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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 22, 23, 25, 26 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 22 recites the limitation "the lid" in line 6. There is insufficient antecedent basis for this limitation in the claim. Claims 23, 25 and 26 ultimately depend from clam 22 and are rejected for the same reason.
For purposes of examination over the prior art, claim 22 will be assumed to further define the nanostructure of claim 1 as having a “lid”.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 25 and 26 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention. These claims recite the option wherein the agent (passed through the DNA origami pore) is a “hydrophobic molecule”. For this particular option, the claims are not enabled.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). Wands states at page 1404,
“Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex parte Forman. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.”
The nature of the invention
The invention is in the class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
The breadth of the claims
The breadth of the claims is not a dispositive issue.
Quantity of Experimentation
The quantity of experimentation needed to enable the passage of hydrophobic molecules through a DNA origami pore would be extensive, with no guarantee of success.
The unpredictability of the art and the state of the prior art
The term “hydrophobic”, by definition, means that the molecule would be insoluble in aqueous environment. DNA, on the other hand, is a charged molecule. If the solution in which the nanostructure is formed is an aqueous environment, then the hydrophobic molecule would be insoluble. While the hydrophobic molecule might partition to the lipid membrane (in which the DNA origami pore is embedded), the hydrophobic molecule would not traverse the pore. On the other hand, if the nanostructure were placed in a non-aqueous solvent (e.g., chloroform, toluene, oil, hexane), although this would provide for solubilization of the hydrophobic agent, it would also dissolve the lipid membrane and disrupt the DNA origami, as DNA is not soluble in such a solvent.
Working Examples
There are no working examples in the disclosure in which a small, hydrophobic agent is passed through the DNA origami pore.
Guidance in the Specification.
There is no guidance in the specification as to how one could pass a small, hydrophobic agent through the DNA origami pore situated in a lipid membrane, given that only in an aqueous environment can the nanostructure/lipid membrane maintain its structure, and in such aqueous environment the hydrophobic agent would be insoluble.
Level of Skill in the Art
The level of skill in the art is deemed to be high.
Conclusion
Given the basic principles of chemistry discussed above, along with the lack of any working examples or guidance, Applicant’s disclosure does not enable claims 25 and 26 as they pertain to the option of passing a “hydrophobic molecule” through the DNA origami pore.
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.
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.
Claim(s) 1, 3, 5, 6, 18-23 and 25 is/are rejected under 35 U.S.C. 103 as being unpatentable over Iwabuchi (Chem. Commun. 57:2990-2993 (2021), IDS ref) in view of Howorka (US 2021/0301334).
Regarding claims 1 and 3, Iwabuchi disclosed a nanostructure comprising:
a base plate sheet comprising a single-duplex layer comprised of DNA origami that is configured in a planar arrangement
See Fig. 1a, where the base plate sheet corresponds to the 42 nm × 42 nm square structure, which Iwabuchi characterizes as “a region that interacts with the lipid membrane”, which “consists of a double-stranded DNA with a length of 42 nm” (last paragraph on page 2990). From the profile view in Fig. 1a and 1b, this appears to have 3 layers:
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The bottom layer of this structure corresponds to the claimed “base plate sheet”.
a pore configured within the center of the base plate sheet
See Fig. 1a, top view showing a 10 nm diameter pore.
wherein the base plate sheet comprises a single-stranded DNA region on the bottom surface
See Fig. 1b, showing 47 strands of single-stranded DNA extending from the bottom.
a lipid membrane anchor covalently linked to a single-stranded DNA sequence which is partially complementary to the single-stranded DNA region of the base plate sheet on the bottom surface
See Fig. 1b, showing a lipid membrane having complementary DNA strands (“Anchor-DNA”), which Iwabuchi disclosed to be cholesterol-modified (last paragraph on page 2990).
Regarding claims 18 and 19, as the specification does not explicitly define the term “about”, Iwabuchi’s 42 nm × 42 nm base plate is “about” 70 nm × 70 nm, and Iwabuchi’s 10 nm × 10 nm pore is “about” 20 nm × 20 nm. In addition, both of these structures are square shaped in Iwabuchi’s Fig. 1.
Regarding claim 20, Iwabuchi’s nanostructure further comprised a lipid bilayer (Fig. 1b).
Regarding claim 22, Iwabuchi’s nanostructure further comprised a “lid”; see Fig. 3. Furthermore, Iwabuchi disclosed (page 2992, second paragraph): “Next, we attempted to regulate molecular transport using “the lid”—ssDNA (Blocker-DNA) that binds across the pore. We modified the design of the nanopore to bind Blocker-DNA by extending the staple DNA strands from the upper part of the pore (Fig. 3a).” Iwabuchi disclosed that a partially closed “lid” blocked passage of 40k dextran, and a fully closed “lid” blocked both 40k dextran as well as calcein (Fig. 3b, c). Additionally, Iwabuchi disclosed (page 2992, paragraph spanning columns): “Furthermore, we attempted to dissociate Blocker-DNA from the nanopore using a strand displacement reaction in situ (supporting note 3, ESI†). The dye influx assay (Fig. S14c, ESI†) showed a result similar to that with 2 Blocker-DNAs (Fig. 3f, middle), though all four Blocker-DNAs were added. It appears that the pore partly opened due to a signal.” According to “supporting note 3” of the supplemental information (included with the reference provided on the IDS), the strand displacement reaction involved providing a “Releaser-DNA”, which corresponds to the claimed “key single-stranded DNA sequence”. The releaser-DNA allowed for the influx of calcein (Fig. S14).
Regarding claim 25, calcein is an ion; see discussion under Table S1 of Iwabuchi’s Electronic Supplementary Information, where Iwabuchi noted that “calcein is negatively charged”.
Iwabuchi did not expressly disclose a multi-duplex layer-thick wall comprising a single-duplex layer comprised of DNA origami that extends downward from the base plate sheet on the periphery of the pore as recited in claim 1, or the specific details about this “wall” recited in claims 5 and 6. In Iwabuchi’s nanostructure, there was a “wall” extending downward (as well as upward) from the base plate sheet which formed the wall of the pore (Fig. 1). However, not enough details were given by Iwabuchi to ascertain whether it was a “multi-duplex layer-thick wall” or a “four-duplex layer-thick” wall. It did, however, extend roughly perpendicularly to the base plate sheet as can be seen in Fig. 1.
Howorka also disclosed DNA origami nanopores for inserting into membranes. In a particular example, shown in Fig. 8 and 9, and described in Examples 5 and 6 (paragraphs [0165]-[0171]), Howorka describes a nanopore structure with a “frame” (analogous to the claimed “base plate sheet”) and a “membrane-spanning partial channel wall” which is “composed of a vertical stack of single duplexed DNA duplexes” (paragraph [0170], referencing Fig. 9). As best seen in Fig. 9C, the “frame” is composed of 2 layers (the bottom analogous to the “base plate sheet”, as was the case with Iwabuchi’s structure), and what appear to be 4 stacked horizontally arranged DNA duplexes extending perpendicularly from the “frame” layers:
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It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to modify the nanostructure of Iwabuchi by providing the membrane spanning wall as configured using a horizontal stack of 4 layers of single-duplexed DNA duplexes, extending downward through the membrane, as this would represent nothing more than selecting an alternative DNA origami arrangement for traversing the lipid membrane.
Regarding claims 21 and 23, it would have been obvious to employ such modified nanostructure in “cell” membranes as both Iwabuchi and Howorka suggest such applications for DNA origami nanopores. Specifically, Iwabuchi references “artificial cells” (abstract, first paragraph and last paragraph of article) and Howorka references the “lipid-based membranes of cells” (paragraph [0093]) or inserting the nanopores into the “membrane of a target cell” (paragraph [0114]).
Claim(s) 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Iwabuchi (Chem. Commun. 57:2990-2993 (2021), IDS ref) in view of Howorka (US 2021/0301334) as applied to claims 1, 3, 5, 6, 18-23 and 25 above, and further in view of Kang (US 2020/0297867).
The teachings of Iwabuchi and Howorka have been discussed. Iwabuchi used cholesterol-modified oligonucleotides to anchor the nanopore structures to the lipid membrane. Iwabuchi did not disclose using fatty alcohols as alternatives.
Kang disclosed stearyl as an alternative to cholesterol for anchoring oligonucleotides to lipid membranes (paragraph [0128]); stearyl is the same as octadecanol.
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to modify the nanostructure suggested by the combined disclosures Iwabuchi and Howorka by substituting cholesterol with stearyl (octadecanol) as it is prima facie obvious to substitute equivalents known for the same purpose (MPEP 2144.06).
Claim(s) 7, 9, 12, 14 and 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Iwabuchi (Chem. Commun. 57:2990-2993 (2021), IDS ref) in view of Howorka (US 2021/0301334) as applied to claims 1, 3, 5, 6, 18-23 and 25 above, and further in view of Andersen (Nature 459:73-76 (2009), IDS ref) and Andersen Supplemental Information ([online] 7 May 2009 [retrieved on 22 July 2026] retrieved from https://www.nature.com/articles/nature07971#Sec18).
The teachings of Iwabuchi and Howorka have been discussed. Iwabuchi does not disclose a lid comprising a single-duplex layer comprised of DNA origami or flexible hinge sequences connecting the lid to the base plate sheet, as recited in claim 7, or the additional limitations in claim 7 or in claims 9, 12, 13, 14, 15 or 17.
Regarding claims 7 and 9, Andersen disclosed a DNA origami box with a lid that could be opened or closed by provision of “key” sequences; see abstract and Fig. 4b. The lid (as well as the other five faces of the box) was comprised of a single-duplex layer (Fig. 1a, b). The lid was connected to the box with flexible hinge sequences comprising single-stranded regions (page 18 of Supplemental Information, describing the 3D staple strands used for connecting face D (the lid) with face E (of the box); these staple strands comprise regions involved in duplex formation as well as single-stranded T4 spacers. The lid comprised two “half-locks” which were complementary to two other “half-locks” on the side of the box opposite the hinged edge; see Fig. 4b.
Regarding claim 12, the key sequences were complementary to the regions of complementarity between the two half-locks, thereby disrupting the pairing between the half-locks and allowing the lid to open; see Fig. 4b.
Regarding claims 14 and 15, Andersen disclosed the lid in both the open and closed configurations; see Fig. 4b.
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to modify the nanostructure suggested by the combined disclosures of Iwabuchi and Howorka by replacing the “lid” used by Iwabuchi with the more sophisticated lid and lock system used by Andersen. At the very least, this is simply substituting one known closing structure for a DNA origami opening with another. In addition, one would have been motivated to modify in this way to achieve a better control over the opening and closing of the lid (including the ability to detect based on FRET whether the lid was opened or closed; see Andersen Fig. 4).
Conclusion
Claims 13 and 17 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SAMUEL C WOOLWINE whose telephone number is (571)272-1144. The examiner can normally be reached 9am-5:30pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, GARY BENZION can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681
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