DETAILED ACTIONPreliminary Amendment
The preliminary amendment filed on April 5, 2024 has been entered. The claims pending in this application are claims 1, 3, 4, 6, 8-10, 13, 15-17, 19, 23-25, and 28. Claims 1, 3, 4, 6, 8-10, 13, 15-17, 19, 23-25, and 28 will be examined.
Claim Objections
Claim 1 is objected to because of the following informalities: (1) no period should appear after the label of each step, e.g., “a.” should be --a)--; (2) “a probe molecule (A₀) and a hybridised splint molecule (C)” should be “a probe molecule A0 and a splint molecule C”; (3) “each A0” in a) should be “the probe molecule A0 of each of the plurality of molecular systems”; (4) “C” in b) should be “the splint molecule C of each of the plurality of molecular systems”; (5) “A0” in b) should be “the probe molecule A0 of one of the plurality of molecular systems”; and (6) “1 to 50 bases in the 5’ direction from the 3'-end of A0” should be “of the probe molecule A0 which is 1 to 50 nucleotides from the 3’-end of the probe molecule A0”.
Claim 6 is objected to because of the following informalities: (1) “A0” should be “the probe molecule A0”; and (2) “DNA or RNA of” in line 2 should be deleted.
Claim 9 is objected to because of the following informality: “the target polynucleotide comprises a site of a genetic mutation and the genetic mutation is present at a low level in the sample compared to wild-type sequences” should be “the target polynucleotide sequences comprise a genetic mutation and compared to wild-type sequences of the target polynucleotide sequences, the genetic mutation is present at a low level in the target polynucleotide sequences of the sample”.
Claim 10 is objected to because of the following informality: “A2” should be “the circular product A2”.
Claim 13 is objected to because of the following informality: “A₀ has a 5’ end which is resistant to exonucleolysis and wherein a 5’-3’ exonuclease is used to digest any nucleic acid molecules which are not rendered resistant to this exonucleolysis, optionally wherein the exonuclease has activity at least partly dependent on the presence of a 5’- phosphate group and the digestion is carried out in the presence of a kinase and a phosphate donor” should be “the probe molecule A0 has a 5’ end which is resistant to exonucleolysis and is not resistant to a digestion of a 5’-3’ exonuclease, optionally wherein the digestion is carried out in the presence of a kinase and a phosphate donor”.
Claim 16 is objected to because of the following informality: “after step (ii) through addition of a pyrophosphatase” should be “by adding a pyrophosphatase after step (ii)”.
Claim 17 is objected to because of the following informality: “detecting the presence of A2 via nucleic acid amplification” should be “detecting the circular product A2 is by a nucleic acid amplification”.
Claim 19 is objected to because of the following informalities: “wherein multiple molecular systems are employed, each comprising A₀ selective for a different target sequence and each A₀ includes an identification region, optionally wherein the identification region is used as a priming site for nucleic acid amplification, enabling detection and identification of A₂; or the identification region is characterised using molecular probes or through sequencing, and optionally wherein step (v) further comprises the steps of: vi. labelling the amplification products from A₂ with a fluorescent signal using one or more oligonucleotide fluorescent binding dyes or molecular probes; vii. measuring the fluorescent signal; viii. exposing the amplification products from A₂ to a set of denaturing conditions; and ix. identifying the polynucleotide target sequence in the analyte by monitoring changes in the fluorescent signal during exposure to the denaturing conditions” should be “wherein the probe molecule A0 of each of the plurality of molecular systems is used for detecting a different target sequence of the target polynucleotide sequences and includes an identification region, optionally wherein the identification region is used as a priming site for a nucleic acid amplification reaction and used for detecting the circular product A2; or the identification region is analyzed by hybridizing the identification region to a molecular probe or by sequencing the identification region, and optionally wherein step (v) further comprises the steps of: vi) producing an amplification product of the circular product A2 and labelling the amplification product with a fluorescent dye; vii) measuring the fluorescent signal from the amplification product labeled with the fluorescent dye; viii) exposing the amplification products labeled with the fluorescent dye to a set of denaturing conditions; and ix) detecting one of the polynucleotide target sequences in the sample by monitoring changes in the fluorescent signal during said exposing the amplification products labeled with the fluorescent dye to the denaturing conditions”.
Claim 23 is objected to because of the following informality: “the different probes A0 comprise” should be “the probe molecule A0 of each of the plurality of molecular systems comprises”.
Claim 28 is objected to because of the following informality: “UDG” is an abbreviation. It can be used only when the whole phrase representing the abbreviation uses once.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 1, 3, 4, 6, 8-10, 13, 15-17, 19, 23-25, and 28 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 1 is rejected as vague and indefinite in view of the phrase “a varying 3’-end” in a) because it is unclear that this phrase means that the probe molecule A0 of each of the plurality of molecular systems has a different nucleotide sequence in its 3’ end or has a random nucleotide sequence in its 3’ end or has a different length in its 3’ end? Furthermore, since a) does not require that the probe molecule A0 of each of the plurality of molecular systems has a double stranded region, it is unclear why the probe molecule A0 of each of the plurality of molecular systems can have a loop region. Please clarify.
Claim 1 is rejected as vague and indefinite in view of the phrase “a varying sequence” in b) because it is unclear that this phrase means that 3’ end of the splint molecule C of each of the plurality of molecular systems has a different nucleotide sequence or has a random nucleotide sequence? Furthermore, since step b) does not require that the splint molecule C has a double stranded region, it is unclear why the splint molecule C can provide a single stranded 3’-overhang having a varying sequence. Please clarify.
Claim 3 is rejected as vague and indefinite because the claim does not make sense. Does this claim mean that the hybridized region between 5’ end of the probe molecule A0 and the splint molecule C has at least 5 complementary nucleotides or 7 complementary nucleotides? Please clarify.
Claim 4 is rejected as vague and indefinite because the claim does not make sense. Does this claim mean that the hybridized region between 3’ end of the splint molecule C and the region located within the loop region of the probe molecule A0 has at least 5 complementary nucleotides or 7 complementary nucleotides? Please clarify.
Claim 8 is rejected as vague and indefinite. Although the preamble of the claim is directed to a method for detecting target polynucleotide sequences in a given nucleic acid analyte, since there is no method step for detecting target polynucleotide sequences in a given nucleic acid, the goal of the claim (see the preamble) cannot be reached. Furthermore, since step i) does not require that a sample contains the target polynucleotide sequences, if the sample does not contain the target polynucleotide sequences, it is unclear why the target polynucleotide sequences in the given nucleic acid analyte can be detected. Please clarify.
Claim 8 is rejected as vague and indefinite because steps ii) to v) do not make sense in view of Figure 4a. Does steps ii) to v) mean ii) producing a first hybridization complex comprising the probe molecule A0 from one of the plurality of molecular systems, the splint molecule C from one of the plurality of molecular systems, and one of the target polynucleotide sequences such that the first hybridization comprises a first duplex formed by 5’ end of the probe molecule A0 and 5’ end of the splint molecule C and a second duplex formed by 3’ end of the probe molecule A0 and the one of the target polynucleotide sequences, and removing the second duplex of the first hybridization complex by treating the first hybridization complex with an enzyme for pyrophosphorolysis, thereby forming a shortened probe A1 comprising the first duplex and a cleaved probe molecule A0; iii) producing a second hybridization complex by hybridizing 3’ end of the cleaved probe molecule A0 with 3’ end of the splint molecule C in the shortened probe A1; iv) forming form a circular product A₂ by ligating 5’ end of the cleaved probe molecule A0 to 3’ end of the cleaved probe molecule A0 in the second hybridization complex; v) detecting the one of the target polynucleotide sequences by detecting the circular product A₂? Please clarify.
Claim 24 recites the limitation “the pyrophosphorolysis reaction” in the claim. There is insufficient antecedent basis for this limitation in the claim because there is no phrase “a pyrophosphorolysis reaction” before “the pyrophosphorolysis reaction”. Please clarify.
Claim 25 recites the limitation “the target nucleic acid sequence” in the claim. There is insufficient antecedent basis for this limitation in the claim because there is no phrase “a target nucleic acid sequence” before “the target nucleic acid sequence”. Please clarify.
Conclusion
No claim is allowed.
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/FRANK W LU/
Primary Examiner, Art Unit 1683
June 24, 2026
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