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
Applicant's election with traverse of Group I in the reply filed on 6/2/2026 is acknowledged. The traversal is on the ground(s) that all claimed inventions share a common special technical feature that constitutes a contribution over the prior art, thus satisfying the unity of invention requirement under 37 C.F.R. § 1.475. Applicant asserts that all claim groups are linked by the same special technical feature: a modular nucleic acid nanostructure platform that integrates (i) one or more targeting agents for specific molecular recognition, (ii) a plurality of dye molecules for signal generation, and (iii) defined spatial organization and attachment geometry. This unified platform architecture constitutes the core inventive contribution and forms the technical backbone of all claimed subject matter. Applicant argues that the product claims of Group I (claims 1-5, 17, and 18) define the fundamental nucleic acid nanostructure comprising the targeting agent(s), dye molecules, and their specific spatial arrangement. The withdrawn method and kit claims (claims 7-16 and 19- 21) are not "completely separate inventions," but rather represent specific applications and embodiments that necessarily depend upon and incorporate the same modular nanostructure platform defined in the elected product claims. Indeed, the method claims expressly require "a nanostructure of claim 1" or "a nanostructure as defined in claim 1," demonstrating their inherent dependency on the elected product claims. Furthermore, the search and examination burden would not be unduly increased by examining all claims together.
This is not found persuasive because the common technical feature of the Groups does not amount to a “special technical feature,” as such the Groups are considered to lack unity of invention because even though the inventions of these groups require the technical feature of a nucleic acid nanostructure comprising one or more targeting agent(s) and a plurality of dye molecules, this technical feature is not a special technical feature as it does not make a contribution over the prior art in view of Chang (US 2015/0017201), as set forth in the previous Office Action, and the Groups may be properly restricted. See MPEP 1893.03(d). It is further noted that at least the independent claim of Group I does not require any defined spatial organization and attachment geometry. The requirement is still deemed proper and is therefore made FINAL.
Status of Claims
Claims 1-5 and 7-21 are pending, of which claims 7-16 and 19-21 are withdrawn from consideration at this time as being directed to a non-elected invention. Claims 1-5, 17 and 18 encompass the elected invention and are examined herein on the merits for patentability.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-3, 5 and 17 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Woehrstein et al. (Sci. Adv., 2017; 3, e1602128).
Woehrstein teaches sub–100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA. A general framework is taught for engineering sub 100-nm–sized tags with digitally tunable optical properties, such as brightness and color, using tools from DNA nanotechnology. Each tag is composed of multiple organic fluorophores, organized in a spatially controlled fashion in a compact subdiffraction volume. This makes the composite fluorophore tag appear similar to a traditional organic fluorophore when visualized under a diffraction-limited microscope. Inspired by the definition of metamaterials, we therefore call this tag a metafluorophore (page 1).
Here, we use a two-dimensional (2D), rectangular DNA origami consisting of 24 parallel DNA double helices with dimensions of 90 × 60 nm2. This specific structure contains 184 uniquely addressable staple strands, which can be functionalized to display a large variety of molecules, such as fluorophores, nano particles, etc. One modular and economic way to attach molecules of interest to this molecular pegboard is the use of so-called “handle” and “antihandle” strands. Here, the staple strand at the position where one wants to attach a molecule is extended with a 21-nt-long single-stranded handle sequence. The complementary antihandle is functionalized with the entity that should be arranged on the DNA origami structure.
Staples carrying the handle sequences and the functionalized antihandle strands are usually part of the one-pot assembly mix. Distinct target species can be attached to the origami pegboard by using orthogonal handle strand sequences. To “label” targets with our DNA origami–based metafluorophore, we could use specific target-binding staple strands. Labeling can either be achieved by direct hybridization to a DNA or RNA strand on the target molecule (handle-/antihandle-binding) or be mediated by using antibodies or small-molecule binders for protein labeling (page 2).
Our structures showed a linear dependence of fluorescence intensity on the number of dyes. We confirmed this linear dependence for Atto 647N, Cy3, and Atto 488 dyes using DNA structures carrying up to 132 dyes per DNA origami (page 2).
See also Figure 4, in which a metafluorophore is programmed to hybridize to part of a specific nucleic acid target. A biotinylated capture strand binds to a second region and thus immobilizes the complex on a streptavidin-coated surface (page 7).
Figure 6 shows a schematic of triggered assembly of triangular metafluorophores constructed from 10 metastable Cy3-labeled DNA hairpin strands. A so-called capture strand (labeled with Alexa 647) is attached to a glass surface via biotin-streptavidin coupling. A long “trigger strand” can hybridize to the capture strand (page 9).
Accordingly, a nucleic acid nanostructure comprising one or more targeting agent(s) and a plurality of dye molecules is disclosed.
Claim(s) 1-5, 17 and 18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yan et al. (US 2019/0240248).
Yan discloses DNA nanostructure nanorobot comprising: a single stranded DNA scaffold strand of about 5,000 to 10,000 bases in length; a plurality of staple strands of DNA, wherein each staple strands are about 20 to 40 bases in length, wherein each staple strand has a unique sequence and is hybridized to a specific position on the DNA scaffold strand, wherein the plurality of staple strands hybridized to the DNA scaffold form a sheet having a top surface and a bottom surface; and one or more fastener strands of DNA, wherein the one or more fastener strands of DNA is capable of fastening the sheet into an origami structure (abstract).
In certain embodiments, the present invention provides a DNA nanostructure nanorobot comprising: a single stranded DNA scaffold strand of about 5000 to 10,000 bases in length; a plurality of staple strands of DNA of about 32 bases in length, wherein each staple strand has a unique sequence and is hybridized to a specific position on the DNA scaffold strand, wherein the plurality of staple strands hybridized to the DNA scaffold form a rectangular sheet having a top surface and a bottom surface, and having four corners; one or more fastener strands of DNA, wherein the one or more fastener strands of DNA is capable of fastening the rectangular sheet into a tube-shaped origami structure; and one or more DNA capture strands, wherein each capture strand is operably linked to a therapeutic agent.
In certain embodiments, the DNA nanostructure nanorobot further comprises DNA targeting strands, wherein each targeting strand is operably linked to a targeting moiety. In certain embodiments, the targeting moiety is an aptamer.
In certain embodiments, the DNA nanostructure nanorobot further comprises DNA imaging strands, wherein each imaging strand is operably linked to an imaging agent. In certain embodiments, the imaging agent is fluorescent dye (paragraph 0090-0096).
In Figure 20, a DNA origami design is shown with functional strands for thrombin loading and for in vitro and in vivo imaging. For thrombin loading on the “top” surface of the rectangular sheet, functional strands were used to replace the original staple strands at the corresponding positions. Functional strands include fasteners for rolling tube origami nanostructures, capture strands for cargo loading, additional aptamer-containing strands for targeting delivery and fluorescent dye-labeled strands for imaging. Strands in red and blue are fasteners (48, 73, 97, 120, 144, and 169) to form the tubular configuration. Twelve thrombin-loading strands (yellow; 43, 44, 57; 64, 65, 78; 139, 140, 153; 160, 161 and 174) are extended at their 5′-end with ssDNA composed of 4 binding sites to capture thrombin-DNA molecules. Eight additional targeting strands (green; 1, 12, 205, 216) with 5′-end extended AS1411 sequences (G-quadruplex format) are placed at the four corners of the rectangle to increase targeting ability. For imaging, thirty-seven imaging strands (magenta) contain extended ssDNA sequences at their 5′-ends. These extensions are complementary to fluorescent dye-labeled ssDNA (the extended parts of the strands are not depicted in the figure).
Accordingly, a nucleic acid nanostructure comprising one or more targeting agent(s) and a plurality of dye molecules is disclosed. With regard to claim 18, it is noted that Yan discloses targeting strands are placed ‘at the four corners of the rectangle”, since the strands are connected by a bond, which is within the scope of a linker, as claimed, the targeting strands are attached to said nanostructure at a distance of <2nm from a corner of said nanostructure, via a linker (bond).
With regard to claim 4, wherein one or more targeting agent(s) is/are attached to said nanostructure at a distance of 3 nm to 15 nm from a corner of said nanostructure, it is noted that the instant specification at published paragraph 0074 states that an attachment position, e.g. a position where a targeting agent is directly attached and/or a position where a linker, e.g. a targeting agent-bound linker (i.e. a linker bound to a targeting agent) is attached, has a distance of <5 nm, preferably <2 nm from a corner of said nanostructure. In one embodiment, a targeting agent is attached to and/or spaced from said nanostructure at a distance of from 3 nm to 15 nm, preferably 7 nm to 9 nm, with respect to a surface of said nanostructure, and is attached, e.g. via a linker, at a position having a distance of <5 nm, preferably <2 nm from a corner of said nanostructure. In one embodiment, a targeting agent is attached at a distal configuration of said nanostructure. In one embodiment, a distal configuration is realized by having the 3′ end of the linker's DNA attachment handle protrude from the nanostructure and by attaching the 5′ end of the complementary linker DNA to the targeting agent. In one embodiment, a distal configuration is realized by having the 5′ end of the linker's DNA attachment handle protrude from the nanostructure and by attaching the 3′ end of the complementary linker DNA to the targeting agent. In one embodiment, a linker has at least 16, preferably at least 20, more preferably at least 26 nucleic acid bases. In one embodiment, a targeting agent is spaced from and/or attached to a nanostructure with a linker having at least 16, preferably at least 20, more preferably at least 26 nucleic acids bases.
Yan discloses in Fig. 2A-2G, analysis of DNA nanorobot-triggered activation and endothelial cell targeting. Scheme of Y-shaped fastener strands and dissociation in response to nucleolin recognition. F and Q represent fluorescent and quencher molecules, respectively. The 15-bp partially complementary duplex switches to the G-quadruplex state to form an AS1411-nucleolin complex in response to the nucleolin target protein. Flow cytometry histograms showing Y-shaped fastener dissociation after a 2 h incubation with HUVECs, as measured by cell labeling with FITC-labeled F50 containing AS1411 sequences. HUVECs treated with fasteners of partially (15-bp, red line) and fully complementary (26-bp, green line) AS1411 duplex are shown.
In paragraph 0045 it is taught that eight additional targeting strands (green; 1, 12, 205, 216) with 5′-end extended AS1411 sequences (G-quadruplex format) are placed at the four corners of the rectangle to increase targeting ability.
Sequences for targeting are also taught at paragraph 0409. Accordingly, targeting sequences having nucleic acid base pair sequences are attached at the corners of the DNA orgigami nanostructures having the claimed length, as evidenced by the instant specification.
Conclusion
No claims are allowed at this time.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LEAH H SCHLIENTZ whose telephone number is (571)272-9928. The examiner can normally be reached Monday-Friday, 8:30am - 12:30pm EST.
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/LHS/
/Michael G. Hartley/ Supervisory Patent Examiner, Art Unit 1618
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