DETAILED ACTION
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.
Claims 93-96, 99-101 and 104-112 are rejected under 35 U.S.C. 103 as being unpatentable over Baumgartner (US 20230407404) in view of Cui (US 20090029348) and/or Eisenbarth (US 20130011860) and/or Sun (US 20090023144).
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.
Baumgartner further teaches that the supramolecular structures in some embodiments may be biotinylated to facilitate attachment to and detection of an analyte, such as a T-cell. Paragraph [0140] describes how a peptide-bound major histocompatibility complex (MHC) is biotinylated in order to couple with a streptavidin conjugated capture agent barcode domain. See also Figs. 4A-4C. It is unclear, however, if this reads on the limitation “a signal is configured to be generated for each analyte molecule bound to a corresponding capture molecule via biotinylation of the analyte molecule”.
Cui discloses a system and method for detecting molecules, such as a HCV analyte. Figs. 1 and 2 depict a strategy in which a capture molecule comprising a coating antigen and a HCV antibody is bound to a substrate. A biotinylated analyte molecule comprising a HCV protein-tag and label binds to the capture molecule when present. This binding event produces a detectable signal due to the label, which may be a fluorescent or radioactive agent. This is described in paragraphs [0016]-[0033].
Eisenbarth discloses a system and method for detecting analyte molecules, such as an insulin autoantibody. Paragraphs [0007]-[0021] teach that a substrate is coated with a streptavidin capture molecule. The analyte molecule is bound to a proinsulin complex, which is biotinylated and labeled. Binding of the analyte molecule to the capture molecule produces a detectable fluorescent and/or luminescent signal.
Sun discloses a system and method for detecting analyte molecules. Paragraph [0003] describes a standard sandwich assay. Sun teaches capturing an analyte using a capture molecule, and then binding the captured analyte with a detection molecule that has been labeled with a reporter molecule, such as biotin and/or a fluorescein. Additional signal generating molecules (e.g., enzyme labeled streptavidin) may be added (“(1) coating a capture antibody onto a solid surface, usually the interior surface of wells of a microtiter plate; (2) adding the sample to be tested into the wells and letting the analyte (the antigen) in the sample bind specifically to the capture antibody and then removing the unbound materials; (3) adding a detection antibody that has been labeled with some kind of reporter molecules (enzymes, biotin, fluorescent groups such as fluorescein, or other types of molecules), letting the detection antibody bind specifically to the captured analyte and then removing the unbound detection antibody; (4) adding relevant reagents necessary for the reporter molecules to generate assay signals (e.g., enzyme-labeled streptavidin, enzyme substrate, etc), or directly detecting the presence of the reporter molecules”).
Before the effective filing date of the claimed invention, it would have been obvious to ensure that the supramolecular structures of Baumgartner are configured such that a signal is generated for each analyte molecule bound to a corresponding capture molecule via biotinylation of the analyte molecule. Cui, Eisenbarth and Sun each teach that the interaction between a biotinylated analyte and capture molecule (e.g., streptavidin) is well established in the art and especially useful for incorporation into detection arrays. Eisenbarth indicates in paragraph [0080] that this detection strategy provides a rapid capture assay that is readily adapted for screening and testing a large number of different analytes and samples simultaneously.
With respect to claims 94-96, 100, 101 and 105-112, Baumgartner, Cui, Eisenbarth and Sun disclose the combination 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) in view of Cui (US 20090029348) and/or Eisenbarth (US 20130011860) and/or Sun (US 20090023144) as applied to claims 93 and 99, and further in view of Fu (US 20160289740).
Baumgartner, Cui, Eisenbarth and Sun disclose the combination as described above, however do 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, wherein the detection system involves the capture of a biotinylated analyte molecule.
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 1-29 and 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, wherein the detection system involves the capture of a biotinylated analyte molecule.
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, wherein the detection system involves the capture of a biotinylated analyte molecule.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
In response to Applicant’s amendment filed 08 May 2026, the previous rejections have been withdrawn. However, upon further consideration, a new ground of rejection is made in view of the combination of Baumgartner with Cui and/or Eisenbarth and/or Sun.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Michael Marcheschi can be reached at (571) 272-1374. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/NATHAN A BOWERS/Primary Examiner, Art Unit 1799
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