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 .
Preliminary Remark
Applicants’ election received on January 8, 2026 was filed with a new claim set, wherein claim 1, marked “original” contains an amendment (marked and notated). While the claim status is incorrect, the Office has decided to accept the response and examine the application for the purpose of compact prosecution. However, subsequent claim set must identify claim 1 as “previously presented” as the claim is not in its original status. Failure to do so will result in the subsequent amendment being held entirely non-responsive.
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-43 in the reply filed on January 8, 2026 is acknowledged.
Claim 44 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 January 8, 2026.
Information Disclosure Statement
The IDS received on May 14, 2024 is proper and being considered by the Examiner.
Drawings
The drawings received on March 30, 2023 are acceptable.
Claim Objections
Claim 1 is objected to because of the following informalities:
Claim 1 contains a period after each sub-step. MPEP 608.01(m) clearly states that each claim begins with a capital letter and ends with a period and that, “[p]eriods may not be used elsewhere in the claims except for abbreviations.”
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 1-43 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 indefinite because the preamble of the claim recites that the method is directed to detecting a target nucleic acid sequence, but the actual steps recite the use of a template nucleic acid sequence. It is unclear whether the template nucleic acid sequence is the target nucleic acid sequence, or there is a missing element that relates the detection of the template nucleic acid into the detection of the target nucleic acid.
Clarification is required.
Claims 22-26 and 34 recite the limitation, “the circular oligonucleotide”. There is an insufficient antecedent basis fort this limitation in the claims. For the purpose of prosecution, the claims have been construed to depend from claim 21.
Claim 35 recites the phrase, “for example T4 gene 32 protein”. Such a phrase is indefinite because it becomes unclear whether the limitation is actively required or not.
Claim 42 is indefinite for analogous reasons as claim 35 for reciting limitations following the phrase, “for example.”
Claim 38 recites the phrase, “the apyrase”. There is an insufficient antecedent basis for this limitation in the claim. For the purpose of prosecution, the claim has been construed to depend from claim 37.
Claim 41 recites the phrase, “the pyrophosphatase”. There is an insufficient antecedent basis for this limitation in the claim. For the purpose of prosecution, the claim has been construed to depend from claim 40.
Claim 43 is indefinite for reciting that the reaction mixture further comprises a hyperbranching primer” but does not integrate how this reagent is to be employed in the method and therefore, is missing an essential element of the steps to integrate the element into the method so as to provide a determinable breadth.
Claims 2-43 are indefinite by way of their dependency on claim 1.
Claim Rejections - 35 USC § 102
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.
Claims 1, 15, 16, 18, 19, 28, 30-33, and 42 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tyagi et al. (U.S. Patent No. 6,277, 607, issued August 2001).
With regard to claim 1, Tyagi et al. teach a primer sequence comprising the below reproduced structure (from Fig. 1):
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As seen, the primer comprises a first nucleic acid probe comprising a first sequence complementary to a template nucleic acid sequence, and further comprising a sequence P at the 3’ end of the first nucleic acid (see element 4, also “primers 1 consists of three parts … a central loop sequence 3, and a 3’-arm sequence 4 … loop 3 and the 3’ arm 4 of the hairpin 1 are complementary to one strand of a target [nucleic acid]”, see column 5, lines 13-17, therefore, loop 3 is synonymous with first sequence, and 3’ arm 4 is synonymous with the sequence P), wherein the sequence P is complementary to a sequence Pc within the first nucleic acid probe and P is annealed to the sequence Pc in the absence of target nucleic acid (see element 2, also “a 5’ arm sequence 2 … a 3’-arm sequence 4 that is complementary to 5’-arm sequence 2”, column 5, lines 13-16; also “[p]rimers according to this invention have stems that do not unravel, or dissociate, unless both the loop and the 3’ arm are complementary to the target”, column 5, lines 28-31);
Tyagi et al. teach that these primers are employed in a nucleic acid polymerase extension reaction, wherein the method requires the step of (a)(i) contacting of a sample comprising a target nucleic acid with a reaction mixture comprising the above-discussed first nucleic acid probes (or primers, see for example, “first reaction was initiated with 20,000 template molecules that contained a target sequence”, column 13, lines 49-52); (ii) the template nucleic acid (or target nucleic acid that serves as a template) comprising the sequence Pc (because template sequence contains the same sequence as the 5’-arm sequence, i.e., Pc), such that sequence P (or 3’-arm sequence) anneals to the sequence Pc in the template nucleic acid upon said contacting the template nucleic acid (“[w]hen the sequence in the loop 3 binds to its complement in the target 5, the stem of the hairpin-shaped primer 1 unravels and the 3’ arm 4 anneals to the target”, column 5, lines 22-23); (iii) a polymerase capable of extending the 3’ end of the nucleic acid probe (“[t]his creates the substrate for enzymatic extension of primer 1”, column 5, lines 24-25); and (iv) a plurality of nucleotides being capable of being incorporated by the polymerase, thereby extending the 3’ end of the first nucleic acid probe (“primers of the present invention permit monitoring of amplification reactions by fluorescence …”, column 6, lines 52-52; also “0.25 mM dATP, 0.25 mM dCTP, 0.25 mM dGTP, 0.50 mM dUTP, 2.5 units of AmpliTaq Gold DNA polymerase …”, column 11, lines 51-55); and detecting the activity of the polymerase (the amplification reaction results in the detection of the activity of the polymerase that extended upon the target nucleic acid when present.
With regard to claims 15 and 16, the detection comprises the detection of fluorescent signal as well as using nucleic acid binding dye (see SYBR Green dye use in Example 1, column 11).
With regard to claims 18 and 19, the nucleic acid is DNA which is a linear molecule (see “20,000 template DNA molecules …”, column 11, line 47).
With regard to claim 28, the primer/probe is a hairpin structure (see above).
With regard to claims 30-32, Tyagi et al. teach that the contacting is performed at a temperature above 37oC (see “55oC annealing”, column 11, line 58).
With regard to claim 33, the polymerase is a thermostable polymerase (AmpliTaq Gold, see above).
With regard to claim 42, the target nucleic acid is RNA (“the presence of target molecules (for example, either wild-type or mutant DNA template molecules, or wild-type or mutant RNA template molecules) …”, column 5, lines 50-54).
Therefore, the invention as claimed is anticipated by Tyagi et al.
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.
Claims 2-5, 13, 14, 20-27, and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Tyagi et al. (U.S. Patent No. 6,277, 607, issued August 2001) in view of Kool et al. (US 2017/0159112 A1, published June 8, 2017).
The teachings of Tyagi et al. have already been discussed above.
Tyagi et al. do not teach every possible means of detection and therefore, do not explicitly teach that the detection can be achieved by detecting incorporation of an ATP-linked nucleotide during polymerization reaction (claims 2 and 5), involving the ATP-linked nucleotide having the structure of claim 3, said nucleotide having sugar base of A, G, C, or T (claim 4), wherein the detection is effected by measuring luminescence (claim 13), via luciferase/luciferase substrate (claim 14).
Tyagi et al. do not teach that the template nucleic acid is a circular oligonucleotide (claims 20 and 21), having a length between 15-200 ntds (claim 22), 15-150 ntds (claim 23), 15-100 ntds (claim 24), 15-75 ntds (claim 25), comprising less than 25% T (claim 26), or no T (claim 27), or using additional probes to anneal to circular nucleic acids (branched RCA, claim 34).
Kool et al. teach a method of detecting the presence of a target polynucleotide of interest, wherein the artisans detect the presence of a target polynucleotide by annealing a primer to the target polynucleotide, followed by its extension with an ATP-linked nucleotide substrates:
“the presence of a target polynucleotide sequence of interest is detected by a polymerization reaction, where the reaction mixture includes … ATP-releasing nucleotides (ARNs)” (section [0010])
“methods are provided for detection of alleles in a polynucleotide sample, where the allelic variation may include … single nucleotide polymorphisms, gene rearrangements … etc. Polynucleotide sample include without limitation, mRNA, or other class of RNA, amplified cDNA, genomic DNA, etc. … reaction mixture includes at least one chimeric nucleoside tetraphosphate dimer in which ATP is the leaving group … the terminal 3’ nucleotide of the primer is designed to be specific to a position of variation …released ATP from a reaction for each of the primers is assayed, where a significantly larger release of ATP is found where there is a perfect match between the primer and the sequence that is present in the polynucleotide sample” (section [0011])
According to the instant specification, the ATP-linked nucleotide of claim 3 is disclosed by the artisan of record (i.e., Kool et al.):
“ARNs are described, for example, in US Application No. 2017/0159112; and Mohsen … ‘Polymerase-amplified release of ATP (POLARA) for detecting single nucleotide variants in RNA and DNA.’ Chemical science 10.11 (2019): 3264-3270” (section [0062])
Kool et al., on Fig. 1B, teach that the ARNs comprise the below formula, which is identical to that claimed in claim 3:
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Kool et al. teach that the detection signal is produced that involve luminescence in the presence of a luciferase and its substrate:
“DNA polymerase uses the ARNs to copy a target strand, releasing one equivalent ATP for every deoxynucleotide incorporated. In a subsequent reaction, luciferase can then process the ATP products to generate light signals in the presence of luciferin” (section [0112])
Kool et al. teach that the RCA can be performed utilizing a circular template comprising the length of up to 50 ntds (“a template can contain a portion of sequence that is complementary to the target sequence … template can be a circular polynucleotide … Circular templates can be for example, up to 50 nt …”, section [0065]; also “may also include a primer for branched RNA”, section [0108]), said template comprising less than 25% T (see sequence on section [0134]).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Tyagi et al. and Kool et al., thereby arriving at the invention as claimed for the following reasons.
As already discussed above, Tyagi et al. teach a method of detecting the presence of a target nucleic acid template in a sample, wherein the artisans employ a hairpin primer, when annealed to its target nucleic acid in a target-specific way, becomes unraveled with its 3’ end extendable in a primer extension reaction, wherein the extension reaction results in the production of a detectable/observable signal.
While Tyagi et al. teach that the detection can be observed by the use of a FRET dye pair found on the hairpin primer itself, or via an intercalator dye (i.e., SYBR Green, see above), one of ordinary skill in the art would have recognized that any prior art known means that produce a detectable signal during a primer extension would have yielded the same benefit (or outcome).
To this end, one of ordinary skill in the art would have been motivated to combine the teachings of Kool et al., so as to produce a detectable signal from the annealed primers of Tyagi et al. during the polymerase extension reaction using the ATP-linked nucleotide substrates.
Since Tyagi et al. not only teach the use of their primers in a thermocycling amplification, but also specifically suggest their use in other known amplification reactions (“[h]airpin primers of this invention are useful in number of nucleic acid amplification processes that employ primers, including polymerase chain reaction (PCR), strand displacement amplification (SDA), nucleic acid sequence based amplification (NASBA), transcription-mediated amplification (TMA), and rolling-circle amplification (RCA), column 7, lines 52-58), one of ordinary skill in the art would have also had a reasonable expectation of success at utilizing the primers of Tyagi et al. in the method of Kool et al. that involve non-denaturing temperatures of Kool et al. (see section [0134] wherein the amplification occurs at 37oC).
In addition, Kool et al. also teach that the use of their method improves the detection signals in comparison to the use of intercalator dyes, such as SYBR Green dye (which was used by Tyagi et al.):
“isothermal miRNA detection via rolling circle amplification reaction has been reported to achieve sensitivity of 30 attomoles (SYBR Green I dye) … Our own experiments confirm an advantage of 1-2 orders of magnitude over DNA-binding fluorescent dyes” (section [0130])
Therefore, in addition to the combination of teachings yielding a predictable outcome of producing a detectable signal during a polymerase extension of a primer, one of ordinary skill in the art would have had a further motivation to combine the detection means of Kool et al. for higher sensitivity.
Lastly, with regard to the circular template comprising no T bases therein, arriving at a template comprising no T would have been well-within the purview of an ordinarily skilled artisan so long as the RCA product produced in the presence of a target nucleic acid would have yielded a concatemer of amplified units to which the primers of Tyagi et al. would anneal to generate a detectable signal therefrom (as motivated by Kool et al. in branched RCA embodiment).
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Claims 6-12 and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Tyagi et al. (U.S. Patent No. 6,277, 607, issued August 2001) in view of Wu et al. (Analytical Chemistry, 2011, vol. 83, pages 3600-3605).
The teachings of Tyagi et al. have already been discussed above.
Tyagi et al. do not teach every possible means of detection and therefore, do not explicitly teach that the detection can be achieved by detecting by the detection of pyrophosphate generation (claim 6), involving ATP sulfurylase (claim 7), adenosine 5’-phosphosulfate (claim 8), dNTP analog comprising dTAPaS (claims 9-12), or an incubation at room temperature (claim 29).
Wu et al. teach a method of generating a detectable signal during a polymerase extension reaction. The detectable signal is generated during a process when a polymerase incorporates dNTP substrates in an extension reaction that releases a pyrophosphate that is converted to ATP by a ATP sulfurylase, said dNTP substrates comprising dATPaS:
“[p]yrosequencing was performed … 2 mM APS [adenosine 5’ phosphosulfate, see Abstract] … 0.1 – 5 mM ATP sulfurylase … recombinant luciferase … 1.6 U/mL apyrase. Sequencing reaction starts by a stepwise elongation of primer strands through sequential additions of four kinds of deoxynucleotide triphosphates” (page 3602, 1st column, bottom paragraph)
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Tyagi et al. and Wu et al., thereby arriving at the invention as claimed for the following reasons.
As already discussed above, Tyagi et al. teach a method of detecting the presence of a target nucleic acid template in a sample, wherein the artisans employ a hairpin primer, when annealed to its target nucleic acid in a target-specific way, becomes unraveled with its 3’ end extendable in a primer extension reaction, wherein the extension reaction results in the production of a detectable/observable signal.
While Tyagi et al. teach that the detection can be observed by the use of a FRET dye pair found on the hairpin primer itself, or via an intercalator dye (i.e., SYBR Green, see above), one of ordinary skill in the art would have recognized that any prior art known means that produce a detectable signal during a primer extension would have yielded the same benefit (or outcome).
To this end, one of ordinary skill in the art would have been motivated to combine the teachings of Wu et al., because the extension reaction from the annealed primers of Tyagi et al. would have resulted in the generation of pyrophosphates and their utilization by combining the reagents of Wu et al. for producing a detectable signal would have been easily adaptable, producing a predictable outcome.
Lastly, pyrophosphate sequencing is known in the art to be performed around 25oC and therefore, would be considered a room temperature and incubation at such a temperature would have been routine, yielding no more than a predictable outcome of providing conditions that are known in the art.
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Claims 6 and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Tyagi et al. (U.S. Patent No. 6,277, 607, issued August 2001) in view of Xie et al. (Biosensors and Bioelectronics, 2018, vol. 102, pages 518-524).
The teachings of Tyagi et al. have already been discussed above.
Tyagi et al. do not teach every possible means of detection and therefore, do not explicitly teach that the detection can be achieved by detecting by the detection of pyrophosphate generation (claim 6) via electrochemical detection of pyrophosphate (claim 17).
Xie et al. teach a method of generating a detectable signal during a polymerase extension reaction. The detectable signal is generated during a process when a polymerase incorporates dNTP substrates in an extension reaction that releases a pyrophosphate that is electrochemically detected:
“we constructed a split aptamer-based electrochemical sandwich assay for ATP detection …” (page 519, 1st paragraph)
“LAMP reaction was performed … ATP sulfurylase were incubated …” (page 520, 1st column)
“The key concept of our method is that converting the byproduct (PPi) generated during LAMP process into adenosine triphosphate (ATP), and then detecting the outputted ATP by constructing an ATP electrochemical aptasensor to achieve indirect quantitative analysis of target genomic DNA.” (page 518, 2nd column)
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Tyagi et al. and Xie et al., thereby arriving at the invention as claimed for the following reasons.
As already discussed above, Tyagi et al. teach a method of detecting the presence of a target nucleic acid template in a sample, wherein the artisans employ a hairpin primer, when annealed to its target nucleic acid in a target-specific way, becomes unraveled with its 3’ end extendable in a primer extension reaction, wherein the extension reaction results in the production of a detectable/observable signal.
While Tyagi et al. teach that the detection can be observed by the use of a FRET dye pair found on the hairpin primer itself, or via an intercalator dye (i.e., SYBR Green, see above), one of ordinary skill in the art would have recognized that any prior art known means that produce a detectable signal during a primer extension would have yielded the same benefit (or outcome).
To this end, one of ordinary skill in the art would have been motivated to combine the teachings of Xie et al., because the extension reaction from the annealed primers of Tyagi et al. would have resulted in the generation of pyrophosphates and their utilization by combining the reagents of Xie et al. for producing a detectable signal would have been easily adaptable, producing a predictable outcome.
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Claim 35 is rejected under 35 U.S.C. 103 as being unpatentable over Tyagi et al. (U.S. Patent No. 6,277, 607, issued August 2001) in view of Kersting et al. (Microchim. Acta, 2014, vol. 181, pages 1715-1723).
The teachings of Tyagi et al. have already been discussed above.
Tyagi et al. do not teach every possible means of amplifying the target nucleic acid, and therefore, do not explicitly teach an amplification means that involve single stranded binding proteins (page 35).
Kersting et al. teach a method of method of detecting a target nucleic acid via amplification wherein the amplification reaction is an RPA that employs a single-stranded binding protein (“promising method is the recombinase polymerase amplification (RPA) which uses a phage recombinase to direct short oligonucleotide primers to a homologous target sequence. In combination with a strand displacing polymerase and single-stranded DNA binding protein an amplification of fewer than ten copies of genomic DNA can be accomplished …”, page 1715, 2nd column to page 1716, 1st column, 1st paragraph).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Tyagi et al. and Kersting et al., thereby arriving at the invention as claimed for the following reasons.
As already discussed above, Tyagi et al. teach a method of detecting the presence of a target nucleic acid template in a sample, wherein the artisans employ a hairpin primer, when annealed to its target nucleic acid in a target-specific way, becomes unraveled with its 3’ end extendable in a primer extension reaction, wherein the extension reaction results in the production of a detectable/observable signal.
While Tyagi et al. teach that the detection can be observed by the use of a FRET dye pair found on the hairpin primer itself, or via an intercalator dye (i.e., SYBR Green, see above), one of ordinary skill in the art would have recognized that any prior art known means that produce a detectable signal during a primer extension would have yielded the same benefit (or outcome).
To this end, one of ordinary skill in the art would have been motivated to combine the teachings of Kersting et al., so as to produce a detectable signal from the annealed primers of Tyagi et al. during the polymerase extension reaction produced via RPA reaction of Kersting et al., or utilize the amplification products produced from the RPA reaction of with the hairpin primers of Tyagi et al., because the extension of the hairpin primers employed in the RPA or on the amplified products of RPA would have yielded a detectable signal that is indicative of the target nucleic acid.
Since Tyagi et al. not only teach the use of their primers in a thermocycling amplification, but also specifically suggest their use in other known amplification reactions (“[h]airpin primers of this invention are useful in number of nucleic acid amplification processes that employ primers, including polymerase chain reaction (PCR), strand displacement amplification (SDA), nucleic acid sequence based amplification (NASBA), transcription-mediated amplification (TMA), and rolling-circle amplification (RCA), column 7, lines 52-58), one of ordinary skill in the art would have also had a reasonable expectation of success at utilizing the primers of Tyagi et al. in the method of Kersting et al. that involve non-denaturing temperatures of Kersting et al. (see page 1717, 2nd column, wherein the amplification occurs at 38oC).
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Claims 36-41 are rejected under 35 U.S.C. 103 as being unpatentable over Tyagi et al. (U.S. Patent No. 6,277, 607, issued August 2001) in view of Wu et al. (Analytical Chemistry, 2011, vol. 83, pages 3600-3605), as applied to claims 6-12 and 29 above, and further in view of Rothberg et al. (US 2002/0012930 A1, published January 31, 2002).
The teachings of Tyagi et al. and Wu et al. have already been discussed above.
While Wu et al. teach a method of generating a detectable signal during a polymerase extension reaction, known as pyrosequencing, the artisans do not explicitly teach that apyrase or phosphatase is contacted with a sample before the sequencing reaction (claims 36 and 37; claims 39 and 40, repectively), wherein said apyrase or phosphatase is provided on a bead (claims 38 and 41, respectively).
Rothberg et al. teach a method of performing pyrosequencing detection on an array platform, wherein apyrase is delivered on a bead (“reactants and enzymes used herein, e.g., the ATP sulfurylase, luciferase, and apyrase, can be attached to the solid surface”, section [0026]).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Tyagi et al. and Wu et al. with the teachings of Rothberg et al., thereby arriving at the invention as claimed for the following reasons.
As already discussed above, Tyagi et al., in combination with Wu et al. teach a method of detecting the presence of a target nucleic acid template in a sample, wherein the artisans employ a hairpin primer, wherein during the extension of the hairpin to a target nucleic acid, results in the generation of a detectable signal via pyrophosphate conversion to ATP and a subsequent signal.
While Wu et al. did not explicitly teach that an apyrase is contacted with the sample before the detection means commences, Rothberg et al. explicitly teach that apyrase is employed to digest the ATP that may produce interfering signals:
“it is desirable to use reagents free of contaminants like ATP and PPi. These contaminants may be removed by flowing the reagents through a precolumn containing apyrase and/or pyrophosphatase bound to resin. Alternatively, the apyrase or pyrophosphatase can be bound to magnetic beads and used to remove contaminating ATP and PPi present in the reagents” (section [0120]).
Therefore, one of ordinary skill in the art would have been motivated to combine the teachings of Tyagi et al. and Wu et al. with the teachings of Rothberg et al. to treat the sample with apyrase or phosphatase for the benefit of reducing the presence of ATP or PPi in a sample that has been prepared for sequencing that may have resulted from the previous amplification reaction.
As to delivering the reagents on a solid-surface, such as beads, doing so would have been well-within the purview of an ordinarily skilled artisan as such delivery means have been conventional, yielding no more than a predictable outcome.
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Claim 43 is rejected under 35 U.S.C. 103 as being unpatentable over Tyagi et al. (U.S. Patent No. 6,277, 607, issued August 2001) in view of Kool et al. (US 2017/0159112 A1, published June 8, 2017), as applied to claims 2-5, 13, 14, 20-27, and 34 above, and further in view of Chen et al. (Harmful Algae, 2015, vol. 47, pages 66-74).
The teachings of Tyagi et al. and Kool et al. have already been discussed above.
While Kool et al. teach RCA, the artisans do no teach hyperbranching primer.
Chen et al. teach a method of performing an RCA wherein the RCA is modified to become hyperbranched using primers, known as HRCA.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Tyagi et al. and Kool et al. with the teachings of Chen et al., thereby arriving at the invention as claimed for the advantage provide by HRCA that improves upon the amplified products from which to provide a detectable signal from, a well-established advantage.
“HRCA is a combination of specific molecular recognition and universal amplification … is a highly efficient amplification method, able to synthesize 109 amplicons from single copy of target sequence within 1 h” (page 67)
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 March 4, 2026
/YJK/