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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 8/14/2025 has been entered.
Status of the Claims
The amended claims were filed on 8/14/2025. Claims 1-3, 7-14, and 19 are under consideration. Claims 4-6, 15-18, 20-22 were cancelled.
Response to Remarks
Withdrawn Rejections - 35 USC § 112: The rejection of Claims 4 and 20 and Claims 5 and 21 re: trademarks/trade names is withdrawn since these claims were cancelled.
Specification Objection
The disclosure is objected to because of the following informalities: The use of the terms, including FAM, HEX, TET, ROX, JOE, TexasRed, BHQ, TAMRA found at least on page 2, TaqMan, noted 37 times, beginning on page 1, and all other registered terms which are trade names or marks used in commerce, have been noted in this application. These terms should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM, or ® following the term.
Appropriate correction is required.
Drawings Objections
The drawings are objected to because the Y axis label is illegible on FIGs. 2-12. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: The numerals “1” and “2” in Fig 2, which appear to reference curves but are not identified; the labels 1-19 in FIG4, 8and 9. Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claim 19 is objected to because of the following informalities.
Please include “A” before the word method. Appropriate correction is required.
Claim Rejections maintained/amended
35 USC § 112(b)
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 8-14 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 8 is indefinite because the claim terminology remains ambiguous regarding how to unequivocally interpret the phrase “starts to be reversely complementary”, and what the metes and bounds of “or a middle of a longer oligonucleotide chain” are. Claims 9, 10,11, 12 depend from and are indefinite in, claim 8, and the issue remains that these have not been examined over the prior art because clear interpretation of claim 8 is still not possible. “Starts to be reversely complementary” could mean that this nucleotide position is the location of the first complement to match and subsequent nucleotides hereafter will match, or it could mean that this is the first reverse complement base pair but that others thereafter may or may not match, or it could mean that this nucleotide position is anywhere in the oligo and this is the first reverse complement. Additionally, reference to “starts to be” can occur “from” an “end” or a “middle”. Metes and bounds of middle and end are simply not definitive: it is unclear where, for example the “middle” begins and ends, and two ordinary artisans may disagree when asked, and similarly whether “end” would reference the first/final base pair only, or if binding occurred for the second base pair from the end, would that also constitute “starts” at an “end”, particularly if this position is not considered “middle”.
Claims 11 and 13 are indefinite in the use of “the two oligonucleotide chains have mutant bases...” making it unclear how to establish metes and bounds of the claim. Claims 12 and 14 depend from claims 11 and 13, respectively, and are indefinite as such. It is unclear what “mutant bases” references exactly, in the context of these claims; there is no indication regarding from what these bases are mutated. For example, this could reference mutation to be different from an original oligonucleotide, or a mutation that is not fitting to be the typical reverse complement of the alternate strand, or a mutation different from a known reference, wildtype sequence or perhaps it references something other than these options. The answer is not clear from the claim as written and there is no “Definitions” section of the Specification to provide an answer, so there is no explicit definition of “mutant base” and upon searching mutant in the Specification, the first hit is to a figure legend, which is also unclear regarding, for example, from what the mutation occurs.
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Claim interpretation
In evaluating the patentability of the claims presented in this application, the claims will be given their broadest reasonable interpretation, in view of the specification, and as set forth at MPEP§ 2111. For clarity of the record, the “two oligonucleotide chains have mutant bases” disclosed above will be interpreted as harboring bases that would differ from the traditionally anticipated base in a hybridizing oligonucleotide.
Maintained Claim Rejections – modified in view of claim amendments
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 1,2,5,7, are rejected under 35 U.S.C. 103 as being unpatentable over by Lei et al. (hereafter, Lei; US 2018/0320223 A1; published Nov 8, 2018) in view of Marras (NA Res 2002 30(21):e122).
Regarding claim 1, Lei described a double-stranded oligonucleotide nucleic acid probe, where one strand has a fluorophore and the other a quencher ([0030], lines 2-3, 5-8) which can each be on either strand (claim 1 iii) and iv)). The two chains are each comprised of preferably 10-50 nucleotides, which is within the claimed range; see paragraph [0035].
probe chains are both able to be hybridized and bound with target DNA/RNA:
The first oligonucleotide sequence is complementary to the target, the second oligonucleotide is complementary to the first, and quenches the fluorophore when hybridized to the first sequence (paragraph [0005]). In the presence of target sequence, the two probe strands will hybridize with the target, which results in fluorescence (paragraph [0045]). See also figure 2B. The first and second oligonucleotides hybridize to produce a first double-stranded blunt end with a fluorophore (claim 4). The first sequence is 100% complementary to the first target sequence (claim 8). The first substrate is linked to the oligonucleotide that is linked to the fluorophore (claim 10)… or to the quencher (claim 11). Detection of different target sequences arose from the combination of fluorophore emission and unique ID of the substrate (paragraph [0048]). See also figure 2B. Lei’s probes have one fluorophore and one quencher on each strand.
Re: both oligonucleotides being linked to a fluorescent group and a quenching group:
Lei did not explicitly disclose two fluorescent and two quenching groups for one double-stranded probe with, the presence of each on both strands, but disclosed relevant factual matter, including that Lei’s probe was flexible in design in that it was capable of being labelled with fluorophore and quencher on either strand ([0005]). For example, the fluorophore and quencher could be on opposed terminal complementary bases of two strands, or both could be on the blunt end of the probe (see Figs). Lei also disclosed using at least two double stranded probes, for example to obtain overlapping sequence [0054]. Thus, a plurality of probes could also be used simultaneously [0015], which meant individual reaction background could impact alternate probe results. Lei disclosed that the probe could have different structures, under different conditions, which was reflected in fluorescence change [0030]. Lei clearly indicated that in the probes, the quencher’s job was to quench the fluorophore when the two oligonucleotides were hybridized ([0005]), so that the probe was non-fluorescent, quenched, here due to the close proximity of the fluorophore and the quencher [0031].
Of significance, Lei pointed out that probes could be adjusted according to optimal quenching [Pg 4 [0036]), indicative of room for improvement with respect to quenching results. Lei disclosed a Table of Fluorophores, and a Table of quenchers [0036], many of which were common in probes at the time. Thus, Lei disclosed a suite of possible fluorophores and quenchers that could have been linked to the oligonucleotides using methods known in the art [0036]. Known to those of ordinary skill in the art and to Marras was that fluorophore quenching was imperfect and impacted by multiple factors, which included proximity (of emitter and quencher, addressed above) and energy transfer (which was to be optimized), as well as other factors (including pH and temperature, as disclosed by Lei [0030])). Marras disclosed that, even for the form of highest efficiency quenching, that induced by contact, imperfect quenching occurred (Table 1, all results <100%) and quenching by FRET typically decreased in efficiency even more than by contact (Table 1). Imperfect quenching resulted in background fluorescence and in the case of Lei, where multiple probes were used simultaneously, there would have been high motivation to consider this issue and to consider alternate designs of their flexibly designed probes, that would provide for additional quenching of background signal, which could impact accurate results.
Lei would have desired accurate results since use of their invention was for diagnostic assays including for detection of important medical issues, like viral infection, cancer, cardiac disease and other serious illnesses, and for determining the presence of said condition in a subject, sometimes single nucleotide mutations being relevant to detection of a condition [0060],[0064].
Prior to the effective filing date of the application it would have been prima facie obvious to the ordinary artisan for Lei to have incorporated the knowledge and results of Marras and to have considered redesign of their probes to improve quenching, particularly given the flexibility in design that Lei had considered, and the value of the modification as an effort to decrease background, which thus would also increase accurate detection. Lei articulated that probes could be adjusted according to optimal quenching [Pg 4 [0036]), thus Lei was motivated to obtain optimal, accurate signal. Lei indicated that it was to be understood that the invention included all possible combinations of the features of the invention, and to the extent possible, features could be used in combination with other aspects and in other embodiments of the invention [0024]. Lei further disclosed that the descriptions were not to be considered limiting the scope of implementation described [0029]. Thus, Lei would have been motivated to explore routine optimization to improve upon the probe at hand so that the medical results they obtained were the most accurate that could be had at the time.
Regarding claim 2, Lei’s double-stranded oligonucleotide probe had a fluorescent or quenching group at a 5’ end or 3’ end of each oligonucleotide chain, respectively and when a 5’ end or a 3’ end of one chain was labelled with the fluorescent group, a 3’ or 5’ end of the other chain was labelled with a quenching group as shown in Fig 1A-Fig 1B, and FIG 2B, which show where the fluorescent group (clear circle, as labelled in Fig 4A) could be at 5’ end or 3’ end, and the other chain was labelled with a quencher at 3’ or 5’ end (dark circle as labelled in Fig 4A).
Regarding claim 7, wherein the two oligonucleotide chains have an equal length or unequal lengths, Lei stated on Page 4, [0044] that “[P]robes having strands of different lengths can spontaneously react with single-stranded oligonucleotides comprising the target sequence in solution, and on Page 5, [0046] the probe is composed of two complementary oligonucleotides of different lengths.
Claims 1,2, and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Kennedy et al. (hereafter Kennedy; Mol Breeding 18:185-193, published Sept 27, 2006) in view of Marras (NA Res 2002 30(21):e122).
Regarding claims 1, 2, and 7 Kennedy designed PCR primers and probes, to be used for SNP detection in the Pi-ta gene, that involved real-time fluorescent PCR (paragraph spanning pages 186-187). Two duplex oligonucleotide probes were made, one duplex probe corresponding to each allele of the target gene (the Pi-ta gene). The duplex probes were labelled with fluorophores at the 5’ end of one strand of the duplex probe (Cy and FAM) and quenched by dark quenchers at the 3’end of the other strand of the duplex probe. Kennedy’s probes each have one fluorophore and one quencher, one on each strand. Re claim 7, Kennedy’s probe strands were unequal in length (pg 187, 1st para).
Kennedy did not design a double-stranded probe with a fluorescent and quenching group on both strands.
Marras’ knowledge on probe-quencher detection and disclosure regarding imperfect quenching (Table 1, all results <100%), as discussed above, could have been of value to Kennedy in subsequent probe design (Table 1) since Kennedy anticipated repeated probe creation for disease (SNP) detection and was willing to try new probe designs to improve performance (Abstract). Kennedy had a goal to accurately identify the presence of low frequency genotypes (Abstract). Kennedy sought low-cost detection methods and developed and probe - LNA based assay and compared them to TaqMan probes (Abstract). The goal was to identify a commercially valuable low-frequency disease resistant rice strain (Abstract). Another goal was to be able to pool samples for screening low frequency alleles in general (Abstract). Kennedy actively sought to identify that which was in low abundance (not just this SNP) developed probes for detection of low frequency strains (Abstract). Kenned discussed TaqMan probes for detection of SNPs in genotyping (Pg.185, right col, para 2), and Locked Nucleic Acids’ improved selectivity (Pg.185, right col, para 2), and the general challenges in developing real time PCR probe systems that detected single base mismatches (Pg 185-186, right col final para, to top left col). Kennedy developed a displacement probe that used fluorophore/quencher labelling and tested disease resistant/susceptible rice strains (Pg. 186 left col para 3; Pg 187, left col para 1, Table 1). Since the methodology involved real-time PCR, fluorescence was detected at the end of each cycle (eg Pg. 187, left col, para 2). While the LNA displacement probe results were clean, the TaqMan probe used produced detectable off target signal (Pg188 left col para 2). Since this was not the sole SNP/ strain Kenned sought to detect, but rather one example of probe use, the recognition, that background signal could generate a problem, particularly with real-time PCR methodology, was crucial for their work. Few relevant real-time studies had been performed previously, related to their work (Pg 190, right col para 1), and while they had off target detection with linear probes, they had good results with this particular displacement probe design (Pg 190 right col, para 1). However, they wanted to pool genomic DNA, but for their goal of detecting single SNP targets in a breeding program, pooling had limitations (Pg 190 right col para 2). Kennedy was focused on background non-specific detection as a challenge in general (Pg 191 right col, final para) and the relevance of alternate probes for future SNP detection may be of significance to them, in cases where background did present as an issue, since it was of interest to them.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to the ordinary artisan for Kennedy to have incorporated the knowledge and results of Marras, particularly given Kennedy’s awareness regarding the topic of background in real-time PCR, and to have considered design changes for subsequent probe development, that incorporated additional signal and quenching. Kennedy would have been motivated to explore routine optimization to improve upon the probe construction for future SNP detection for commercially relevant disease since he was aware of the limitations that could arise related to signal and signal quenching in probe design.
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)(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.
Claims 1,2, 3,7 13 and 14 are rejected under 35 U.S.C. 102(a)(2) as being anticipated over Coull (US 6,361,942 B1; published: March 26, 2003).
Regarding claim 1, Coull developed a double stranded probe structure with base-paired chains, and donor and acceptor moieties, used to detect a target sequence, including presence, absence and quantity (Abstract). The interacting groups were complementary nucleobases of all, or portions, of the sequence of component polymers (23, lines 29-31). The interacting groups included probing and/or annealing polymers (23, 13-14). Probing segments were selected typically to be stable, with 5-50 subunits, most preferably being 12-20 in length (22, lines 50, 52-52), with working Example 13 referencing Fig 1B, where the probe was 15 nucleotides in length ((50, lines 20-23). Fig 1A depicted one type of detection probe between 6 and 50 oligonucleotides, with a single donor and single acceptor moiety (labelled 1, and 2, respectively) (20, lines 49-54). In some examples, both chains were linked to fluorescent groups and to quenching groups (FIG 1B, labels: 5,3 on left and 6, 4 on right, FIG1C has even multiple labels per strand, and FiG 3B is clearly labelled, F1, and Q on one strand and F2 and a second Q (quencher) on the alternate strand).
Regarding claim 2, probe with fluorescent or quenching groups at 5’ or 3’ end of each chain, and where alternate ends have other label, Fig 3B depicted a fluorescent group at 5’ and quencher at 3’ of both probe strands.
Regarding claim 3, where two ends of one chain are both labelled with the fluorescent group and two ends of the other chain, a quencher
Figure 3A depicted a probe structure with a fluorophore donor and an acceptor moiety on a duplex probe, with fluorophores on two ends of one chain and quenchers on two ends of the other chain.
Regarding claim 7, oligonucleotide chains have equal or unequal length, claim 13, where the two chains have equal length and both have mutant bases, and claim 14, the number of mutant bases ranges from 1-10,
Fig 1B, 3A and 3B depict chains of equal length. Regarding Figs 1B and 1C, bulges (26) may result because the nucleobases of the component polymers are non-complementary and therefore do not interact (23, lines 52, 60-62). Also disclosed are non-interacting segments of each component polymer are shown to bulge (21, 15). Fig 1C depicts multiple locations of bulging such that it would not be possible for just a single strand to drive the mismatch depicted in the figure since alternate strands would then pair not present as bulge. Further, there is no limitation in the recitation that says that non-complementary strands may not arise from more than one chain, nor any stated or implied reason for the expectation that the result with this probe, were two chains non-complementary with one another, at for example the first two positions in the bulge, one difference arising on one chain and the second difference arising on a second chain, to differ from only one of the chains being non-complementary, since the disclosure explicitly indicates the non complementary bases do not interact, which does not limit this disclosure to a single chain (23, 60-62).
MPEP 2112 states: The express, implicit, and inherent disclosures of a prior art reference may be relied upon in the rejection of claims under 35 U.S.C. 102 or 103. “The inherent teaching of a prior art reference, a question of fact, arises both in the context of anticipation and obviousness.” In re Napier, 55 F.3d 610, 613, 34 USPQ2d 1782, 1784 (Fed. Cir. 1995) (affirmed a 35 U.S.C. 103 rejection based in part on inherent disclosure in one of the references). See also In re Grasselli, 713 F.2d 731, 739, 218 USPQ 769, 775 (Fed. Cir. 1983).
Re: claim 14, number of bases 1-10: In working Example 13, it was stated that the detection complex was constructed by design, “with two 5 bp stem regions at each end of the complex, with a 5 bp bulge in the center of the polymer where there are no complementary nucleobases (see FIG 1B)”, which falls between the requisite 1-10 mutant bases (50, lines 20-23).
Claim Rejections - 35 USC § 103
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Kennedy et al. (hereafter Kennedy; Mol Breeding 18:185-193, published Sept 27, 2006) in view of Coull (US 6,361,942 B1; published: March 26, 2003) further in view of Heid (Gen Res, 6:986-994; published 1996).
Regarding Claim 19, method for using probe of claim 1, in real-time fluorescent PCR or reverse transcription fluorescent PCR, comprising (1) designing the probe and primers
Kennedy used a method to detect SNPs, where PCR primers and probes were designed to be used for SNP detection in the Pi-ta gene (Pg 186, right col, last para), wherein two oligonucleotide probes per target sequence (specific for PiTa), were labelled with fluorophores at 5’ end (Cy and FAM) and quenched by dark quenchers at 3’end such as BHQs (Pg 187, left col, first para). Specific genes (e.g. Pi-ta) with alleles associated with disease resistance/susceptibility, were amplified in particular rice samples (disease resistant Doongara and disease susceptible BL14) then sequenced, then the probe was used in a real-time PCR assay (Pg 187, 4th para). PCR with BL14 gDNA template and a PiTaCy5 probe generated an amplification curve that was not generated with PiTaFAM, and Doongara generated an amplification curve only with FAM (Pg 187, 4th para), where competitive quenching played a role in detection specificity (Pg 190 right col para 1).
(2) A PCR amplification reaction solution with primers, probe, template, PCR buffer, magnesium/manganese ions, dNTPs and TAQ and (3) tube with PCR reaction solution to thermal cycler to perform real-time fluorescent PCR for 25-50 cycles, and recording fluorescence….
Each PCR was performed in tubes containing primer, probe, gDNA (template), master mix (hence buffer, TAQ, dNTPs) (Pg 187, left col, 2nd para). Cycling conditions… 40 cycles at 95 degrees C…. with fluorescence detected at the end of each cycle (Pg 187, left col, 2nd para). Fig 1. Detection of displacement probe PCR showing fluorescence (Y axis) as a function of number of cycles (X axis) (Pg 188, Fig. 1).
(4) Performing regression on a cycle number of threshold fluorescence with a log (initial template concentration), preparing standard curve, performing qualitative/quantitative analysis of NA to be detected.
Kennedy disclosed labelled probe, and used fluorescence and quenching but did not disclose the dual fluorescent/quenching of both strands of the instant claim.
Coull did disclosed a probe meeting the limitations of claim 1, as described in the previous rejection.
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the invention to have substituted the labelled probe of Coull into the work of Kennedy to have benefitted from the double fluorescent and double quenching labels of Coull in the invention of Kennedy, since Kennedy’s goal was to detect mutant genotypes (small changes, meaning sensitivity was required) and to distinguish them from non-mutant genotypes, which he did through real time PCR, fluorescence and quenchers. Kennedy’s goal also included developing SNP detecting probes in general, and specifically generating probes that were sensitive and reduced background, including through quenching contributing to specificity (Pg. 190 right col, para 1). Kennedy wanted to pool samples and wanted to limit the problems of off-target detection of other methods and wanted to maximize quenching, as well
Kennedy did not mention magnesium in the reactions or performing a regression analysis to generate a standard curve.
Heid indicated the use of magnesium in optimization reactions, specifically to identify valuable magnesium concentrations for a given probe, to yield the highest intensity fluorescent signal from the reporter in a real-time PCR product detection assay (Pg 987, right para, lines 26-30).
Heid also demonstrated measuring PCR product through fluorogenic probe use (Abstract). On page 988, Figure 1 Heid depicted regressing cycle number of threshold fluorescence as a function of log (input genomic DNA = template) in Fig 1C. An example of a Heid standard curve was shown in on Page 992, Fig 4B, where mean Ct (here, for pF8TM) was plotted on a standard curve of serial dilutions of pF8TM, and Fig 4C depicted the same plot type for B-actin, which was used a housekeeping gene, for use in data normalization). These figures depict standard NA output, and Table 1 depicts Ct per sample run, with three runs per sample, which are expected to be very similar to one another, as well as mean, sd, and CV providing metrics for sample comparison (here for two concentrations of starting gDNA).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the invention, to use the magnesium recommended by Heid, and the software used by Heid in the methodology used by Kennedy to generate signal, and to generate useful output data after real-time PCR using fluorescent probes. This would allow the brightest signal to be emitted from the probe, and qualitative/quantitative interpretation of results by Kennedy after using the methodology of real-time PCR.
Response to Arguments
Re: 35 USC § 112 Claims 8-12: Applicant argues that the two oligonucleotides could be incompletely reversely complementary thus there is a specific position from which the chain starts to be reversely complementary from a 5’end, 3’end or middle of a longer chain. Before such point, the chains are not complementary. The examiner understands the applicant’s point and perhaps even intent, and previously understood this point, but believes the applicant is not taking into consideration alternative possible readings/interpretations of the words on the page, and is making singular assumptions about what, for example starts to be incompletely reversely complementary means, without taking into consideration all interpretations of the phrase.
For example, the claim could be interpreted to be referencing the first base pair binding at the “start” of a reverse complement sequence (only portions of which may bind), OR this may make references to the first nucleotide that is a reverse complement, which are two possible interpretations. Applicant’s argument appears to only address the case where oligos are not fully complementary and at a given sequence position, binding occurs and then it sounds as though applicant is saying all other nucleotides are reverse complements, which is not what the words in the claim state. Thus, the interpretation is not definite and it remains unclear. Re: middle…it is indefinite what comprises the middle… two individuals of ordinary skill might not know whether for example base position 16 is part of the “middle” or not as a heuristic example (position 16 is selected at random, and could be position 8 or 3, etc). Perhaps a specific nucleotide position where the reverse complement region begins is being referenced. The recitation of “or a middle of a longer oligonucleotide chain”, is addressed in the 112b rejection and further clarification is necessary for additional feedback.
Applicant traverses the rejection 35 USC § 102 of Lei (Pg 2-3), articulating that Lei depicts one fluorescent and one quenching group on the probe and applicant has amended the claim to include additionally, “bot the two nucleotide chains being linked to a fluorescent group and a fluorescent quenching group” and offers that the amendment overcomes the rejection. The rejection has been modified in view of amendment and now includes Lei in view of Marras (NA Res 2002 30(21):e122). The rejection is maintained and has been modified to address the new claimed limitation recited above, as articulated in the rejection.
Next (Pg 3) applicant indicates that Kennedy and Coull (Pg 10) also no longer apply based upon the claimed amendment. The rejection is maintained and is modified in view of the amendments and is articulated above.
Next Applicant indicates that 35 USC § 103 (Kennedy in view of Heid) also no longer applies based upon amendment, namely both oligonucleotides are linked to fluorescent/quenching groups and the number of fluorescent/quenching groups linked to each chain is one or more. Applicant then describes the attributes of their probe, articulating the value of their system (to Page 7) and then (Pg 7) indicates that Heid fails to disclose (the amendment) “both the two oligo chains are linked to fluorescent and quenching groups” and “the number is one or more, respectively”, and thus Heid combined with Kennedy to not render the amended claim obvious. The rejection is maintained and modified in view of the amendments as is articulated in the rejection.
Conclusion
No claim is allowed.
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/LISA HORTH/ Examiner, Art Unit 1681
/GARY BENZION/ Supervisory Patent Examiner, Art Unit 1681