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 I, E. coli, Polymerase, clustering composition in the reply filed on 11/21/2025 is acknowledged. 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Claims 9, 15-23 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 11/21/2025.
Priority
The instant application was filed 09/27/2023 and claims priority from provisional application 63411965 , filed 09/30/2022
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4/4/2024 and 5/1/2024 are being considered by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - The incorporation by reference paragraph required by 37 CFR 1.834(c)(1), 1.835(a)(2), or 1.835(b)(2) is missing, defective or incomplete.
Required response - Applicant must:
• Provide a substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
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 1-5, 7-8, 10-14 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 recites, “An amplification composition”. The specification states, “[0091] By "amplification composition" is meant a composition that is suitable for the amplification of a target nucleic acid template. By contrast, a "cluster composition" refers to a composition that is suitable for the amplification of a (single) target sequence into a cluster (i.e. the composition is suitable for cluster generation, particularly for the generation of a monoclonal cluster) as described above, not just for any amplification method.” However the independent claim merely requires, “comprising ATP sulfurylase.” Thus the metes and bounds of the claim are confusing and unclear as does not appear an ATP sulfurylase is by itself suitable for amplification of a target nucleic acid.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-5, 7-8, 10-14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural occurring product of an ATP sulfurylase. This judicial exception is not integrated into a practical application because the claims provide no limitations which specifically require the hand of man. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because claims provide no limitations which specifically require the hand of man.
Claim analysis
The instant claim 1 is directed towards An amplification composition comprising ATP sulfurylase. This encompasses naturally occurring protein ATP sulfurylase.
Dependent claims set forth further limitations to about the concentration of the ATP sulfurylase, additional elements of composition, source of the ATP sulfurylase, the presence of a buffer, etc.
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case the Step 1 requirement is satisfied as the claims are directed towards a composition.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, natural phenomena or composition .
With regards to claim 1, the claim recites, ATP sulfurylase.” This encompasses a naturally occurring composition
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? The answer is no as the claims provide no limitations which require the hand of man..
Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No as the claims provide no limitations which require the hand of man.
Thus the claims encompass naturally occurring products and thus are not patent eligible.
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) 1, 3, 5, 7, 10, 12- 13 are rejected under 35 U.S.C. 102(a)(1)/102 (a)(2) as being anticipated by Fang (US 20070009925).
As noted in the MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Further, a preamble is generally not accorded any patentable weight where it merely recites the purpose of a process or the intended use of a structure, and where the body of the claim does not depend on the preamble for completeness but, instead, the process steps or structural limitations are able to stand alone. See In re Hirao, 535 F.2d 67, 190 USPQ 15 (CCPA 1976) and Kropa v. Robie, 187 F.2d 150, 152, 88 USPQ 478, 481 (CCPA 1951). Accordingly, the claim language of "an amplification composition” merely sets forth the intended use or purpose of the claimed composition, but does not limit the scope of the claims.
Fang is drawn to, “The disclosed teachings provide methods and kits for determining the sequence of a gDNA target region comprising multiple amplification steps and sequencing at least part of the amplification product of one or more amplification reactions.” (abstract).
With regards to claim 1 and 13, Fang teaches, “0039] According to certain disclosed methods, an amplification composition comprises at least one of an extending enzyme, an ATP sulfurylase, a luciferase, and an apyrase.” Thus Fang anticipates claim 1.
With regards to claim 3, Fang teaches, “[0042] The term "ATP sulfurylase", also known as sulfate adenylyltransferase, refers to a polypeptide that, under suitable conditions, catalyzes the reaction: ATP+sulfate=pyrophosphate+adenylyl sulfate (see, e.g., Nyren and Lundin, Analyt. Biochem. 151:504-09, 1985; and Agah et al., Nucl. Acids Res. 32:e166, 2004). Expressly within the intended scope of the term ATP sulfurylase are enzymatically active mutants or variants thereof.”
With regards to claim 5, Fang teaches “[0040] The term "extending enzyme" refers to a polypeptide that, under suitable reaction conditions, catalyzes the synthesis of a complementary nucleotide strand in a template-dependent manner. In some embodiments, an extending enzyme catalyzes the 5'-3'extension of a hybridized primer. In some embodiments, an extending enzyme binds to a double-stranded DNA promoter, separates the two strands, and uses the 3'-5' strand as a template to synthesize a complementary 5'-3' strand comprising ribonucleotides. Extending enzymes are typically: (1) DNA polymerases, including (a) RNA-dependent DNA polymerases, including reverse transcriptases, and (b) DNA-dependent DNA polymerases; and (2) RNA polymerases, including (a) DNA-dependent RNA polymerases and (b) RNA-dependent RNA polymerases. In certain embodiments, an extending enzyme is a reverse transcriptase, for example but not limited to, retroviral reverse transcriptases such as Avian Myeloblastosis Virus (AMV) reverse transcriptase and Moloney Murine Leukemia Virus (MMLV) reverse transcriptase. In certain embodiments, an extending enzyme is a DNA-dependent DNA polymerase, including Taq DNA polymerase and the Klenow fragment of DNA polymerase I. Certain DNA-dependent DNA polymerases possess reverse transcriptase activity under some conditions, for example but not limited to, the DNA polymerase of Thermus thermophilus (Tth DNA polymerase, E.C. 2.7.7.7) which demonstrates reverse transcription in the presence of Mn.sup.2+, but not Mg.sup.2+ (see also, GeneAmp.RTM. AccuRT RNA PCR Kit and Hot Start RNA PCR Kit comprising a recombinant polymerase derived from Thermus species Z05, both from Applied Biosystems). Likewise, certain reverse transcriptases possess DNA-dependent DNA polymerase activity under certain reaction conditions, including AMV reverse transcriptase and MMLV reverse transcriptase. In some embodiments, an amplification reaction comprises transcription, including in vitro transcription, and an extending enzyme comprises a DNA-dependent RNA polymerase, for example but not limited to bacteriophage T3, SP6, and T7 RNA polymerases. Descriptions of extending enzymes can be found in, among other places, Lehninger Principles of Biochemistry, 3d ed., Nelson and Cox, Worth Publishing, New York, N.Y., 2000 ("Lehninger"), particularly Chapters 26 and 29; Twyman, Advanced Molecular Biology: A Concise Reference, Bios Scientific Publishers, New York, N.Y., 1999; Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., including supplements through April 2005 ("Ausubel et al."); and Enzymatic Resource Guide: Polymerases, Promega, Madison, Wis., 1998. Expressly within the intended scope of the term extending enzyme are enzymatically active mutants or variants thereof, and incluidng enzymes modified to confer different temperature-sensitive properties (see, e.g., U.S. Pat. Nos. 5,773,258; 5,677,152; and 6,183,998; and DNA Amplification: Current Techniques and Applications, Demidov and Broude, eds., Horizon Bioscience, 2004, particularly in Chapter 1.1):
With regards to claim 7, Fang teaches, “recombinant S. cerevisiae ATP sulfurylase,” (0093)
With regards to claim 10, Fang does not teach PEG and thus anticipates the claim.
With regards to claim 12, Fang teaches sequencing by synthesis (0093)
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) 1-3, 5, 7-8, 10-15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fang (US 20070009925), Liu (Biochemistry1994, 33, 2042-2047) and Uniprot (A0A0F3TAE2;, Jun 24, 2015)
As noted in the MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Further, a preamble is generally not accorded any patentable weight where it merely recites the purpose of a process or the intended use of a structure, and where the body of the claim does not depend on the preamble for completeness but, instead, the process steps or structural limitations are able to stand alone. See In re Hirao, 535 F.2d 67, 190 USPQ 15 (CCPA 1976) and Kropa v. Robie, 187 F.2d 150, 152, 88 USPQ 478, 481 (CCPA 1951). Accordingly, the claim language of "an amplification composition” merely sets forth the intended use or purpose of the claimed composition, but does not limit the scope of the claims.
Fang is drawn to, “The disclosed teachings provide methods and kits for determining the sequence of a gDNA target region comprising multiple amplification steps and sequencing at least part of the amplification product of one or more amplification reactions.” (abstract).
With regards to claim 1 and 13, Fang teaches, “0039] According to certain disclosed methods, an amplification composition comprises at least one of an extending enzyme, an ATP sulfurylase, a luciferase, and an apyrase.” Thus Fang anticipates claim 1.
Fang does not specifically teach E coli ATP sulfurylase, reaction conditions, or SEQ ID NO 1 or a fragment thereof.
However, Liu teaches isolation of E. coli K12 ATP sulfurylase. (title, abstract, materials and methods). Liu teaches synthesis of APS using ATP sulfurylase at 0.92µM at pH 8.0 with MgCl2(synthesis of 18O APS, page 2043)
Uniprot (A0A0F3TAE2) teaches a E. coli ATP sulfurylase sequence comprising SEQ ID NO 1.
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 to use coli K12 ATP sulfurylase or SEQ ID NO 1 at concentration, pH and MgCl2 concentrations taught by the art. Thea artisan would be motivated to look to the art of Liu and Uniprot as Fang does not specifically teach the conditions for ATP sulfurylase or sequences. The artisan would be motivated to use conditions and specific amino acid sequence in which ATP sulfurylase was known to work. The artisan would have a reasonable expectation of success as the artisan is merely using known reagents in known conditions.
With regards to claim 3, Fang teaches, “[0042] The term "ATP sulfurylase", also known as sulfate adenylyltransferase, refers to a polypeptide that, under suitable conditions, catalyzes the reaction: ATP+sulfate=pyrophosphate+adenylyl sulfate (see, e.g., Nyren and Lundin, Analyt. Biochem. 151:504-09, 1985; and Agah et al., Nucl. Acids Res. 32:e166, 2004). Expressly within the intended scope of the term ATP sulfurylase are enzymatically active mutants or variants thereof.”
With regards to claim 5, Fang teaches “[0040] The term "extending enzyme" refers to a polypeptide that, under suitable reaction conditions, catalyzes the synthesis of a complementary nucleotide strand in a template-dependent manner. In some embodiments, an extending enzyme catalyzes the 5'-3'extension of a hybridized primer. In some embodiments, an extending enzyme binds to a double-stranded DNA promoter, separates the two strands, and uses the 3'-5' strand as a template to synthesize a complementary 5'-3' strand comprising ribonucleotides. Extending enzymes are typically: (1) DNA polymerases, including (a) RNA-dependent DNA polymerases, including reverse transcriptases, and (b) DNA-dependent DNA polymerases; and (2) RNA polymerases, including (a) DNA-dependent RNA polymerases and (b) RNA-dependent RNA polymerases. In certain embodiments, an extending enzyme is a reverse transcriptase, for example but not limited to, retroviral reverse transcriptases such as Avian Myeloblastosis Virus (AMV) reverse transcriptase and Moloney Murine Leukemia Virus (MMLV) reverse transcriptase. In certain embodiments, an extending enzyme is a DNA-dependent DNA polymerase, including Taq DNA polymerase and the Klenow fragment of DNA polymerase I. Certain DNA-dependent DNA polymerases possess reverse transcriptase activity under some conditions, for example but not limited to, the DNA polymerase of Thermus thermophilus (Tth DNA polymerase, E.C. 2.7.7.7) which demonstrates reverse transcription in the presence of Mn.sup.2+, but not Mg.sup.2+ (see also, GeneAmp.RTM. AccuRT RNA PCR Kit and Hot Start RNA PCR Kit comprising a recombinant polymerase derived from Thermus species Z05, both from Applied Biosystems). Likewise, certain reverse transcriptases possess DNA-dependent DNA polymerase activity under certain reaction conditions, including AMV reverse transcriptase and MMLV reverse transcriptase. In some embodiments, an amplification reaction comprises transcription, including in vitro transcription, and an extending enzyme comprises a DNA-dependent RNA polymerase, for example but not limited to bacteriophage T3, SP6, and T7 RNA polymerases. Descriptions of extending enzymes can be found in, among other places, Lehninger Principles of Biochemistry, 3d ed., Nelson and Cox, Worth Publishing, New York, N.Y., 2000 ("Lehninger"), particularly Chapters 26 and 29; Twyman, Advanced Molecular Biology: A Concise Reference, Bios Scientific Publishers, New York, N.Y., 1999; Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., including supplements through April 2005 ("Ausubel et al."); and Enzymatic Resource Guide: Polymerases, Promega, Madison, Wis., 1998. Expressly within the intended scope of the term extending enzyme are enzymatically active mutants or variants thereof, and incluidng enzymes modified to confer different temperature-sensitive properties (see, e.g., U.S. Pat. Nos. 5,773,258; 5,677,152; and 6,183,998; and DNA Amplification: Current Techniques and Applications, Demidov and Broude, eds., Horizon Bioscience, 2004, particularly in Chapter 1.1):
With regards to claim 7, Fang teaches, “recombinant S. cerevisiae ATP sulfurylase,” (0093)
With regards to claim 10, Fang does not teach PEG and thus anticipates the claim.
With regards to claim 12, Fang teaches sequencing by synthesis (0093)
Claim(s) 1, 3- 5, 7, 10, 12- 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fang (US 20070009925) and ORTAC (WO2021102210).
As noted in the MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Further, a preamble is generally not accorded any patentable weight where it merely recites the purpose of a process or the intended use of a structure, and where the body of the claim does not depend on the preamble for completeness but, instead, the process steps or structural limitations are able to stand alone. See In re Hirao, 535 F.2d 67, 190 USPQ 15 (CCPA 1976) and Kropa v. Robie, 187 F.2d 150, 152, 88 USPQ 478, 481 (CCPA 1951). Accordingly, the claim language of "an amplification composition” merely sets forth the intended use or purpose of the claimed composition, but does not limit the scope of the claims.
Fang is drawn to, “The disclosed teachings provide methods and kits for determining the sequence of a gDNA target region comprising multiple amplification steps and sequencing at least part of the amplification product of one or more amplification reactions.” (abstract).
With regards to claim 1 and 13, Fang teaches, “0039] According to certain disclosed methods, an amplification composition comprises at least one of an extending enzyme, an ATP sulfurylase, a luciferase, and an apyrase.” Thus Fang anticipates claim 1.
With regards to claim 3, Fang teaches, “[0042] The term "ATP sulfurylase", also known as sulfate adenylyltransferase, refers to a polypeptide that, under suitable conditions, catalyzes the reaction: ATP+sulfate=pyrophosphate+adenylyl sulfate (see, e.g., Nyren and Lundin, Analyt. Biochem. 151:504-09, 1985; and Agah et al., Nucl. Acids Res. 32:e166, 2004). Expressly within the intended scope of the term ATP sulfurylase are enzymatically active mutants or variants thereof.”
Fang does not specifically teach a concentration of APS.
However, Ortac teaches ATP sulfurylase/luciferase signaling amplification loop using MgCl2, ATP sulfurylase, and 200 micromolar of APS (0276)
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 to use 200 micromolar of APS. The artisan would be motivated to look to the prior art such as Ortac as Fang provides no specific concentrations for APS. The artisan would have a reasonable expectation of success as the artisan is merely using known concentration of a known reactant,
With regards to claim 5, Fang teaches “[0040] The term "extending enzyme" refers to a polypeptide that, under suitable reaction conditions, catalyzes the synthesis of a complementary nucleotide strand in a template-dependent manner. In some embodiments, an extending enzyme catalyzes the 5'-3'extension of a hybridized primer. In some embodiments, an extending enzyme binds to a double-stranded DNA promoter, separates the two strands, and uses the 3'-5' strand as a template to synthesize a complementary 5'-3' strand comprising ribonucleotides. Extending enzymes are typically: (1) DNA polymerases, including (a) RNA-dependent DNA polymerases, including reverse transcriptases, and (b) DNA-dependent DNA polymerases; and (2) RNA polymerases, including (a) DNA-dependent RNA polymerases and (b) RNA-dependent RNA polymerases. In certain embodiments, an extending enzyme is a reverse transcriptase, for example but not limited to, retroviral reverse transcriptases such as Avian Myeloblastosis Virus (AMV) reverse transcriptase and Moloney Murine Leukemia Virus (MMLV) reverse transcriptase. In certain embodiments, an extending enzyme is a DNA-dependent DNA polymerase, including Taq DNA polymerase and the Klenow fragment of DNA polymerase I. Certain DNA-dependent DNA polymerases possess reverse transcriptase activity under some conditions, for example but not limited to, the DNA polymerase of Thermus thermophilus (Tth DNA polymerase, E.C. 2.7.7.7) which demonstrates reverse transcription in the presence of Mn.sup.2+, but not Mg.sup.2+ (see also, GeneAmp.RTM. AccuRT RNA PCR Kit and Hot Start RNA PCR Kit comprising a recombinant polymerase derived from Thermus species Z05, both from Applied Biosystems). Likewise, certain reverse transcriptases possess DNA-dependent DNA polymerase activity under certain reaction conditions, including AMV reverse transcriptase and MMLV reverse transcriptase. In some embodiments, an amplification reaction comprises transcription, including in vitro transcription, and an extending enzyme comprises a DNA-dependent RNA polymerase, for example but not limited to bacteriophage T3, SP6, and T7 RNA polymerases. Descriptions of extending enzymes can be found in, among other places, Lehninger Principles of Biochemistry, 3d ed., Nelson and Cox, Worth Publishing, New York, N.Y., 2000 ("Lehninger"), particularly Chapters 26 and 29; Twyman, Advanced Molecular Biology: A Concise Reference, Bios Scientific Publishers, New York, N.Y., 1999; Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., including supplements through April 2005 ("Ausubel et al."); and Enzymatic Resource Guide: Polymerases, Promega, Madison, Wis., 1998. Expressly within the intended scope of the term extending enzyme are enzymatically active mutants or variants thereof, and incluidng enzymes modified to confer different temperature-sensitive properties (see, e.g., U.S. Pat. Nos. 5,773,258; 5,677,152; and 6,183,998; and DNA Amplification: Current Techniques and Applications, Demidov and Broude, eds., Horizon Bioscience, 2004, particularly in Chapter 1.1):
With regards to claim 7, Fang teaches, “recombinant S. cerevisiae ATP sulfurylase,” (0093)
With regards to claim 10, Fang does not teach PEG and thus anticipates the claim.
With regards to claim 12, Fang teaches sequencing by synthesis (0093)
Claim(s) 1, 3, 5, 7, 10, 12- 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fang (US 20070009925) and Nemiroski (US2019/0338352)
As noted in the MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Further, a preamble is generally not accorded any patentable weight where it merely recites the purpose of a process or the intended use of a structure, and where the body of the claim does not depend on the preamble for completeness but, instead, the process steps or structural limitations are able to stand alone. See In re Hirao, 535 F.2d 67, 190 USPQ 15 (CCPA 1976) and Kropa v. Robie, 187 F.2d 150, 152, 88 USPQ 478, 481 (CCPA 1951). Accordingly, the claim language of "an amplification composition” merely sets forth the intended use or purpose of the claimed composition, but does not limit the scope of the claims.
Fang is drawn to, “The disclosed teachings provide methods and kits for determining the sequence of a gDNA target region comprising multiple amplification steps and sequencing at least part of the amplification product of one or more amplification reactions.” (abstract).
With regards to claim 1 and 13, Fang teaches, “0039] According to certain disclosed methods, an amplification composition comprises at least one of an extending enzyme, an ATP sulfurylase, a luciferase, and an apyrase.” Thus Fang anticipates claim 1.
Fang does not specifically teach a clustering composition.
However, Nemiroski teaches pyrosequencing method using ATP sulfurylase and using clusters (0075). Nemiroski teaches, “[0081] A method set forth herein can use any of a variety of amplification techniques. Exemplary techniques that can be used include, but are not limited to, polymerase chain reaction (PCR), rolling circle amplification (RCA), multiple displacement amplification (MDA), bridge amplification, or random prime amplification (RPA). In particular embodiments, one or more primers used for amplification can be attached to a surface in a vessel, such as a flow cell. Methods that result in one or more features on a solid support, where each feature is attached to multiple copies of a particular nucleic acid template, can be referred to as ‘clustering’ methods.
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 to provide a clustering composition with the ATP sulfurylase. The artisan would be motivated to provide multiple copies a nucleic acid template to enable easier detection. The artisan would have a reasonable expectation of success as the artisan is merely using known methods.
With regards to claim 3, Fang teaches, “[0042] The term "ATP sulfurylase", also known as sulfate adenylyltransferase, refers to a polypeptide that, under suitable conditions, catalyzes the reaction: ATP+sulfate=pyrophosphate+adenylyl sulfate (see, e.g., Nyren and Lundin, Analyt. Biochem. 151:504-09, 1985; and Agah et al., Nucl. Acids Res. 32:e166, 2004). Expressly within the intended scope of the term ATP sulfurylase are enzymatically active mutants or variants thereof.”
Fang does not specifically teach a concentration of APS.
However, Ortac teaches ATP sulfurylase/luciferase signaling amplification loop using MgCl2, ATP sulfurylase, and 200 micromolar of APS (0276)
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 to use 200 micromolar of APS. The artisan would be motivated to look to the prior art such as Ortac as Fang provides no specific concentrations for APS. The artisan would have a reasonable expectation of success as the artisan is merely using known concentration of a known reactant,
With regards to claim 5, Fang teaches “[0040] The term "extending enzyme" refers to a polypeptide that, under suitable reaction conditions, catalyzes the synthesis of a complementary nucleotide strand in a template-dependent manner. In some embodiments, an extending enzyme catalyzes the 5'-3'extension of a hybridized primer. In some embodiments, an extending enzyme binds to a double-stranded DNA promoter, separates the two strands, and uses the 3'-5' strand as a template to synthesize a complementary 5'-3' strand comprising ribonucleotides. Extending enzymes are typically: (1) DNA polymerases, including (a) RNA-dependent DNA polymerases, including reverse transcriptases, and (b) DNA-dependent DNA polymerases; and (2) RNA polymerases, including (a) DNA-dependent RNA polymerases and (b) RNA-dependent RNA polymerases. In certain embodiments, an extending enzyme is a reverse transcriptase, for example but not limited to, retroviral reverse transcriptases such as Avian Myeloblastosis Virus (AMV) reverse transcriptase and Moloney Murine Leukemia Virus (MMLV) reverse transcriptase. In certain embodiments, an extending enzyme is a DNA-dependent DNA polymerase, including Taq DNA polymerase and the Klenow fragment of DNA polymerase I. Certain DNA-dependent DNA polymerases possess reverse transcriptase activity under some conditions, for example but not limited to, the DNA polymerase of Thermus thermophilus (Tth DNA polymerase, E.C. 2.7.7.7) which demonstrates reverse transcription in the presence of Mn.sup.2+, but not Mg.sup.2+ (see also, GeneAmp.RTM. AccuRT RNA PCR Kit and Hot Start RNA PCR Kit comprising a recombinant polymerase derived from Thermus species Z05, both from Applied Biosystems). Likewise, certain reverse transcriptases possess DNA-dependent DNA polymerase activity under certain reaction conditions, including AMV reverse transcriptase and MMLV reverse transcriptase. In some embodiments, an amplification reaction comprises transcription, including in vitro transcription, and an extending enzyme comprises a DNA-dependent RNA polymerase, for example but not limited to bacteriophage T3, SP6, and T7 RNA polymerases. Descriptions of extending enzymes can be found in, among other places, Lehninger Principles of Biochemistry, 3d ed., Nelson and Cox, Worth Publishing, New York, N.Y., 2000 ("Lehninger"), particularly Chapters 26 and 29; Twyman, Advanced Molecular Biology: A Concise Reference, Bios Scientific Publishers, New York, N.Y., 1999; Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., including supplements through April 2005 ("Ausubel et al."); and Enzymatic Resource Guide: Polymerases, Promega, Madison, Wis., 1998. Expressly within the intended scope of the term extending enzyme are enzymatically active mutants or variants thereof, and incluidng enzymes modified to confer different temperature-sensitive properties (see, e.g., U.S. Pat. Nos. 5,773,258; 5,677,152; and 6,183,998; and DNA Amplification: Current Techniques and Applications, Demidov and Broude, eds., Horizon Bioscience, 2004, particularly in Chapter 1.1):
With regards to claim 7, Fang teaches, “recombinant S. cerevisiae ATP sulfurylase,” (0093)
With regards to claim 10, Fang does not teach PEG and thus anticipates the claim.
With regards to claim 12, Fang teaches sequencing by synthesis (0093)
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.
Claims 1-5, 7-8 and 10-14 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-7, 9-15 of copending Application No. 18/476015. Although the claims at issue are not identical, they are not patentably distinct from each other because they are 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 n amplification composition comprising ATP sulfurylase.
The claims of 015 are drawn to An amplification composition comprising an ATP sulfurylase, wherein the ATP sulfurylase is a thermophilic ATP sulfurylase.
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the claims of 015 are a species which is encompassed by the instant claims. Thus the species anticipates the genus.
Summary
No claims are allowed.
Conclusion
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/Steven Pohnert/ Primary Examiner, Art Unit 1683
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