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 .
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.
Claims 93-103 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Independent claims 93 and 99 each require a “signal generation system”, however it is unclear specifically what structures read on this “signal generation system”. The specification describes in paragraph [0011] of the printed publication that the signal generating system “enabl[es] a signal to generate based on a supramolecular structure in an excited state”. Paragraph [0008] states that, at least in some embodiments, a signal is generated by “tagging each analyte molecule linked with a corresponding supramolecular structure in the excited state with a dye molecule, thereby generating the fluorescence signal”. Paragraph [0009] describes another strategy that involves a “nanoparticle that scatters light”, and paragraph [0010] describes the use of a second capture molecule that is fluorescently labelled. Accordingly, the specification appears to broadly describe a few exemplary signal generation methods, but fails to specifically indicate what physical features constitute the claimed “signal generation system”. For example, it is unclear if the signal generation system includes the dye, a subunit of the supramolecular structure (and, if so, which subunits specifically), the analyte, a nanoparticle, a label, or something else.
Independent claim 93 recites the limitation "the substrate" in line 4. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 102/103
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.
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.
Claims 93-96, 99-101 and 104-112 are rejected under 35 U.S.C. 102(a)(2) as anticipated by or, in the alternative, under 35 U.S.C. 103 as obvious over Baumgartner (US 20230407404).
With respect to claims 93, 99 and 104, Baumgartner discloses a system and method for detecting analyte molecules comprising a plurality of supramolecular structures (Figure 1:102). Each supramolecular structure includes at least one capture molecule (Figure 1:107) configured to bind to an analyte molecule and a barcode (Figure 1:105) that can be used to map the location of each respective supramolecular structure on the substrate. This is described in paragraphs [0130]-[0139]. Baumgartner indicates that the supramolecular structures may be bound to a substrate, such as a feature (Figure 1:101) or a plate (Figure 6:632). The substrate includes a plurality of binding locations that are configured to be mapped using the barcodes, thereby allowing the creation of a map of unique capture molecule locations on the substrate. This is described in paragraphs [0128], [0153] and [0154]. Paragraph [0265] further teaches that a signal generation system is provided to generate a signal for each analyte molecule bound to a corresponding capture molecule. Paragraphs [0159]-[0161] state that the generated signals are detected by a detection system.
As for apparatus claims 93 and 99, it is further noted that limitations relating to signal generation, detection and mapping are intended use recitations that describe how the claimed system should or can be operated. Apparatus claims cover what a device is, not what a device does. A claim containing a recitation with respect to the manner in which a claimed apparatus is intended to be employed does not differentiate the claimed apparatus from a prior art apparatus if the prior art apparatus teaches all the structural limitations of the claim. See MPEP 2114.
In the alternative, if Baumgartner does not expressly teach the particulars of the claimed mapping step using the disclosed barcodes, it would have been obvious to do so. Baumgartner states that the purpose of the barcode is to provide information as to the location or position of an analyte, and that each barcode is unique relative to other barcodes. The references teaches that the spatial barcodes identify one or more cells, and/or contents of the one or more cells, as associated with a particular spatial location. See also paragraphs [0153], [0154] and [0162] (“ sequence information for a spatial barcode associated with an analyte is obtained, and the sequence information can be used to provide information about the spatial distribution of the analyte in the biological sample. Various methods can be used to obtain the spatial information. In some embodiments, specific capture probes and the analytes they capture are associated with specific locations in an array of features on a substrate. For example, specific spatial barcodes can be associated with specific array locations prior to array fabrication, and the sequences of the spatial barcodes can be stored (e.g., in a database) along with specific array location information, so that each spatial barcode uniquely maps to a particular array location”). Baumgartner further discuses training a machine learning module to identify relationships between spatial barcode data and image data. This is believed to either read directly on the claimed “mapping” and “creating a map” limitations or describe a similar and obvious variation.
With respect to claims 94-96, 100, 101 and 105-112, Baumgartner discloses the system and method as described above. Baumgartner teaches that barcodes are linked to capture molecules, and that the capture molecules are configured to interact with the same or different analytes. It would have been obvious to perform mapping at essentially any time during processing, including when the substrate is manufactured, prior to contacting the substrate with the analyte, and after immobilization of capture molecules. See paragraph [0153] (“During analysis of spatial information, sequence information for a spatial barcode associated with an analyte is obtained” and “specific spatial barcodes can be associated with specific array locations prior to array fabrication”). Baumgartner further discloses the creation of heat maps used to quantify concentrations of different analyte molecules.
Claims 97, 98, 102 and 103 are rejected under 35 U.S.C. 103 as being unpatentable over Baumgartner (US 20230407404) as applied to claims 93 and 99, and further in view of Fu (US 20160289740).
Baumgartner discloses the apparatus as described above, however does not appear to teach that the supramolecular structures are DNA origami structures.
Fu discloses a system for detecting analyte molecules comprising a substrate comprising a plurality of binding locations. Each binding location is configured to receive a supramolecular structure having at least capture molecule configured to bind to an analyte molecule. Paragraph [0008] state that the supramolecular structure may include a barcode to enable mapping (“providing a plurality of oligonucleotides immobilized on a substrate; contacting a sample with the plurality of oligonucleotides immobilized on the substrate; hybridizing the target with a probe that specifically binds to the target; capturing an image showing the locations of the target; capturing an image of the sample; and correlating the image showing the locations of the target and the image of the sample to spatially barcode the target in the sample”). Fu teaches in paragraphs [0147]-[0151] that the supramolecular structure may be configured as scaffolded DNA origami structures, such that the capture molecules are attached through DNA hybridization.
Before the effective filing date of the claimed invention, it would have been obvious to support the Baumgartner capture molecules and barcodes on a supramolecular structure configured as a scaffolded DNA origami structure. Fu states that DNA origami structures can change shape and conformation in response to one or more certain environmental stimuli, which allows for the selective exposure of an inner surface. Fu further indicates that the DNA origami folding may also sterically preclude compounds in a sample from interacting with an inner surface, except through one or more openings of a predetermined size.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 93-112 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 210-234 of copending Application No. 18/245,131 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other. The claims of copending Application No. 18/245,131 include limitations drawn to a system and method for detecting analyte molecules comprising a plurality of supramolecular structures (“providing a supramolecular structure…”), at least one capture molecule (“a capture molecule linked to the core structure at a first location”), and a barcode (“the capture molecule is linked to the core structure through a capture barcode, wherein the capture barcode comprises a first capture linker”). The claims of copending Application No. 18/245,131 further require the provision of a detection system and a signal generation system.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 93-112 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-32 of copending Application No. 17/708,786 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other. The claims of copending Application No. 17/708,786 include limitations drawn to a system and method for detecting analyte molecules comprising a plurality of supramolecular structures (“attaching a plurality of supramolecular structures to a surface of a substrate…”), at least one capture molecule (“one or more affinity binders”), and a barcode (“the one or more unique identifiers comprise barcode sequences”). The claims of copending Application No. 17/708,786 further require the provision of a detection system and a signal generation system.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 93-112 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-36 and 38-42 of copending Application No. 17/677,255 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other. The claims of copending Application No. 17/677,255 include limitations drawn to a system and method for detecting analyte molecules comprising a plurality of supramolecular structures (“ a supramolecular structure of the array comprising: a core structure comprising a plurality of core molecules…”), at least one capture molecule (“a capture molecule linked to the core structure”), and a barcode (“associating the detected analyte molecule with the supramolecular structure based on an identity of the capture barcode”). The claims of copending Application No. 17/677,255 further require the provision of a detection system and a signal generation system.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. The Bava (US 20210238664) and Gopinath (US 20190323002) references teaches the state of the art regarding barcoded supramolecular structures used for detecting analyte molecules.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NATHAN ANDREW BOWERS whose telephone number is (571)272-8613. The examiner can normally be reached M-F 7am-5pm.
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/NATHAN A BOWERS/Primary Examiner, Art Unit 1799