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 .
Election/Restrictions
Claims 19-20 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 7/31/25.
Oligosaccharides in claims 5 and 15 and adenovirus and bacterial toxins in claims 6 and 16 stand withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 7/31/25.
NOTE: the amendment filed on 3/18/26 contained an amendment (typographical error) to claims 8 and 10 with no status identifier indicated that the claims were amended. Applicant filed a supplemental amendment that is identical to the amendment filed on 3/18/26 to correct the error for claims 8 and 10 to the claims 8 and 10 filed on 7/31/25. Claims 8 and 10 were updated to correct this typographical error in the originally filed office action response. The claims filed in the supplemental amendment were entered because they removed the issue of claims 8 and 10 being amended without the proper status identifier in the amendment filed on 3/18/26. Thus, the claims filed on 3/18/26 were not entered.
The objection to claims 8 and 10 is withdrawn because the periods are for an abbreviation (No.) for the term ‘number’.
Response to Arguments
Applicant’s arguments, see pages 6-8, filed 3/18/26 and 4/8/26, with respect to the rejection(s) of claims 1-18 under 102 by Chang (US 11242533); Veneziano (WO 2017189870); and US 20210137479); and under 103 by US 20200237903 and Chang and WO 2017176762 and Wilner have been fully considered and are persuasive. Therefore, the rejection has been withdrawn because of the amendment to the independent claims to recite: binder regions are configured so that binders can bind a plurality of epitopes on the surface of a target according to the spatial pattern of the plurality of epitopes on the surface of the target.
Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
In addition, new rejection(s) are required because of the amendment to the independent claims 1 and 13 and the addition of new claims 21-22.
Claim Interpretation
The amended claims now embrace an oligonucleotide scaffold comprising a plurality of binders incorporated into binder insertion regions, wherein the regions are arranged for the binders (peptides, aptamers, small molecules, oligosaccharides or combinations thereof) to bind to a spatial pattern of a plurality of epitopes on a surface of a target molecule (e.g., virus, bacteria, bacterial toxin, antigen). A skilled artisan would possess the knowledge that epitopes are regions on an antigen. The oligonucleotide scaffold is used for multivalent binding interaction between the binders and epitopes. The specification does not appear to provide a definition of the term “spatial pattern” but provides an example of the term (Figure 1). The broadest reasonable interpretation of the term embraces any multivalent structure that binds to a pattern of a plurality of epitopes on a target molecule.
The limitation recited in the pre-amble “for pattern-recognized targeting of disease” in independent claims 1 and 13 is directed to an intended of the claimed product and does not add an patentable weight to the claimed invention because it does not add any structural limitations to the instant claims.
Claim Rejections - 35 USC § 102
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1-18 and 21-22 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kwon et al. (BioRxiv, pages 1-25, April 13, 2019, cited on an IDS, and Supplementary Information (pages 1-36). NOTE: the symbol "&" on the first page of the publication indicates that several authors (Paul S Kwon, Shaokang Ren, Seok-Jook Kwon, Megan E. Kizer, Lolo Kuo) who were listed or not listed as a joint inventor on the instant application contributed equally to the work.
As to claims 1 and 13 and new claim 22, Kwon discloses a method of making a structure for pattern-recognized targeting of diseases, comprising: an oligonucleotide scaffold including a plurality of binder insertion regions, wherein the binder insertion regions are arranged in a pattern conforming to a plurality of epitopes of a target (page 3, paragraph 2); "Herein, we demonstrate a unique strategy for potent viral detection and inhibition through a precise, spatial pattern- recognizing display of weak binders in two-dimensional (2D) space"; page 6 paragraph 1; "we designed a star-shaped DNA nanostructure (called "DNA star" herein) that was assembled from 21 DNA oligonucleotides of programmed sequences (Figs. 1b and 1c)"); and a plurality of binders incorporated into the binder insertion regions, wherein the binders are configured to bind at least one of the plurality of epitopes (Abstract; "a star-shaped DNA architecture, carrying five molecular beacon-like motifs, was constructed to display ten dengue virus envelope protein domain-III (ED3)-binding aptamers into a 2D pattern precisely matching the pentagonal arrangement of ED3 clusters on the dengue viral surface"; pg 5 para 2; "DENV was chosen because its envelope protein binding-domain III (ED3), a viral surface epitope, is organized into a complex icosahedral shape with alternating clusters of three or five ED3 sites (Fig. 1a) By connecting the clusters of ED3 sites linearly, we determined that a star-shape, consisting of an interior pentagon connected to five exterior triangles, would provide an optimal multivalent scaffold (Fig. s1b)"). As to claim 2 and new claim 21, Kwon further discloses that one or more functional domains having an activity, wherein the activity includes inhibition (pg 8 para 2; "DNA star for viral detection and inhibition of DENV (serotype 2, referred to as just DENV) was prepared by placing a ED3-binding aptamer (called "aptamer" herein) at all ten vertices of the DNA star to form a star-aptamer complex that geometrically matches and targets ED3 clusters (Fig. 2a). DENV was chosen"). As to claim 3, Kwon further discloses that the functional domains exhibit a first activity when unbound and a second activity when bound to the plurality of epitopes (pg 9 para 2; "the hairpins would be pulled apart and converted to ssDNA (single- stranded DNA) as the aptamers arranged on the DNA star bind to ED3 sites on the DENV surface. The potent multivalent interactions, promoted by the matched geometric aptamer-ED3 pattern, would therefore cause a separation of the FAM fluorophores from BHQ-1 quenchers to afford a fluorescent readout"). As to claim 4, Kwon discloses that the functional domains include a hybridized fluorophore and a quencher, wherein the quencher inactivates the fluorophore as the first activity, and wherein the quencher separates from the fluorophore upon binding of the plurality of binders to generate a detectable fluorescent signal as the second activity (pg 8 para 2; "A FAM (fluorophore)or BHQ-1 (quencher) molecule-carrying ssDNA was hybridized to each inner edge strand flanking the hairpin to turn the star-aptamer complex into a viral sensor"; pg 9 para 2; "the hairpins would be pulled apart and converted to ssDNA (single-stranded DNA) as the aptamers arranged on the DNA star bind to ED3 sites on the DENV surface. The potent multivalent interactions, promoted by the matched geometric aptamer-ED3 pattern, would therefore cause a separation of the FAM fluorophores from BHQ-1 quenchers to afford a fluorescent readout"). As to claim 5, Kwon further discloses that the binders include aptamers (abstract; "Specifically, a star-shaped DNA architecture, carrying five molecular beacon-like motifs, was constructed to display ten dengue virus envelope protein domain-lii (ED3)-binding aptamers'). As to claim 6, Kwon further discloses that the target is Dengue virus (pg 5 para 2). As to claim 7, Kwon discloses that the scaffold includes one or more interior scaffold segments and one or more exterior edge segments (pg 6 para 1; "The DNA star contains ten 15-nm long double-stranded (dsDNA) external edges in which each inner vertex is comprised of a 4-arm junction. Each inner edge carries a single-stranded DNA (ssDNA) region that can form a hairpin (stem loop) structure with a 6-bp (base-pair) long stem"). In addition, the Supplementary Information for the Kwon publication (pages 24-34) disclose the instant SEQ ID NOs: in claims 8 and 10. As to claim 9, Kwon discloses that the interior scaffold segments include a stem-loop structure (pg 6 para 1; "Each inner edge carries a single-stranded DNA (ssDNA) region that can form a hairpin (stem loop) structure with a 6-bp (base-pair) long stem'). As to claims 11 and 18, Kwon discloses that five aptamers attached to interior scaffold segments (see pg 15 fig 4C; illustration of full star aptamer complex indicates 5 aptamers attached to interior scaffold segments), wherein the aptamers attach to the interior scaffold segments at the 3' ends of the interior scaffold segments (see pg 9 fig 2A; aptamers attached at 3' ends); and five aptamers attached to exterior edge segments (see pg 15 fig 4C; illustration of full star aptamer complex indicates 5 aptamer attached to exterior edge scaffold segments), wherein the aptamers attach to the exterior edge segments at the 3' ends of the exterior edge segments (see pg 9 fig 2A; aptamers attached at 3' ends). As to claim 12, Kwon further discloses that the interior scaffold segments and exterior edge segments are arranged in a 3D pattern (pg 20 para 1; "various DNA 2D/3D structures can be designed and synthesized on-demand to mimic simpler surface epitope patterns of pathogenic viruses").
Response to Arguments
Applicant’s arguments filed on 3/18/26 are based on the declaration filed under 130(a) that all inventive concepts of the Kwon article were derived only from the inventors of the current application and will be addressed below.
The Declaration under 37 CFR 1.130(a) filed on 3/18/26 is insufficient to overcome the 102(a)(1) rejection of claims 1-18 (and new claims 21-22) based on Kwon et al. (BioRxiv 2019, pages 1-25 and supplementary information, pages 1-36).
Dr. Kwon states: the remaining co-authors, Shaokang Ren, Megan E. Kizer, Lili Kuo, Feng Zhou, Fuming Zhang, Domyoung Kim, Keith Fraser, Laura D. Kramer, Nadrian C. Seeman, and Jie Chao designed, planned, and carried out experiments, designed and synthesized specific sequences of DNA star, and contributed to the data analysis and manuscript preparation. None of these remaining co-authors contributed to the conception of subject matter in currently pending claims 1-20 in the US 17/612,000 patent application.
The statement by Dr. Kwon regarding the remaining co-authors “designed and synthesized specific sequences of DNA star” embraces several sequences recited in the instant claims (e.g., claims 8 and 10). Based on the standard for inventorship in MPEP 2109 § II, “designing” the claimed sequence counts as having conceived of that sequence. A co-author who designed, planned, and carried out experiments, designed and synthesized specific sequences of DNA star appears to have contributed to the conception of the invention.
Furthermore, “‘conception is established when the invention is made sufficiently clear to enable one skilled in the art to reduce it to practice without the exercise of extensive experimentation or the exercise of inventive skill.’ Hiatt v. Ziegler, 179 USPQ 757, 763 (Bd. Pat. Inter. 1973)” (MPEP 2138.04). Someone would be considered to have conceived of the invention if they “designed [and] planned … experiments” that generated data that the inventors are relying on to provide an enabling disclosure. The statement that the co-authors not listed as inventors in the application, “designed” and “planned” experiments would indicate that the one or more of those co-authors not listed as an inventor “conceived of” the claimed invention.
Regarding the statement “these authors contributed equally to this work” on page 1 of Kwon et al. directed to several co-inventors (Paul S Kwon and Seok-Jook Kwon) and non-inventors (Shaokang Ren, Megan E. Kizer, Lolo Kuo), the declaration doesn’t sufficiently explain the statement “these authors contributed equally to this work”, without a more detailed explanation that shows what the non-inventors contributed for the Kwon publication that doesn’t count as conceiving of the invention.
In view of the reasons set forth above, the inventive concepts of the Kwon article do not appear to be derived only from the inventors of the current application. Thus, the declaration is insufficient to overcome the 102(a)(1) rejection over Kwon et al. (supra).
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1-3, 5, 7, 9, 12-15, and 21-22 are rejected under 35 U.S.C. 103 as being unpatentable over taken with Zhang et al. (US 2021/0137479, effective filing date 9/16/18) taken with Xu et al. (Chinese Sci Bull 55: 2169-2174 2010).
'479 teaches a nucleic acid assembly composition for use in targeted delivery (pages 128-130; Fig 5A). The composition in figure 5a has interior scaffold and exterior edge segments. The composition has interior scaffold segments having shRNAs, which are stem-loop structures (also see paragraphs 610-625). DNA origami methods were known in the prior art to design scaffold oligonucleotides (paragraph 73). The composition can be used to deliver an oligonucleotide to a targeted cell. A nucleic acid assembly can include a single stranded scaffold nucleic acid sequence that is modified to include one or more sequences of nucleic acids that bind one or more functional moieties, such as nucleic acids, proteins or small molecules (paragraph 275). The scaffold can include one or more moieties at the 5’ or 3’ ends or internal functionalizing sequence or moiety, for example, within one or more nucleic acids that form part of an edge of the assembly. The nucleic acid assembly can be modified to include one or more antibodies that function by binding to one or more epitopes (paragraphs 274-310 and 672 and 680). The antibodies or an antigen binding fragment thereof can bind a conformational epitope that includes a 3-D surface feature, shape or tertiary structure at the surface of the target cell.
'479 teaches a nucleic acid assembly composition that would read on the oligonucleotide scaffold comprising one or more functional moieties (binders incorporated into binder insertion regions) that bind one or more epitopes, except ‘479 does not specifically teach the amended claims directed to a composition comprising an oligonucleotide scaffold comprising a plurality of binders inserted into binder regions on the scaffold, wherein the binder insertions regions are configured to bind a plurality of epitopes on the surface of a target according to the spatial pattern of the plurality of epitopes on the surface of the target.
However, Xu et al. teach antibodies interact with antigen proteins through the epitope area, where the epitope are found to be discontinued or spatial or conformational rather than linear on the protein surface (abstract). Xu et al. studied B-cell discontinuous epitope prediction for protein antigens (pages 2170-2174). Computational tools can be used by one of ordinary skill in the art to identify spatial pattern on the protein surface of a target based on accumulation of 3D structures of antibody-antigen complexes in publicly available databases (page 2170).
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to combine the teaching of ‘479 taken with Xu et al. to make multivalently arrange binders in a spatial pattern to conform to the spatial pattern of a plurality of epitopes on the surface of a target molecule to assists in targeted cell delivery. A person of ordinary skill in the art would have been motivated to use the identifying steps for a spatial pattern of a plurality of epitopes on the surface of a desired target cell as taught by Xu et al. in a method of preparing the nucleic acid assembly taught by ‘479. Depending on the target, a person of ordinary skill in the art can make binders (antibodies) in the nucleic acid assembly bind to a plurality of epitopes on the surface of the target, wherein the plurality of the epitopes is the same epitope. See MPEP 2143(I)B. One of ordinary skill in the art would have been motivated to combine the teaching to detect a target molecule or for targeting delivery of a nucleic acid (CRISPR-Cas complex or gRNA) to a desired cell type. Depending on the chosen functional moiety, it would have an activity including inhibition, signaling, therapeutic or combinations thereof and would have an activity after the nanostructure binds to the desired cell. ‘479 teaches the scaffold having one or more interior scaffold segments and one or more exterior edge segments arranged in a 3D pattern (Fig 5a). The composition has interior scaffold segments having shRNAs, which are stem-loop structures.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Claims 1-3, 5, 7, 12-15, 17 and 21-22 are rejected under 35 U.S.C. 103 as being unpatentable over Veneziano et al. (WO 2017189870, of record) taken with Xu et al. (Chinese Sci Bull 55: 2169-2174 2010).
'870 teaches making a polyhedral nucleic acid nanostructure, wherein the nanostructure comprises a single-stranded scaffold sequence including one or more nucleic acid sequences complementary to a nucleic acid sequence corresponding to one or more of an mRNA, DNA, or an epitope recognized by a DNA binding protein. The nanostructures would have one or more interior scaffolds and one or more exterior edge segments and be arranged in a 3D structure pattern. The nanoparticles can include functional moieties displayed at the surface of the nanoparticle or located within the inner volume of the nanoparticle.
The nanostructure further comprising a molecule selected from the group consisting of PNA, protein, lipid, carbohydrate, a small molecule, a dye and RNA. For example, see pages 65-110 and 155-164 and Figures 1-18. The nanostructure can include oligonucleotide staples extended at either the 5' or 3' ends by an unpaired region of nucleic acid and the nucleic acid can includes a binding site for one or more functional moieties such as nucleic acids, proteins or small molecules (page 79). The protein can be antibodies and the RNA can be aptamers having affinity to one or more targets (pages 20-26 and 78-100). Antibodies can include an antigen binding site that binds to an epitope on the target cell. The epitope can be a linear epitope or bind a conformational epitope that includes a 3-D surface feature, shape, or tertiary structure at the surface of the target cell. Methods of determining spatial conformation of epitopes include for example, x-ray crystallography and 2-dimensional nuclear magnetic resonance. Targeting elements can be added to the nanostructure to exploit the surface markers specific to a group of cells to be targeted (pages 82-90).
‘870 teaches a DNA nanostructure comprising one or more antibodies attach to the nanostructure, wherein the antibodies comprise an antigen binding site that binds to one or more epitopes on a target and spatial conformations of epitopes are well-known in the prior art, but does not specifically teach the claims now directed to a composition comprising an oligonucleotide scaffold comprising a plurality of binders inserted into binder regions on the scaffold, wherein the binder insertions regions are configured to bind a plurality of epitopes on the surface of a target according to the spatial pattern of the plurality of epitopes on the surface of the target.
However, Xu et al. teach antibodies interact with antigen proteins through the epitope area, where the epitope are found to be discontinued or spatial or conformational rather than linear on the protein surface (abstract). Xu et al. studied B-cell discontinuous epitope prediction for protein antigens (pages 2170-2174). Computational tools can be used by one of ordinary skill in the art to identify spatial pattern on the protein surface of a target based on accumulation of 3D structures of antibody-antigen complexes in publicly available databases (page 2170).
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to combine the teaching of ‘870 taken with Xu et al. to make multivalently arrange binders in a spatial pattern to conform to the spatial pattern of a plurality of epitopes on the surface of a target molecule to assist in detecting a target or delivery of a molecule to a desired cell. A person of ordinary skill in the art would have been motivated to use the identifying steps for a spatial pattern of a plurality of epitopes on the surface of a desired target cell as taught by Xu et al. in a method of preparing the nucleic acid assembly taught by ‘870. ‘870 teaches that one of ordinary skill in the art can add one or more functional domains having activity to the nanostructure (page 161). Depending on the domain chosen, it would have an activity including inhibition, signaling, therapeutic or combinations thereof and would have an activity after the nanostructure binds to the desired cell. ‘870 teaches that the nanostructure would include one or more interior scaffolds and one or more exterior edge segments and the segments are arranged in a 3D pattern (e.g., figures 1-18). Depending on the target, a person of ordinary skill in the art can make binder in the nucleic acid assembly bind to a plurality of epitopes on the surface of the target, wherein the plurality of the epitopes is the same epitope. See MPEP 2143(I)B.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over ‘870 and Xu et al. as applied to claims 1-3, 5, 7, 12-15, 17 and 21-22 above, and further in view of Hamaguchi et al. (Analytical Biochemistry 294, 126-131, 2001, cited on a new IDS).
‘870 and Xu et al. do not specifically teach using a hybridized fluorophore and a quencher in the nucleic acid nanostructure.
However, Hamaguchi teaches that design of aptamer beacons for detecting a wide range of ligands (pages 126-131). The beacon can be a sensitive tool for detecting proteins and other chemical compounds. A fluorescence quencher pair is used to report changes in formation induced by ligand binding.
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to combine the teaching of ‘870 and Xu taken with Hamaguchi to use an aptamer beacon in the nucleic acid nanostructure for detection of proteins in a diagnostic method, namely to arrive at the claimed invention.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Claims 6 and 16 are rejected under 35 U.S.C. 103 as being unpatentable over ‘870 taken with Xu et al. as applied to claims 1-3, 5, 7, 12-15, 17 and 21-22 above, and further in view of Zhang et al. (Nat Struct Mol Biol. 2013, 20:105-110).
‘870 and Xu et al. do not specifically teach the target is from Dengue virus, Zika virus, influenza virus, adenovirus, bacterial toxin or combinations thereof.
However, spatial patterns of antigens on Dengue viral particles is available using Cryo-EM data as taught by Zhang et al. In addition, one of ordinary skill in the art would possess the knowledge that viruses, bacteria and toxins are known to have unique spatial patterns of antigens on their surfaces. “Prior art is not limited to the references being applied, but includes the understanding of one of ordinary skill in the art. See MPEP 2141(II)(C).
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to combine the teaching of ‘870 and Xu et al. taken with Zhang et al. to use the spatial patterns of antigens on Dengue viral particles or other viruses in the nucleic acid nanostructure for detecting the virus.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Conclusion
See attached PTO-326 for disposition of claims.
The art made of record and not relied upon is considered pertinent to applicant's disclosure. US 20230417749 (EFD 11/18/20) appears to teach or suggest the claimed invention, but was filed or published or has a filing date after the EFD (5/17/19) of the instant application.
US 20230019867 cites a publication (Kwon et al. Nature Chem: 12, 26-35, 2020) published after the EFD, including several of the applicant’s (paragraph 4).
Shaw et al. (Nature Methods 11, 2014, pages 841-846) investigated bivalent interactions of ligand nanospacing in EphA2 receptor activation.
Shaw et al. (Nature Nanotechnology Vol. 14, February 2019, 184-190) disclose attaching antigens to DNA origami nanostructures and studying the binding to antibodies based on the spatial tolerance of the antibodies. The nanostructure had two aptamers, wherein each aptamer binds to a different exosite, which is not an epitope.
Rinker et al. (Nature Nanotechnology Vol. 3, 418-422, 2008) teach self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding.
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.
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/BRIAN WHITEMAN/ Primary Examiner, Art Unit 1636