthetic DNA polynucleotide" lacks antecedent basis. The claim does not previously introduce or recite any " synthetic DNA polynucleotide." Accordingly, it is unclear what element this term refers to.
Second, the use of parenthesis in "(or selector polynucleotide)" creates further ambiguity. It is unclear whether "synthetic DNA polynucleotide" and "selector polynucleotide" are intended to be interchangeable terms referring to the same element, or whether they are alternative terms each having distinct meanings. The specification does not provide express definition for these terms, under BRI and within the context of the claim, "synthetic DNA polynucleotide" appear to be broader in scope than "selector polynucleotide," as the claim requires "selector polynucleotide" to comprise additional structural elements such as a selector nucleotide residue.
As such, the scope of this limitation is unclear, rendering the claim indefinite.
C) Regarding claim 11, it recites in part (e): "contacting the newly created nucleic acid duplex with a ribonuclease enzyme," which is indefinite because "the newly created nucleic acid duplex" lacks antecedent basis. The claim does not specifically recite in any prior steps, newly creating a nucleic acid duplex. As such, it is unclear what "the newly created nucleic acid duplex" refers to.
Part (c) recites a contacting step for generating a nucleic acid duplex by pairing a selector polynucleotide with a template DNA polynucleotide.
Part (d) recites contacting the nucleic acid duplex with a DNA polymerase enzyme, thereby producing a "new extended DNA polynucleotide."
It is unclear whether "the newly created nucleic acid duplex" refers to the "nucleic acid duplex" in (c), or the "new extended DNA polynucleotide" in (d).
For the purpose of compact prosecution and applying prior art under 35 USC§ 102 and 103, any prior art method that teaches contacting a nucleic acid duplex with a ribonuclease enzyme is considered to meet this limitation "contacting the newly created nucleic acid duplex with a ribonuclease enzyme."
D) Claim 1 recites in part (e) a step of "contacting the newly created nucleic acid duplex with a ribonuclease enzyme, wherein optionally the ribonuclease enzyme is thermostable," and further recites contingent limitations in a wherein clause:
" (ii) if the selector nucleotide residue (optionally a single ribonucleotide residue) is retained in the extended selector polynucleotide and is matched to a deoxyribonucleotide residue, then the thermostable ribonuclease enzyme cuts at the selector nucleotide residue (optionally a single ribonucleotide residue) thereby detaching the portion of the extended synthetic DNA polynucleotide (or selector polynucleotide that was 5' to the selector nucleotide residue (optionally a single ribonucleotide residue). “
Therefore, part (ii) refers to the use of a thermostable ribonuclease enzyme to cut at the selector nucleotide residue. However, the thermostable ribonuclease enzyme is explicitly recited as optional within the claim. This creates ambiguity because it raises the question of whether the thermostable ribonuclease enzyme is truly optional.
E) Regarding claim 11, part (e)(ii) recites "the extended synthetic DNA polynucleotide (or selector polynucleotide that was 5' to the selector nucleotide residue (optionally a single ribonucleotide residue)," which is indefinite.
First, the term "the extended synthetic DNA polynucleotide" lacks antecedent basis. The claim does not previously introduce or define an "extended synthetic DNA polynucleotide," and it is therefore unclear what structure this term refers to.
Second, the recitation contains uneven and unbalanced parentheses, which renders the scope unclear. It is not reasonably certain which language is intended to be optional, which language modifies which element, and what limitations are required by the claim.
Third, claim 11 further recites additional limitations in parentheses, such as "(optionally a single selector ribonucleotide residue)," which is indefinite.
In the claims, parentheses are typically permitted only to enclose abbreviations for a term or reference characters corresponding to drawings and description. Use of parentheses for other purposes should be avoided, as it introduces indefiniteness issues for it cannot be determined if the limitations in parenthesis are intended to be further limiting or something entirely different. Applicant is advised to revise the claim language to remove ambiguity and clearly set forth the required limitations, without reliance on unclear parenthetical expressions.
Claims 13 and 34-42 are rejected for depending from claim 1 and not remedying the indefiniteness.
D) Regarding claim 13, it recites "the reagent," which lacks antecedent basis. The claim does not previously recite an reagent.
E) Regarding claim 35, it recites "the rare allele," which lacks antecedent basis.
F) Claim 36 recites limitations in parentheses, such as "(optionally a single ribonucleotide residue)," which is indefinite because it cannot be determined if the limitations in parenthesis are intended to be further limiting or something entirely different.
G) Claim 38 recites limitations in parentheses, such as "(optionally a single ribonucleotide residue)," which is indefinite because it cannot be determined if the limitations in parenthesis are intended to be further limiting or something entirely different.
H) Regarding claim 39, it recites "the production of amplicons of interest," which lacks antecedent basis. The claim does not previously recite any production step for "amplicons of interest."
I) Regarding claim 40, it recites "wherein the selector polynucleotide is a single selector ribonucleotide residue," which is indefinite. Specifically, the term "polynucleotide" generally refers to a polymer comprising multiple nucleotide residues. In contrast, a "single selector ribonucleotide residue" refers to a single nucleotide unit. These terms have inconsistent and conflicting meanings. Therefore, it is unclear how a polynucleotide can be limited to a single ribonucleotide residue.
Applicant is advised to use full, clear, concise, and exact terms, and to apply such terms consistently throughout the claims, to distinctly point out the patentably novelty of the invention. See 37 CFR 1.111 and MPEP § 714.02.
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.
Claims 11, 13 and 34-42 are rejected under 35 U.S.C. 103 as being unpatentable over Cahill (Cahill et al.; Exo-proofreading, a versatile SNP scoring technology. Genome Res. 2003 May;13(5):925-31. doi: 10.1101/gr.939903. Epub 2003 Apr 14. PMID: 12695330; PMCID: PMC430895), in view of Sagawa (Sagawa et al.; CA2417798A1 - Method of amplifying nucleic acid ; Published 2003-01-30) .
A) Cahill teaches an exonuclease proofreading assay for allele detection that takes advantage of the 3' to 5' proofreading activity of DNA polymerase, utilizing primers labeled at the 3' end with a detectable tag (Abstract; Figure 1).
Regarding claim 11, Cahill teaches a method for amplifying nucleic acid for differentiating a first nucleic acid sequence from a second nucleic acid sequence
wherein the first and the second nucleic acid are in the same amplification reaction mixture (Figure 1; Figure 2; page 929, right-hand col, “Exo-Proofreading Assay”; “Allele Frequency”), comprising:
providing or having provided a selector polynucleotide,
wherein the selector polynucleotide contains therein a selector nucleotide residue (Figure 1 and legends, primer labeled with a detectable tag on the 3’ nucleotide base),
wherein the at least single residue selector nucleotide is structurally or chemically unlike any other residue within the region or section of the selector polynucleotide necessary for binding of the selector polynucleotide to a target nucleic acid (Figure 1; Table 1; page 929, right-hand col, “Oligonucleotide Primers”) , and
the selector polynucleotide has a 3' end that can be: extended by a DNA polymerase, or processed to have a 3' end that can be extended by a DNA polymerase (Figure 1) ;
providing or having provided a DNA polynucleotide or plurality of DNA polynucleotides (Figure 1),
contacting, annealing or hybridizing, the selector polynucleotide to the DNA polynucleotide or plurality of DNA polynucleotides (Figure 1),
wherein the DNA polynucleotide or plurality of DNA polynucleotides acts as a template DNA polynucleotide to the selector polynucleotide under conditions wherein the selector polynucleotide anneals or specifically hybridizes to a complementary sequence or substantially complementary sequence in the DNA polynucleotide, thereby generating a nucleic acid duplex;
wherein the selector polynucleotide is either paired to the template DNA polynucleotide at the position of the selector nucleotide residue or is not paired to the template DNA polynucleotide at the position of the selector nucleotide residue;
contacting the duplex with a DNA polymerase enzyme having 5' to 3' extension activity and having a 3' to 5' exonuclease activity (Figure 1 and legends) ,
wherein
(i) the selector nucleotide residue is mismatched between the selector polynucleotide and the DNA polynucleotide or plurality of DNA polynucleotides, and the 3' to 5' exonuclease activity results in enzymatically removing portions of the selector polynucleotide from the 3' end including the selector nucleotide residue and all nucleotides 3' of the selector nucleotide prior to the DNA polymerase extending what remains of the selector polynucleotide into a new extended DNA polynucleotide that does not retain the selector nucleotide residue (optionally a single ribonucleotide residue) (Figure 1 and legends, see Figure 1A, allele 2 ).
Cahill discloses that its exo-proofreading assay distinguishes alleles using primers labeled at the 3' terminus with a detectable tag. If the primer is mismatched to the template, the labeled nucleotide is removed by the polymerase's proofreading activity, and the tag is not incorporated into the amplified nucleic acid duplex. Cahill further teaches retaining the 5’ portion of its primer comprising 3’ tag, upon removal of the tagged nucleotide, thereby allowing for exponential amplification via PCR (Figure 1 and legends). However, Cahill does not explicitly teach contacting the nucleic acid duplex with a ribonuclease enzyme.
Sagawa teaches methods for highly sensitive and specific amplification of target nucleic acid, using chimeric oligonucleotide primers having a ribonucleotide provided at the 3'-terminus or in the 3'-terminal side. (abstract).
Regarding claim 11, Sagawa teaches contacting the newly created nucleic acid duplex with a ribonuclease enzyme (Figure 35, step 3), where the duplex comprises a ribonucleotide-containing primer extension product that is cleavable by RNase H. Because the chimeric oligonucleotide primers used to generate the duplex comprise a ribonucleotide being positioned at the 3'-terminus, the ribonucleotide is recognized and cleaved by RNase H when incorporated into a nucleic acid duplex, thereby initiating strand-displacement amplification, specifically for those nucleic acids comprising a cleavable ribonucleotide (page 50, lines 22-25 to page 51, lines 1-10).
Sagawa further teaches advantages of its amplification method, including high sensitivity, scalability, low cost, compatibility with other nucleic acid amplification techniques, and adaptability to various detection means (pages 109-110) .
Accordingly, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the exo-proofreading allele detection assay of Cahill by incorporating the ribonucleotide-containing primer design strategy and RNase H-initiated strand-displacement amplification taught by Sagawa. Both references relate to nucleic acid amplification assays that utilize modified primers at the 3' terminus. Cahill uses a detectable 3' tag to distinguish alleles based on proofreading activity, followed by purification and fluorescent measurement. Sagawa provides an alternative 3' modification that support an improved target detection approach ꟷ namely, a ribonucleotide ꟷ that enables RNase H-driven, target-specific amplification.
The skilled artisan would have been motivated to make the modification in order to leverage the potential advantages suggested by Sagawa's teachings. Incorporating the ribonucleotide modification into the primers of Cahill would have provided a predictable benefit: allele-specific amplification driven by RNase H cleavage of correctly incorporated ribonucleotide-containing primers, thereby enhancing sensitivity and expanding detection options beyond fluorescence-based readout.
The person of ordinary skill would have had a reasonable expectation of success in making this modification. As discussed above, both references are directed to the same field of nucleic acid amplification using modified primers and disclose technically compatible teachings. Therefore, a skilled artisan would have reasonably expected that combining these teachings would have yielded the predictable result of large amount of allele-specific amplification products suitable for various nucleic acid detection options.
B) Regarding claim 13, it recites "wherein the reagent used to cut on the 5' side of the single selector ribonucleotide is a ribonuclease H2." This limitation is obvious in view of the combined teachings of Cahill and Sagawa because it does not further limit the claimed method.
Per MPEP 2111.04, a wherein clause can limit a method claim if it contributes meaning and purpose to the manipulative steps.
In this instant case, the "wherein" clause does not introduce any additional steps or modify any existing step. It does not make a manipulative difference to the claim scope, and merely describes "the reagent," which is not recited in any of the steps in the claimed method.
Therefore, this claim language is interpreted as descriptive statement without any associated active steps and do not distinguish the claims from the prior art.
Regarding claim 34, Cahill teaches detecting the presence or absence of an allele in a biological specimen (Figure 1).
Regarding claim 35, it recites:
"wherein detecting the presence or absence of the rare allele in the biological specimen is for non-invasive pre-natal testing (NIPT), or to assess tissue compatibility or detecting donor-derived nucleic acid following organ transplant (optionally solid organ or bone marrow transplant), or to assess anti-microbial resistance (AMR) or early detection of microbial resistance in the individual in need thereof, or assessing the presence of minimum residual disease (MRD)."
This limitation is obvious in view of the combined teachings of Cahill and Sagawa because it does not further limit the claimed method.
Per MPEP 2111.04, a wherein clause can limit a method claim if it contributes meaning and purpose to the manipulative steps.
In this instant case, the "wherein" clause does not introduce any additional steps or modify any existing step. It merely lists intended applications of the method and does not make a manipulative difference to the claim scope. Therefore, this claim language is interpreted as descriptive statement without any associated active steps and do not distinguish the claims from the prior art.
Regarding claim 36, Sagawa teaches a second selector polynucleotide or primer, that is identical to a first selector polynucleotide, except that the selector nucleotide residue is replaced by a corresponding normal deoxyribonucleotide to create a DNA amplification primer (page 195, lines 12-16, Seq ID NO 76 is a non-chimeric control of the chimeric primer in SEQ ID NO: 74), and specific amounts of this DNA amplification primer are mixed with the first selector polynucleotide (page 195, lines 18-25).
Regarding claim 37, Cahill teaches the sequence of the new extended DNA polynucleotide, is determined by DNA sequencing (page 930, right-hand col, “Confirmation Sequencing”).
Regarding claim 38, Cahill teaches the identity of the nucleotide corresponding to the position of an original selector nucleotide residue is determined by extension of a primer over the site of interest (Figure 1; Figure 5).
Regarding claim 39, Sagawa teaches DNA chip array, which is an equivalent quantification method to qPCR (See Morey et al., Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR. Biol. Proced. Online 8, 175–193 (2006). doi.org/10.1251/bpo126; in abstract ).
Regarding claim 40, Sagawa teaches a single ribonucleotide residue (page 50, lines 22-25 to page 51, lines 1-2).
Regarding claim 41, it recites:
"wherein:
(a) the DNA polynucleotide or plurality of DNA polynucleotides are derived from a cell genome, a microbial genome or a viral genome;
(b) the genome, cDNA, cDNA library or genomic library is derived from a eukaryote or a prokaryote, a plant, an animal, or a mammal;
(c) the genome, cDNA, cDNA library or genomic library is derived from a human, (d) the genome, cDNA, cDNA library or genomic library is derived from a microorganism,
(e) the genome, cDNA, cDNA library or genomic library is derived from a bacterium, an algae, a protist, an Archea or a fungus, or
(f) the genome, cDNA, cDNA library or genomic library is derived from a virus or a bacteriophage."
This limitation is obvious in view of the combined teachings of Cahill and Sagawa because it does not further limit the claimed method.
Per MPEP 2111.04, a wherein clause can limit a method claim if it contributes meaning and purpose to the manipulative steps.
In this instant case, the "wherein" clause does not introduce any additional steps or modify any existing step. Instead, it merely provides alternatives for the source of the DNA polynucleotides or its optional derivation in (b)-(f). The claimed method does not include any steps for extracting, isolating, or preparing the polynucleotides from materials. Thus, this wherein clause only describes the origin of the DNA polynucleotides and does not make a manipulative difference to the claim scope.
Therefore, this claim language is interpreted as descriptive statement without any associated active steps and do not distinguish the claims from the prior art.
Regarding claim 42, Sagawa teaches the single selector nucleotide residue is located at the first position from the 3' end, or the ultimate position of the polynucleotide (page 50, lines 22-25 to page 51, lines 1-2).
Conclusion
Claims 11, 34 and 37-38 are objected to; claims 11,13 and 34-42 are rejected. No claims are allowed.
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/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
1 Claims 12 and 14 are withdrawn as being drawn to non-elected species B.
2 Claims 30-32 and 43 are withdrawn as being drawn to non-elected species A-1.