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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 8/5//2025 has been entered.
Claim Status and Formal matters
This action is in response to papers filed 8/5//2025.
Claims 1-10, 12, 14-17, 19-21, 46, are pending.
Claims 1, 12, and 46 have been amended.
The instant response traverses the withdraw of claim 46.
Newly submitted claim 46 is directed to an invention that is independent or distinct from the invention originally claimed for the following reasons: the product of claim 46 requires a flow cell, an optical detector configured to generate an electrical signal responsive to the fluorescence from the fluorophore; and circuitry configured to detect the at least one of the single-stranded oligonucleotides comprising the abasic site responsive to the electrical signal. Thus it has a materially different design and affect and is not obvious variants of composition which does not require an optical detector configured to generate an electrical signal responsive to the fluorescence from the fluorophore; and circuitry configured to detect the at least one of the single-stranded oligonucleotides comprising the abasic site responsive to the electrical signal or flow cell.
Since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits. Accordingly, claim 46 withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
To preserve a right to petition, the reply to this action must distinctly and specifically point out supposed errors in the restriction requirement. Otherwise, the election shall be treated as a final election without traverse. Traversal must be timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are subsequently added, applicant must indicate which of the subsequently added claims are readable upon the elected invention.
Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the inventions unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other invention. The response of 4/9/2025 traverses the restriction asserting claim depends 46 depends from claim 12 and provides further limitations. This argument has been thoroughly reviewed but is not considered persuasive as claim 12 is to a composition while claim 12 is a device. Thus a device is different in scope and is not an obvious variant of a composition. Searching a device would not inherently provide art on the composition. While claim 46 has been amended to require a composition consistent with claim 12, a device is still different than a composition, it requires different limitations, which require an additional serious search and examination burden for the office.
The response of 6/27/205 repeats the arguments addressed above as non-persuasive. The response further provides arguments with respect to US patent 10,648,022. The arguments with respect to US patent 10,648,022 are not persuasive as each application is examined on its own merits. Further the fact pattern between the instant application and US patent 10,648,022 are different. Claim 46 of the instant application is an independent claim to a device, however claim 22 of US patent 10,648,022 recites, “A system including the composition of claim 21.” Thus this claim can be construed to be dependent claim 21 and is not explicitly an independent claim. Further the device of instant claim 46 requires a flow cell, wherein the surface is located within the flow cell;an optical detector configured to generate an electrical signal responsive to the fluorescence from the fluorophore; andcircuitry configured to detect the at least one of the single-stranded oligonucleotides comprising the abasic site responsive to the electrical signal. These limitations differentiate the device from the composition, providing limitation which provide a serious search burden on the office.
Applicant’s election of group II, 9-(2-carboxy-2-cyanovinyl)-julolidine (CCVJ1) (claim 17);
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(claim 18); and hydroxylamine (claims 20 and 21). in the reply filed on 6/21/2023 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 1-10, 21, 46 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention or species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 6/21/2023.
Claims 12, 14-17, 19-20 are being examined.
Priority
The instant application was filed 09/10/2021 Claims Priority from Provisional Application 63077119 , filed 09/11/2020.
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 12, 14-17, 19-20 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 12 has been amended to recite, “the single-stranded oligonucleotides comprise amplification primers, and wherein the at least one of the single- stranded oligonucleotides comprising the abasic site comprises a damaged amplification primer..” The specification later on page 11 states, “As used herein, the term "primer" refers to a polynucleotide to which nucleotides may be added via a free 3' OH group.” It is unclear what is required in view of the amendment. It is unclear if the claim is intended to require a primer site which includes an abasic site or in view of 0043 if the claim fails to further limit as single stranded oligonucleotide with an abasic site could be interpreted to be a primer. Further Belhocine (WO2019157529) states, “Illumina full P5 sequence, partial P5 sequence.” Thus the metes and bounds are unclear about what is require by the recitation of P5 and P&.
Response to Arguments
The response traverses the rejection asserting the limitations of claims 43 and 44 are definite. This argument has been thoroughly reviewed but is not considered persuasive in view of the teachings of 0043 of the specification.
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) 12, 19-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Armour (WO2013/191775), Schwartz (US20100216132), Hoeijmakers (Nature Protocols (2011) volume 6, pages 1026-1036), Belhocine (WO2019157529)
With regards to claim 12, Armour teaches use of a polynucleotide or fragment thereof comprising a fluorescently labelled abasic site (0077-0078).
While Armour teaches use of a polynucleotide or fragment thereof comprising a covalently fluorescently labelled abasic site (0077-0078).
Armour teaches random or specific primers can be used for synthesizing nucleic acids (0002). Armour teaches, “set of primers specific to the adaptor sequences.” (0017, 0023) Armour teaches “The DNA molecules are then annealed to a sequencing primer and sequenced in parallel base-by-base using a reversible terminator approach. Typically, the Illumina Genome Analyzer System utilizes flow-cells with 8 channels, generating sequencing reads of 18 to 3 6 bases in length, generating > 1. 3 Gbp of high quality data per run. Accordingly, the methods of the invention are useful for sequencing by the method commercialized by Illumina, as described U.S. Pat. Nos. 5,750,341; 6,306,597; and 5,969,119.” (0174)
Armour teaches, “[0041] As used herein, the term "polynucleotide" refers to a molecule that includes a sequence of nucleotides that are bonded to one another. A polynucleotide is one nonlimiting example of a polymer. Examples of polynucleotides include deoxyribonucleic acid (DNA), ribonucleic acid (RiNA), and analogues thereof. A polynucleotide may be a single stranded sequence of nucleotides, such as RNA or single stranded DNA, a double stranded sequence of nucleotides, such as double stranded DNA, or may include a mixture of a single stranded and double stranded sequences of nucleotides. Double stranded DNA (dsDNA) includes genomic DNA, and PCR and amplification products. Single stranded DNA (ssDNA) can be converted to dsDNA and vice-versa.”
Armour teaches polynucleotides attached to a solid support for further detection or amplification (0091, 0140, 0155, 0167, 174).
Armour teaches in 00140, “some cases the methods of the invention can create a "polymerase colony technology", or "polony", referring to a multiplex amplification that maintains spatial clustering of identical amplicons.” Armour further teaches methods of amplification 00156-00168).
Thus Armour teaches a single stranded oligonucleotide with an abasic site with a fluorophore attached couple to substrate with a surface. The fluorophore allows fluorescence detection.
While Armour renders obvious the coupling of an oligonucleotide to a substrate with a fluorescently labeled abasic site that can be amplified, Armour, Armour does not teach the label is a Alexa flour 488 hydroxylamine, oxime, or the presence
However, Schwartz teaches the detection of DNA damage using different labels including fluorescent. (abstract). Schwartz teaches, “[0002] The present invention relates to compounds and methods used to label biomolecules for detection and diagnosis. In particular, it relates to fluorescent and pro-fluorescent, chromogenic and pro-chromogenic, hydrazine compounds that when bound to deoxyribonucleic acid ("DNA"), detect damage caused by ionizing radiation, oxidizing chemicals and cellular defects.” Thus Schwartz is related to the abasic sites of Armour,
Schwartz teaches, “0005] An attractive and comprehensive alternative is to use the chemical reactivity of some oxidized bases to detect their presence in purified DNA and/or in permeabilized cells. The Aldehyde Reactive Probe ("ARP", N-(aminooxyacetyl)-N'-(D-biotinoyl) hydrazine (Ide et al., Biochemistry 32:8276, 1993; Kubo et al., Biochemistry 31:3703, 1992)) represents the most comprehensively studied chemical-based method to detect lesions on DNA caused by oxidative stress. ARP detects abasic sites on DNA by forming an oxime between a substituted aminoxy reagent and the aliphatic aldehyde produced on de-purination.”
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 that an abasic site or reactive group would have an aldehyde and use oxime. The artisan would be motivated as Schwartz teaches ARP targets the aldehyde of the abasic site through the aldehyde and is attractive and comprehensive alternative is to use the chemical reactivity of some oxidized bases to detect their presence in purified DNA. The artisan would have a reasonable expectation of success as the artisan is merely using known abasic labeling dyes to label abasic sites.
While, Armour teaches sequence specific primers and adapter’s including for use with Illumina sequencing, Armour does not specifically teach the use of P5 or P& primer sequences.
However, Belhocine teaches, “[00228] In some cases, the nucleic acid molecule can comprise a functional sequence, for example, for attachment to a sequencing flow cell, such as, for example, a P5 sequence for Illumina® sequencing. In some cases, the nucleic acid molecule or derivative thereof (e.g., oligonucleotide or polynucleotide generated from the nucleic acid molecule) can comprise another functional sequence, such as, for example, a P7 sequence for attachment to a sequencing flow cell for Illumina sequencing. In some cases, the nucleic acid molecule can comprise a barcode sequence. In some cases, the primer can further comprise a unique molecular identifier (UMI). In some cases, the primer can comprise an Rl primer sequence for Illumina sequencing. In some cases, the primer can comprise an R2 primer sequence for Illumina sequencing.” Belhocien teaches, “[00391] A modification for blocking primer extension by a polymerase may be a carbon spacer group of different lengths or a dideoxynucleotide. In some cases, the modification may be an abasic site that has an apurine or apyrimidine structure, a base analog, or an analogue of a phosphate backbone, such as a backbone of N-(2-aminoethyl)-glycine linked by amide bonds, tetrahydrofuran, or , 2’-Dideoxyribose..”
Hoeijmakers teaches, “i) subsequent cDNA synthesis is initiated from a primer complementary to adapter A (P5, Fig. 2 and Table 1), resulting in the exclusive conversion of fragments with A-B/B-A adapters (B-B-type fragments are not converted into cDNA and removed by RNA degradation; Fig. 2). The resulting library can be directly used for Illumina deep sequencing.” (1026, 2nd column, last full paragraph)
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 P7, P5 or P7 and P5 adapters as part of the sequence for the single stranded oligonucleotides. The artisan would be motivated as Belhocine and Hoeijmakers teach P5 and P7 were known and used in commercial sequencing machines. Thus the artisan would be motivated as P7 and P5 were well known, well studied and commonly used in commercially available sequencing machines. The artisan would have a reasonable expectation of success as the artisan is merely using known sequences in known composition.
With regards to claims 19 and 20, Schwartz teaches, “ARP detects abasic sites on DNA by forming an oxime between a substituted aminoxy reagent and the aliphatic aldehyde produced on de-purination.”(0005)
Schwartz further teaches in 0060 the use of Alexa Fluor 488 hydroxylamine (elected compound of claim 18)to label nucleic acids in the described 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 use Alexa Fluor 488 hydroxylamine to label abasic sites. The artisan would be motivated as Schwartz suggest the use of Alexa Fluor 488 hydroxylamine label nucleic acids for analysis of abasic sites. The artisan would have a reasonable expectation of success as the artisan is merely using known labels to label nucleic acids.
Response to Arguments
The response traverses the prior rejection with respect to P5/P7 primers providing arguments with Aigrain. This argument is not persuasive as Aigrain is not relied upon.
The response continues by asserting Armour is limited to depleting or reducing non-desired nucleic acids, implying sequencing is outside the scope of Armour teachings. This argument has been thoroughly reviewed but is not considered persuasive as Armour teaches, “The present invention provides methods, compositions and kits for the generation of next generation sequencing (NGS) libraries in which non-desired nucleic acid sequences have been depleted or substantially reduced.” Thus Armour is to production of libraries for sequencing and thus is of similar art to Hoeijmakers and Becherer.
The response continues by asserting Schwartz is to detection of damaged DNA. This argument has been thoroughly reviewed but is not considered persuasive as Schwartz teaches, “[0002] The present invention relates to compounds and methods used to label biomolecules for detection and diagnosis. In particular, it relates to fluorescent and pro-fluorescent, chromogenic and pro-chromogenic, hydrazine compounds that when bound to deoxyribonucleic acid ("DNA"), detect damage caused by ionizing radiation, oxidizing chemicals and cellular defects.” Thus Schwartz is related to the abasic sites of Armour.
The response further provides arguments with respect to the number of known primers. This argument has been thoroughly reviewed but is not considered persuasive as the rejection does not rely on the enormous genus taught in public databases. The rejection is based on the use of P5 or P7 primers sequences which are used with Illumina sequencing platforms and are common to sequencing. It is noted the specification provides no evidence of unexpected result using either of the recited primer sequences.
Thus the rejection is maintained.
Claim(s) 14-17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Armour (WO2013/191775), Schwartz (US20100216132), Hoeijmakers (Nature Protocols (2011) volume 6, pages 1026-1036), Belhocine (WO2019157529)
as applied to claim12, 19-20 above, and further in view of WU (.Sensors and Actuators B206(2015)449–455) and Goh ( J Am Chem Soc (2014) volume 136, pages 6159-6162)
The teachings of Armour, Schwartz, Hoeijmakers, and Belhocine are set forth above.
While Armour, Schwartz, Hoeijmakers, and Belhocine renders obvious the coupling of an oligonucleotide to a substrate with a fluorescently labeled abasic site, Armour, Schwartz, Hoeijmakers, and Belhocine do not teach the label is a molecular rotor dye or CCVJ1.
However, Wu provides an article on detection of DNA abasic sites by uses of fluorescence (title abstract). Wu teaches, “we found that 9-dicyanovinyljulolidine (DCVJ) can selectively target the apurinic site (namely, the orphan base is pyrimidine)and its fluorescence is significantly enhanced only when the flanking base is guanine.”(abstract). Wu teaches, “DCVJ serves as a fluorescent molecular rotor and has been widely used in probing fluidic viscosity [49] and in protein studies [50,51].” (450, 2nd column top).
Goh teaches CCJV1 is a molecular rotor dye for detection of bimolecular interactions (title).
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 substitute CCVJ1 for the fluorescent dye of Armour, Schwartz, Hoeijmakers, and Belhocine. The artisan would be motivated to see if molecular rotor dyes had improved performance relative to the labels of Armour in view of teachings of Wu. The artisan would be motivated to see if CCVJ had different specificity than DCVJ. The artisan would have a reasonable expectation of success as the artisan is merely substituting one fluorescent dye for another to examine presumed improved qualities.
Claim 14-17 base on dependency appear to merely provide for limitations which would flow from the use of CCVj1 or DCVJ and thus are obvious over the art.
Response to Arguments
The response provides no specific arguments to this rejection. Thus the rejection is maintained.
Summary
No claims are allowed.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEVEN C POHNERT PhD whose telephone number is (571)272-3803. The examiner can normally be reached Monday- Friday about 6:00 AM-5:00 PM, every second Friday off.
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/Steven Pohnert/Primary Examiner, Art Unit 1683