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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 8/3/2026 has been entered.
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claims 17-24 remain withdrawn. Claims 25-27 have been added. Claims 1-16 and 25-27 are pending and are examined on the merits herein.
Response to Applicant’s Amendments
35 USC 112(b) Rejections
Claims 1-16 were rejected due to indefiniteness issues associated with instant claim 1. In light of Applicant’s amendments to the claims submitted 8/3/2026, this rejections have been withdrawn.
35 USC 103 Rejections
Claims 1-12 and 15 were rejected under 35 U.S.C. 103 as being unpatentable over Cass et al. (WO 2018/189530 A1; cited in Applicant’s IDS) in view of Lu et al. (ACS Sensors, 2018).
Claims 13-14 were rejected under 35 U.S.C. 103 as being unpatentable over Cass et al. (WO 2018/189530 A1; cited in Applicant’s IDS), in view of Lu et al. (ACS Sensors, 2018), as evidenced by Pfeffer et al. (Drug Development Research, 2015).
Claim 16 was rejected under 35 U.S.C. 103 as being unpatentable over Cass et al. (WO 2018/189530 A1; cited in Applicant’s IDS) in view of Lu et al. (ACS Sensors, 2018), and further in view of Meller et al. (US 2013/0203610 A1).
Applicant’s arguments and amendments have been thoroughly reviewed and considered. These rejections have been maintained for all currently pending claims. See “Free of the Prior Art” below for newly added claims 25-27. See also “Response to Applicant’s Arguments” below.
Response to Applicant’s Arguments
Regarding the 35 USC 103 Rejections, Applicant argues that Lu does not teach a carrier-binding moiety as claimed, and that incorporating Lu’s triplex molecular beacon into the carrier-based nanopore system of Cass would require a redesign to Lu’s structure to introduce an additional nucleic acid carrier-binding function to the stem-forming oligonucleotide (sfO). This redesign to arrive at Cass in view of Lu as described by the Examiner would not be obvious, as the claimed carrier is more than merely an attachment (Remarks, page 11). The claimed carrier is designed to “provide a nanopore-translocating scaffold, to prolong dwell time, or to generate a distinguishable electric signature,” which allegedly cannot be done with the sfO of Lu. Moreover, Applicant argues that it would not be apparent to the ordinary artisan where a carrier-binding sequence could be introduced into the tMB of Lu without affecting its operation (Remarks, page 12). Finally, Applicant argues that Lu teaches away from a flexible system, as the reference shows that changes to the tMB structure have effects on performance (Remarks, pages 12-13).
Though the carrier nucleic acid molecule of the claimed invention may be intended by Applicant to be used for various purposes as recited in the Remarks, in the claims, the carrier nucleic acid binds to the nucleic acid moiety of the detection element to form a complex, and then moves through a nanopore. The “nanopore-translocating scaffold” function of the carrier is accomplished by the complex moving through the nanopore with the carrier. As to the other argued functions of the carrier, there is no requirement that the carrier specifically perform any additional functions related to dwell time, or that this molecule in particular solely generates the electrical signal. Furthermore, while in Cass, the electrical detection with the nanopore is in part due to the charge associated with the carrier molecule (see page 10, para. 4), the carrier itself can simply be a DNA or RNA molecule, which naturally has a charge and so would naturally accomplish this goal (page 3, para. 3). In Cass in view of Lu, the carrier is DNA, and so would be capable of generating an electrical signal upon entering the nanopore.
Additionally, in Cass in view of Lu, the design constraints discussed in the actual 35 USC 103 Rejections, namely that, “this would simply amount to designing said sequences so that they appropriately hybridize to one another, that the molecular beacon aptamer is complementary to the target in its loop section, and that the molecular beacon aptamer contains a fluorophore and quencher at each end,” (page 34 of the Final Rejection) are already present in the tMB-sfO complex of Lu, and so no additional design is required. Lu detects miR-21, and as no particular analyte is required by instant claim 1, the tMB-sfO complex of Cass in view of Lu already meets each limitation of the claim as is. In the Response to Applicant’s Arguments associated with the Final Rejection, the Examiner states, “As the molecular beacon and stem-forming oligonucleotide already form a stable complex structure with a target that can be optically detected (and Lu notes that tMBs have excellent selectivity, similar to an aptamer, see page 2438, column 1, para. 1), the only changes that may be required of the design of the tMB would be those that allow it to be detected during nanopore translocation, such as changes in molecular weight and charge (see Cass page 10, para. 4). Thus, it is possible that the combination of Cass in view of Lu would require redesign of the specific molecular beacon and stem-forming oligonucleotide of Lu. However, Lu already teaches that the structure of the tMB need not be rigidly fixed in order to be a functional detection mechanism – see Figures 1-3 and 5 for example, which show tMBs with slight differences in design from one another,” (para. 10 of the Final Rejection). However, even with the adjustments shown in Lu, though some might result in higher fluorescence levels than others, all are still capable of detection and none are inoperable.
MPEP 2143.01 V states, “‘[a] given course of action often has simultaneous advantages and disadvantages, and this does not necessarily obviate motivation to combine’" (quoting Medichem, S.A. v. Rolabo, S.L., 437 F.3d 1157, 1165, 77 USPQ2d 1865, 1870 (Fed. Cir. 2006). Thus, though slightly altering the design of the tMB to ensure successful use in the method of Cass in view of Lu may make said design process more complex and may result in a decrease in fluorescence depending on the final design, this alone does not obviate the obviousness rationale used to combine these references, particularly in view of the advantages gained by combining the references (e.g. early disease diagnosis, more accurate detection of a target due to use of two types of detection, etc.).
Furthermore, Applicant argues that showing the differences in results for the various parameters of Lu is evidence that Lu teaches away from flexibility in their tMB system. However, the results shown by Lu are a means of optimizing the tMB-sfO system both generally and for their specific miR-21 target (see pages 2441-2443 of Lu). While different properties of the system may have particular optimized parameters, Lu does not at any point teach away from particular variations associated with the system, though certain parameters may be preferred. As stated in MPEP 2145 X (D) 1, “"the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed…." In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004).” Lu in fact concludes that tMBs can become “a universal strategy for the detection of miRNAs and biomarkers with a suitable aptamer, which holds great potential for the early clinical diagnostics of diseases,” (page 2444 column 2, para. 1), where new targets would likely require their own optimization protocols for detection. This flexibility is what the Examiner is referring to in the Final Rejection.
Finally, Applicant argues about introducing a carrier-binding sequence into the tMB of Lu and how this would not be obvious to the ordinary artisan to include. In Cass in view of Lu, the molecular beacon is analogous to the claimed detection element, where it contains a fluorophore and quencher, a region for binding to an analyte, and a region for binding to the carrier (i.e. the sfO), thus acting as the claimed nucleic acid moiety. No additional sequence would be required to be added.
Thus, these arguments are not considered persuasive.
Rgearding the dependent claims, Applicant first states that the combination of references including Pfeffer does not arrive at the inventive concept of the claimed invention (Remarks, pages 16-17). Pfeffer is used as an evidentiary reference only to provide additional information about the target described in Lu (miR-21). Therefore, the arguments concerning Cass in view of Lu described above also apply here.
Regarding Meller, Applicant argues that as Cass in view of Lu does not meet the limitations of the instant claims, Meller must do so alone or in combination with Cass and Lu, which Meller allegedly does not do because the reference teaches methods concerning labelled analytes (Remarks, pages 17-18).
Applicant’s arguments here conflate the addition of the guidance of Meller to the obviousness rejection with the use of the specific molecular beacon/nanopore sequencing methods of Meller. In para. 46 of the Final Rejection, it states, “Meller teaches that measurements of fluorescence and current can be made for multiple samples (the examples in paras. 241-244 provide evidence of this, as they use two samples), and teaches comparison of simultaneous emission/current peaks with total emission/current measurements. Meller also teaches that these methods can be used to distinguish particular nucleotides from one another, and teaches that the methods of their invention can be used to detect mutations and single nucleotide polymorphisms (para. 96). Taken together, these would motivate the ordinary artisan to compare control and target samples to detect changes in nucleotide sequences, which could indicate a mutation in the target sequence… Meller teaches classifying sequences based on the resulting peak measurements (see para. 245 and Figures 5c), and so the ordinary artisan would be able to determine mutations in a target sequence regardless of the direction of difference present between control and target measurements.” Thus, the analysis methods of Meller are used with Cass in view of Lu to arrive at the claimed invention. Cass in view of Lu would produce similar simultaneous emission/current measurements to those shown in Figures 3-5 of Meller, and so the ordinary artisan would be capable of analyzing the results of Cass in view of Lu in the same manner as presented in Meller utilizing ordinary skill and creativity in the art. The specific molecular beacon methods described by Meller are not actually being implemented in Cass, in view of Lu, and further in view of Meller, and so no principle of operation of Meller is being altered.
Thus, these arguments are not considered persuasive.
As Applicant’s arguments regarding the rejections of record in the Final Rejection mailed 3/3/2026 are not considered persuasive, these rejections have been maintained and are reiterated below.
On pages 13-16 of their Remarks, Applicant discusses the newly added claims, and argues that Cass in view of Lu does not teach the limitations associated with these claims. The Examiner agrees that Cass in view of Lu alone does not teach these limitations. See the “Free of the Prior Art” section below.
Priority
The disclosure of the prior-filed application, Application No. GB 1902630.1, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. Specifically, this application fails to provide support for instant claims 11-14 and 16, as this application makes no mention of the analyte being miRNA (instant claims 11-12), cancer being detected (instant claims 13-14), or the comparative methods described by instant claim 16. Subsequently, these claims will be given the priority date of the effective filing date of the PCT application, 2/27/2020.
Claim Objections
Claim 1 is objected to because of the following informality: it is recommended that the “v)” be removed from the wherein clause underneath the description of the detection element, as the wherein clause does not describe an added structural element for the detection element. Appropriate correction is required.
Claims 2-16 and 25-27 are objected to due to their dependence on objected to claim 1.
Claim 26 is objected to because of the following informality: in the second wherein clause of the claim, it is recommended that “wherein the at least one analyte-binding moieties in each detection element bind to different analytes” read “wherein the at least one analyte-binding moiety in each detection element binds to a different analyte” to better match the language used in claim 1. Appropriate correction is required.
Claim 27 is objected to due to its dependence on objected to claim 26.
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.
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.
Claims 1-12 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Cass et al. (WO 2018/189530 A1; cited in Applicant’s IDS) in view of Lu et al. (ACS Sensors, 2018).
Cass teaches methods of detecting one or more analytes using a carrier nucleic acid that contains at least one single-stranded region and an aptamer specific for the analyte that comprises a single-stranded portion complementary to the single-stranded region of the carrier nucleic acid. The carrier and aptamer are then contacted with the analyte in the sample, forming a complex. The complex is then detected (pages 2-3, joining text). The aptamer here thus is analogous to the detection element in the present invention (instant claim 4). The complex may be detected by voltage-driven translocation through a nanopore, where a change in nanopore conductance versus a control over time indicates the presence and location of the analyte in the complex (page 3, paras. 5-6). Several figures also show measurements of current over time (e.g. Figures 3B, 4D, 8A-8C, 9B, and 10A-10B).
Multiple aptamers can be present that are complementary to different single-stranded regions on the carrier nucleic acid, with no limit to how many can be provided (page 3, para. 1; instant claim 3).
The nanopore provided can be at the tip of a nanopipette (page 4, para. 1; instant claim 5). Cass shows that quartz nanopipettes may specifically be used (page 7, Figures 14 and 15 captions; instant claim 6).
Cass also teaches the use of lambda DNA for the carrier element (page 5, Figures 2 and 4 captions; instant claim 7).
The analyte of interest can be detected in serum (page 1, para. 1 and page 5, para. 1; instant claim 15).
Cass also teaches that detection can additionally be achieved by fluorescence detection (page 4, para. 2). This fluorescence detection was used in conjunction with nanopore detection in the embodiment shown in Figure 9 and explained on page 15, paras. 2-4. In particular, Cass shows both optical and electrical signals plotted simultaneously, and notes that “synchronized detection [was] visible on several occasions,” and “This work demonstrates that simultaneous electrical and optical detection is possible,” (page 15, para. 4). In the embodiment of their invention that uses this detection however, the target molecule has a fluorophore, and not the aptamer (page 15, para. 3). Thus, Cass does not teach that the aptamer may have a fluorophore and quencher.
Lu teaches the use of a triplex molecular beacon that is used to detect miR-21 (Abstract). Scheme 1 shows the basics of this structure and how it acts in the presence of a target (the structure is described in the joining para. of pages 2439-2440). The molecular beacon contains a fluorophore and quencher at either end, and contains a loop portion that is complementary to the target miRNA. The stem portion is complementary to a labelled stem-forming oligonucleotide. When the molecular beacon and oligonucleotide are bound, the fluorophore is quenched (see also Figure 1A). Upon target binding, the fluorophore present on the molecular beacon can be detected (Figure 1A). Lu also teaches that triplex molecular beacons can be used in nanopore sensing to detect specific macromolecules (page 2439, column 1, para. 1). This reference teaches that miR-21 in particular is a well-known biomarker for cardio-cerebrovascular disease (Abstract), and also notes the important and wide-ranging uses for molecular beacons (page 2438, column 1, para 1). Overall, Lu concludes that the triplex molecular beacon can be very useful in the early diagnosis of disease and can be used as a universal strategy for detecting miRNAs (page 2444, column 2, para. 1).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Lu in the method of Cass to arrive at the method of claims 1-2 and 10-12. Specifically, the ordinary artisan would be able to use the molecular beacon and stem-forming oligonucleotide structures of Lu as the aptamer and carrier molecules, respectively, in the method of Cass. As Cass already teaches that these structures comprise nucleotide sequences, this would simply amount to designing said sequences so that they appropriately hybridize to one another, that the molecular beacon aptamer is complementary to the target in its loop section, and that the molecular beacon aptamer contains a fluorophore and quencher at each end. Both Cass and Lu teach well-known fluorophores (Cass page 15, para. 3 and Lu Abstract), and Lu also teaches the well-known Black Hole Quencher (Abstract). Lu provides a reasonable expectation of success in creating these structures, as this reference shows that they can be both created and successfully used. Lu also provides motivation for the ordinary artisan by teaching the broad uses for molecular beacons, as well as diagnostic implications for their use. These would additionally motivate the ordinary artisan to detect miR-21 in the serum samples taught by Cass in order to provide early detection of cardio-cerebrovascular disease in patients. By providing early detection and potential diagnosis, medical interventions could be made earlier, improving patient outcomes. As Lu already teaches that the molecular beacon and stem-forming oligonucleotide can be designed to detect this particular microRNA, there would be a reasonable expectation of success.
Finally, the ordinary artisan would be motivated to include the fluorophore/quencher on the molecular beacon aptamer and not on the target (as described by Cass alone) so that in the absence of the target, there would not be any fluorescence, and so that the ordinary artisan would not need to worry about adding a fluorophore to a target that may or may not be present in a sample – simplifying the method protocol once the required components and reagents are present. In the embodiment of Cass on pages 2-3 of the reference, the analyte is not stated to be labeled (contrast the method on pages 2-3 with that of page 4, which does describe the use of a labeled analyte). In the examples of Cass, several unlabeled analytes are used. Page 11, para. 6 states that human serum may contain targets with no indication of a label on said targets, and page 13 notes that unlabeled targets such as acetylcholinesterase and thrombin proteins were used. Additionally, compare the methods of claims 1 and 11 of Cass, where claim 1 is a method where the analyte need not be labeled and claim 11 describes labeling of the analyte. In Lu, the miRNA is the analyte, and this analyte is not labeled – see the Abstract, Scheme 1, and Figure 1. Therefore, both Cass and Lu are considered to teach the use of label-free analytes, providing the ordinary artisan with a reasonable expectation of success that the analyte could be unlabeled while the aptamer is labeled and the method would overall still function as intended.
Thus, claims 1-7, 10-12, and 15 are prima facie obvious over Cass in view of Lu.
Regarding claims 8-9, Cass teaches that multiple aptamers can be provided that are specific for different analytes, and that each aptamer can be specific to a different single-stranded region on the same carrier nucleic acid (page 3, para. 1). Cass also teaches the fluorophore Atto 488 (page 15, para. 3). As noted above, Lu teaches the fluorophore FAM (Abstract). It would be prima facie obvious to the ordinary artisan to use different fluorophores for different aptamer structures specific to different analytes and carrier nucleic acids, as this would allow for the detection of specific targets, rather than just the presence of any target. If one analyte is present and another is absent, it may indicate a different clinical meaning than if both analytes are present or absent. It is noted that instant claim 8 requires a minimum of two fluorophores, corresponding to the at least two single-stranded regions described in i) of the claim. As Cass and Lu teach two fluorophores (FAM and Atto 488), the use of these two fluorophores in the manner described above meet the limitations of this claim.
Thus, claims 8-9 are prima facie obvious over Cass in view of Lu.
Claims 13-14 are rejected under 35 U.S.C. 103 as being unpatentable over Cass et al. (WO 2018/189530 A1; cited in Applicant’s IDS), in view of Lu et al. (ACS Sensors, 2018), as evidenced by Pfeffer et al. (Drug Development Research, 2015).
Cass in view of Lu teaches the methods of claims 1-12 and 15, as described above. This method involves the detection of miR-21.
Pfeffer teaches that this miRNA can be a biomarker for various different cancers (Abstract). These include lung, ovarian, and prostate cancers (page 271, column 1, paras. 1-2), thereby meeting the limitations of instant clams 13-14.
Thus, claims 13-14 are prima facie obvious over Cass, in view of Lu, as evidenced by Pfeffer.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Cass et al. (WO 2018/189530 A1; cited in Applicant’s IDS) in view of Lu et al. (ACS Sensors, 2018), and further in view of Meller et al. (US 2013/0203610 A1).
Cass in view of Lu teaches the methods of claims 1-12 and 15, as described above. Regarding claim 16, Cass teaches a method where comparing the change in nanopore conductance of a target versus a control indicates the presence of an analyte. Specifically, the location of the change in conductance can indicate the position of the aptamer (page 3, para. 6). However, Cass does not teach these control compared conductance measurements in conjunction with fluorescence measurements, or any calculations similar to those described in instant claim 16.
Meller teaches use of molecular beacons and nanopore sequencing (Abstract). Particularly, Meller provides methods detailing simultaneous fluorescence emission and nanopore current measurements (Figures 3-5 and paras. 241-245). Using different combinations of two fluorophores on one or two molecular beacons, particular nucleotides could be examined, and these were viewed in light of nanopore current results. Fluorescent peaks were found to correspond with electrical peaks, and these were tallied in light of all detected signals to create ratio measurements (paras. 243-244 and Figures 4-5).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Meller in the method of Cass in view of Lu to arrive at the method of claim 16. Specifically, Cass in view of Lu already teaches simultaneous measurements of fluorescence emissions and current responses, as described above in the rejection of claim 1. Cass then goes on to teach that it is possible to measure control and target analytes with their methods, which would render it obvious to the ordinary artisan that this could also be done with the simultaneous fluorescence and current measurements. Meller teaches that measurements of fluorescence and current can be made for multiple samples (the examples in paras. 241-244 provide evidence of this, as they use two samples), and teaches comparison of simultaneous emission/current peaks with total emission/current measurements. Meller also teaches that these methods can be used to distinguish particular nucleotides from one another, and teaches that the methods of their invention can be used to detect mutations and single nucleotide polymorphisms (para. 96). Taken together, these would motivate the ordinary artisan to compare control and target samples to detect changes in nucleotide sequences, which could indicate a mutation in the target sequence. As to whether the ratio as taught by Meller would be a higher or lower value for the target sequence relative to the control, this would depend on the particular mutation that occurred and the resulting sequence. Meller teaches classifying sequences based on the resulting peak measurements (see para. 245 and Figures 5c), and so the ordinary artisan would be able to determine mutations in a target sequence regardless of the direction of difference present between control and target measurements.
Thus, claim 16 is prima facie obvious over Cass, in view of Lu, and in view of Meller.
Free of the Prior Art
Claims 25-27 are free of the prior art. Claim 25 is considered free of the prior art because no known prior art could be found that teaches, alone or in combination, using multiple carrier nucleic acids in a method analogous to the instantly claimed method. Grossman et al. (Angew. Chem. Int. Ed., 2007) teaches that triplex molecular beacons can be used in conjunction with several different stem-forming oligonucleotides (sfO; Figure 1B and page 5223, column 2, para. 3), and compares the use of sfOs with 6-11 adenine residues (page 5223, column 2, para. 5). The reference teaches various means of using and evaluating these sfOs, but they are not used in conjunction with one another, and there is no teaching where a detection element binds to multiple carriers in single solution.
Claims 26-27 are free of the prior art as they are dependent on claim 25.
Conclusion
No claims are currently allowable.
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/FRANCESCA FILIPPA GIAMMONA/Examiner, Art Unit 1681
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