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 July 21, 2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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 110 and 111 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 110 recites the limitation “the complex”. There is insufficient antecedent basis for this limitation in the claim. Claim 101 in which 110 is dependent upon, does not mention a complex.
Claim 111 recites the limitation “hybridized to the decoy oligonucleotide”. There is insufficient antecedent basis for this limitation in the claim. Claim 111 is dependent upon 110. Claim 101 in which 110 is dependent upon mentions the “first and second hybridization regions”, however, does not mention a specific step of hybridization taking place.
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.
Claim(s) 101-111,113, and 117-120 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bava et. al. (US 20230037182 A1, filed 7/29/22) in view of Kühnemund et. al. (US 20220195498 A1; filed 10/22/21 cited on IDS).
The applied reference has a common assignee with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C.
102(a)(2).
This rejection under 35 U.S.C. 103 might be overcome by: (1) a showing under 37 CFR
1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly
from the inventor or a joint inventor of this application and is thus not prior art in accordance
with 35 U.S.C.102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure
under 35 U.S.C. 102(b)(2)(B); or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing
that, not later than the effective filing date of the claimed invention, the subject matter
disclosed and the claimed invention were either owned by the same person or subject to an
obligation of assignment to the same person or subject to a joint research agreement. See
generally MPEP § 717.02.
Bava teaches a method for analyzing a biological sample, comprising: a) contacting the biological sample with a circularizable probe or probe set and a decoy oligonucleotide, wherein: the biological sample comprises a target nucleic acid comprising a target region, the circularizable probe or probe set comprises a first hybridization region and a second hybridization region which, upon hybridization to the target region, are ligatable, and the decoy oligonucleotide comprises a decoy region capable of hybridizing to the first and/or second hybridization regions; b) allowing the circularizable probe or probe set and the target nucleic acid to hybridize at one or more locations in the biological sample; c) circularizing the circularizable probe or probe set to generate a circular probe by ligating the first and second hybridization regions using the target region as template; d) generating a rolling circle amplification (RCA) product of the circular probe; and e) detecting the RCA product at the one or more locations, thereby detecting the target nucleic acid in the biological sample ([0004], [0031], [0015], instant claim 101).
Bava teaches contacting the sample containing the target nucleic acid with a circularizable probe and a blocking strand (that equates to the decoy oligonucleotide of the instant claim) simultaneously ([0221], instant claim 102).
Bava teaches that the target sequence is hybridized to a blocking strand before being contacted with a probe ([0193], instant claim 103).
Bava teaches displacement of the blocking strand if the interrogatory region is complementary to the region of interest, to allow the hybridization region to be available for hybridizing to the target nucleic acid or the circularizable probe ([0017], instant claim 104).
Bava teaches hybridization in step b) and the ligation in step c) are carried out under the same reaction condition, optionally wherein a ligase that performs the ligation is added prior to, during, and/or after the hybridization in step b). ([0275], [0335], instant claim 105).
Bava teaches that probes that do not specifically hybridize to target nucleic acids in the sample can be disassociated from the target nucleic acids in the sample by washing before the amplification step D, and optionally before the ligation step C; indicating the washing does not have to take place prior to step C, teaching the limitations of instant claims 106 and 107 ([0381]).
Bava teaches in step 1 of Figure 1A probe hybridization (with optional blocking strand) where an interrogatory sequence of the probe matches a region of interest comprised by the target nucleic acid, the padlock probe displaces the blocking strand. The reference recites the blocking strand as being an optional component in the first step of 1A that takes place prior to the ligation in step 3 of FIG 1B above. Therefore, the blocking strand-probe hybridized complex could be optionally present in the biological sample before ligation occurs, teaching instant claims 108 and 109.
Bava teaches wherein in the complex, the decoy oligonucleotide comprises one or more mismatches with the circularizable probe or probe set at or near a ligation junction ([0213], instant claim 110).
Bava teaches the blocking strand is hybridized to the hybridization region in the probe and the blocking strand can be hybridized to the hybridization region of the target nucleic acid. If the interrogatory region is not complementary to the region of interest, the blocking strand is not displaced and the hybridization regions in the target nucleic acid and the probe are unavailable for binding to each other, preventing generation of the circular probe ([0213], instant claim 111).
Bava teaches the ligase is present in and/or added to a reaction buffer for the hybridization in step b) ([0335], instant claim 113).
Bava teaches methods involving the use of one or more probes analyzing one or more target nucleic acids present in a cell or a biological sample, such as a tissue sample ([0089], instant claim 118).
Bava teaches probes and probe sets can be hybridized to an endogenous analyte and/or a labelling agent and each probe may comprise one or more barcode sequences. The one or more barcode sequences or complements thereof can be detected by: i) contacting the biological sample with one or more detectably-labeled probes that directly or indirectly bind to the one or more barcode sequences or complements thereof, ii) detecting signals associated with the one or more detectably-labeled probes ([0186], [0070], instant claim 119).
Bava teaches a method for analyzing a biological sample, comprising: a) contacting the biological sample with a circularizable probe or probe set and a decoy oligonucleotide, wherein: the biological sample comprises a target nucleic acid comprising a target region, the circularizable probe or probe set comprises a first hybridization region and a second hybridization region which, upon hybridization to the target region, are ligatable, and the decoy oligonucleotide comprises a decoy region capable of hybridizing to the target region; b) allowing the circularizable probe or probe set and the target nucleic acid to hybridize at one or more locations in the biological sample; c) circularizing the circularizable probe or probe set to generate a circular probe by ligating the first and second hybridization regions using the target region as template; d) generating a rolling circle amplification (RCA) product of the circular probe e) detecting a signal associated with the RCA product at the one or more locations, thereby detecting the target nucleic acid in the biological sample ([0004],[0256], instant claim 120).
Bava does not teach the probe or probe set and decoy oligonucleotide provided as the first complex, however, Kühnemund teaches a method for nucleic acid sequence detection where the first and second probes can be contacted with the interfering agent to form a second probe/ interfering agent hybridization complex ([0009], instant claim 117).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Bava to incorporate the teaching of Kühnemund to provide the decoy oligonucleotide and probe as the first hybridization complex in order to prevent the generation of an amplification product and ultimately regulate gene expression.
Claim(s) 112 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bava et. al. (US 20230037182 A1, filed 7/29/22) and Kühnemund et. al. (US 20220195498 A1; filed 10/22/21 cited on IDS) as applied to claims 101-111,113, and 117-120 above, and further in view of Harada et. al. (US 10550429 B2; filed 5/30/19 cited on IDS) .
The teachings of Bava and Kühnemund are discussed above. Bava and Kühnemund fail to teach a decoy oligonucleotide possessing a terminating group. However, Harada teaches in FIG 21 an oligonucleotide 2110 with a modification for blocking primer extension located on the 3’ end (shown as “X”). When oligonucleotide 2110 and unbarcoded ssDNA 2120 bind to each other in a primer extension reaction, only unbarcoded ssDNA 2120 can be extended. Harada further teaches that a modification for blocking primer extension by a polymerase may be a carbon spacer group of different lengths or a dideoxynucleotide. Paragraph [0069] of the instant application teaches that in some instances; the decoy target comprises a 3' chain terminating nucleotide or modification such as a 3' dideoxynucleotide. ((174), (175), instant claim 112)).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Bava and Kühnemund to incorporate the teaching of Harada to attach a terminating group to the decoy oligonucleotide for the purpose of preventing continuous amplification of additional decoy oligonucleotides that can interfere with probe generation and amplification during synthesis.
Claim(s) 114 and 115 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bava et. al. (US 20230037182 A1, filed 7/29/22) and Kühnemund et. al. (US 20220195498 A1; filed 10/22/21 cited on IDS) as applied to claims 101-111,113, and 117-120 above, and further in view of Urdea et. al. (US 5635352 A; published 6/3/97 cited on IDS) as evidenced by
Behind the Bench Staff (Behind the Bench Staff, ThermoFisher Scientific, 2019).
The teachings of Bava and Kühnemund are discussed above. Bava and Kühnemund fail to teach the degree of complementarity between the decoy oligonucleotide and the hybridization probe duplex compared to the complementarity of the hybridization region to either the target or off-target nucleic acid.
Urdea teaches an amplification assay carried out with two distinct amplification multimers that are bridged by one or more label probes. Each label probe contains regions that are complementary to corresponding regions in each amplification multimer. The length of the complementary regions is selected so as to ensure that the melting temperature of the complex formed between the label probe and a single amplification multimer will be lower, preferably at least about 10 degrees Celsius lower than the melting temperature of the complex formed between the two amplification multimers ((17), instant claim 114).
Urdea further teaches a first nucleic acid sequence (L-1) comprising a nucleic acid sequence complementary to a region in repeating oligonucleotide subunits of an amplifier probe. L-1 and the corresponding complementary sequences in the amplifier probes are selected such that the melting temperature of the complex formed from both amplifier probes and the label probes is preferably at least about 10 degrees Celsius higher than the melting temperature of the complex formed between the label probe and a single amplifier multimer ((49), instant claim 115). As evidenced by Behind the Bench Staff, nucleotide base complementarity impacts the melting temperature (Tm), G and C result in higher melting temperatures than A and T. If the Tm of a primer is very low, finding a sequence with greater GC content can increase Tm. A higher/lower G-C content in oligo strands is correlated with a higher/lower melting temperature and indicates complementarity between the base pairs.
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Bava and Kühnemund to incorporate the teaching of Urdea for routine optimization by biasing the GC content and influencing preferential binding of the decoy oligo strand and probe with the target nucleic acid to reduce noise and yield the desired amplification result within the biological sample.
Claim(s) 116 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bava et. al. (US 20230037182 A1, filed 7/29/22) and Kühnemund et. al. (US 20220195498 A1; filed 10/22/21 cited on IDS) as applied to claims 101-111,113, and 117-120 above, and further in view of Guo et. al. (WO2020102094A1; filed 11/11/19 cited on IDS) .
The teachings of Bava and Kühnemund are discussed above. Bava and Kühnemund fail to teach percentage of complementarity between the decoy oligonucleotide and the hybridization region in the probe. However, Guo teaches a method for analyzing biomolecules in a tissue sample, and duplex formation between two oligonucleotides containing mismatched base pairs. Paragraph [0058] recites “For example, nucleotide sequences that are complementary to each other have mismatches at less than 20% of the bases, at less than about 10% of the bases, preferably at less than about 5% of the bases, and more preferably have no mismatches.” Mismatches of 5% to 20% of the base pairs between the oligonucleotides corresponds to 80% to 95% complementarity, teaching the limitations of instant claim 116.
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Bava and Kühnemund to incorporate the teaching of Guo to allow a decoy oligonucleotide to have a lower percentage of mismatches to equate to a higher percentage of complementarity to the hybridization region of the probe to influence preferential binding of the decoy to probe over the off-target region. Upon hybridization to the hybridization region, the decoy oligonucleotide may not be capable of generating a product that is detectable by detectable probes configured to detect the probe or probe set, further preventing amplification within a biological sample.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Avanda Harvey-Butler whose telephone number is (571)272-6511. The examiner can normally be reached M-F, 9-5 ET.
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/A.H.B./Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683