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 .
Status of Claims
Claims 1-9, 12-13, 15-17, 19, 21, 24-25, and 31-32 are pending.
Priority
Claims 1-9, 12-13, 15-17, 19, 21, 24-25, and 31-32 are a 371 of PCT/US 2022/032822 filed on June 9, 2022, which has priority to PRO 63/208725 filed on June 9, 2021.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on December 11, 2023, was filed before the mailing of the First Office Action on March 7, 2026. The Non-Patent Literature is in compliance with the provisions of 37 CFR 1.97 and are being considered by the examiner.
Drawings
The drawings are objected to because:
Figs. 1A – D are not legible.
Figs. 2A – G are not legible.
Figs. 3A – C are not legible.
Figs. 4A – K are not legible.
Figs. 5A – G are not legible.
Figs. 6A – D are not legible.
Figs. 7A – D are not legible.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
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.
Claim 16, 24, 25, and 31-32 is 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.
Nature of the Invention:
The invention is directed to structural DNA nanotechnology applied to viral encapsulation, specifically involving triangular DNA nanoscale structures assembled to form a macromolecular cylindrical shell for encapsulating filamentous viral particles.
Breadth of the Claims:
The claims encompass encapsulation of filamentous viral particles without any limitation to viral species, particle dimension, structural variability, or required assembly tolerances. Because of this, the claims cover a broad and structurally diverse genus of viral particles.
Amount of Direction or Guidance present in the Application:
The specification provides only a conceptual designs and theoretical descriptions. Paragraph [0165] expressly states “the conceptual designs, illustrated in Figs. 9-16…triangular subunits that can self-assemble to form cylindrical shell systems will be prepared and tested against filamentous virus particles…”. Based on this, an artisan would view the claimed invention as prospective and unverified, rather than supporting any operative teachings. Additionally, the specification lacks any discussion or guidance related to size matching between cylindrical shell type and viral particles, mechanical tolerances required for encapsulation, assembly conditions compatible with filamentous viral structures, or mechanisms for accommodating viral flexibility and polydispersity.
Presence or Absence of Working Examples:
The specification provides no working examples that include successful encapsulation of any filamentous viral particle.
Relative Skill of Those in the Art:
It is argued that the relative skill in the art, is that of a scientist with several years’ experience in the field, but that the Art itself is a recognition of what is understood by the Artisan, and thus, as seen below, does not make the breadth of the claims more predictable.
Predictability or lack thereof in the Art:
The art is highly unpredictable. As explained by Zanotti and Grinzato, filamentous viruses exhibit dynamic structural properties, including variability in particle length, bending, and surface organization [Structure of filamentous viruses, Current Opinion in Virology, 2021]. These features introduce substantial uncertainty into any encapsulation scheme based on rigid or semi-rigid nanoscale assemblies.
Quantity of Experimentation Needed:
The field of art is unpredictable and would require extensive experimentation. This would include such things as determination of compatible shell diameters and geometries, accommodating viral particle flexibility and curvature, selecting and/or optimizing targeting moieties, and validation across multiple viral systems given the diverse nature of filamentous viral particles. This amount of experimentation would be substantial given the exploratory nature of the experimentation that would be required to practice the invention as claimed.
Conclusion:
Given this, the specification fails to provide sufficient disclosure to allow one or ordinary skill in the art to make and use the claimed invention without undue experimentation.
Claims 16, 24, 25, and 31 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 written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 16 uses the generic phrase “encapsulate a filamentous viral particle” in the context of a cylindrical shell that is self-assembled using triangular DNA nanostructures that include a targeting moiety.
Claim 24 uses the generic phrase “encapsulate a filamentous viral particle” as it relates to a method of encapsulating said viral particle where the three-dimensional DNA molecular structures self-assemble around the said viral particle.
Claim 25 uses the generic phrase “encapsulates a filamentous viral particle” as it relates to a macromolecular cylindrical shell assembled from three-dimensional DNA molecular structures.
Claim 31 uses the generic phrase “encapsulates filamentous viral particles” as it relates to a method of treating an individual for a viral infection. The same generic scope “encapsulates filamentous viral particles” is present in each of the dependent claims, i.e. Claim 32.
The specification provides antecedent basis for a cylindrical shell configured to encapsulate a filamentous virus particle [¶ 0015].
The specification states “…macromolecular cylindrical shell forms a physical barrier that encapsulates filamentous viral particles at the site of viral infection, thereby treating the individual” [¶ 0015]. The specification goes on to give examples in the drawings where single-stranded DNA, single-stranded circular DNA, single gold nanoparticles, and gold labeled single-stranded DNA were encapsulated [¶ 0027]. In ¶ [0079], the specification again states encapsulation of filamentous viral particles along with other viral particle shapes. The specification mentions “encapsulate” 3 more times at paragraphs [0147], [0087], and [0093]. However, the specification does not provide any examples or experimental data demonstrating that a macromolecular cylindrical shell can encapsulate a filamentous viral particle. In fact, at paragraph [0165], the specification states that the “conceptual designs illustrated in Figs. 9-16, and the nucleic acid sequence illustrated in Tables 11-28 below, triangular subunits that can self-assemble to form cylindrical shell systems will be prepared and tested against filamentous virus particles such as…influenza A virus particles and non-infectious Ebola virus-like particles”. Filamentous virus particles exhibit substantial variability in diameter, length, rigidity, and surface composition as discussed in Zanotti & Grinzato, Structure of filamentous viruses [Current Opinion in Virology, 2021]. Because the specification has not demonstrated possession of the claimed invention as it relates to claim 16, a person of ordinary skill in the art would not be able to quantify all of the different variations that would be required under the scope of claim 16.
Given the generic scope of “wherein the cylindrical shell is configured to encapsulate a filamentous virus particle” in the context of a cylindrical shell that is self-assembled using triangular DNA nanostructures that include a targeting moiety, and the absence of teaching what, if any, the claimed invention could encapsulate specific filamentous virus particles, the Artisan would not understand Applicant to be in possession of the generic scope of “encapsulate a filamentous virus particle”.
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 3, 6-9, 13 and 16 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 3 recites “nanoscale triangular subunits mate”. It is unclear what “mate” means considering there is only one mention in the specification with no definition. Is “mate” referencing base pair hybridization, helix stacking, physical proximity or other structural interactions? Without further meaning, it is unclear what the scope of the claim is.
Claim 3 recites “subunits mate with only one of the other two edges”. It is unclear what “edges” are being referred to. Is the triangular subunit being folded where one edge “mates” with the opposite edge of the same subunit? Is it referring to an edge of one triangular subunit “mating” with a specific edge of another triangular subunit. As written, a person of ordinary skill would not understand what is meant by “each of the three edges of the nanoscale triangular subunits mate with only one of the other two edges”. For purposes of examination, Claim 3 is being interpreted to mean one edge of the triangular subunit “mates” with only one edge of a separate triangular subunit.
Claim 6 recites “ss-DNA molecule is positioned along a base surface of the nanoscale triangular subunit”. “base surface” is unclear. What is considered the base surface? Without a directional reference or coordinate system, a “base surface” is unclear. As the subunits assemble, they may flip or rotate and without a clear definition, a person of ordinary skill would be unable to determine what or where the “base surface” is located. The specification confounds this by assigning a definition of “base surface” to the inner surface of the nanostructure in reference to coating a virus shell [pg. 12 ¶ 0056]. However, base surface is also used in context to refer to a base surface of a triangular DNA nanoscale subunit [¶ 0056, 0057, 0068].
Claim 7 recites “ss-DNA molecule is positioned along a base surface of the nanoscale triangular subunit”. “base surface” is unclear. What is considered the base surface? Without a directional reference or coordinate system, a “base surface” is unclear. As the subunits assemble, they may flip or rotate and without a clear definition, a person of ordinary skill would be unable to determine what or where the “base surface” is located. The specification confounds this by assigning a definition of “base surface” to the inner surface of the nanostructure in reference to coating a virus shell [pg. 12 ¶ 0056]. However, base surface is also used in context to refer to a base surface of a triangular DNA nanoscale subunit [¶ 0056, 0057, 0068].
Claims 8 and 9 are also rejected based on dependency to claim 7.
Claim 13 recites “further comprises a linking agent that binds to two edge-to-edge stacked nanoscale triangular subunits”. “linking agent” is unclear and is not defined in the specification. The only mention of linking agent in the specification is at [¶ 0072]. What constitutes a linking agent? Given this, a person of ordinary skill would not understand what is meant by the term “linking agent”. Additionally, “binds to two edge-to-edge stacked nanoscale triangular subunits” is also unclear based on the term “linking agent”. Does this involve hybridization-based, covalent, electrostatic, etc.? Can the linking agent also be a single-stranded DNA?
Claim 16 recites “The macromolecular cylindrical shell according to claim 16”. Claim 16 improperly depends upon itself and renders the claim indefinite given a person of ordinary skill in the art would not be able to determine the meets and bounds of the claimed invention.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 1-9, 12-13, 15, 17, 19, and 21 are rejected under 35 U.S.C. §103 as being unpatentable over Tikhomirov et al. [Triangular DNA origami tilings, Journal of American Chemical Society, 2018], in view of Fraden et al. [Bioinspired DNA origami capsids, Brandies University et al., 2020], in view of Rothemund [Folding DNA to create nanoscale shapes and patterns, Nature, 2006], in view of Cao et al. [Mulivalent aptamer-modified DNA origami as drug delivery system for targeted cancer therapy, Chemical Research in Chinese Universities, 2020] in view of Williams-Rice (Hereinafter Rice) [The best nanotube edges have ‘armchairs’ and ‘zigzags’, Futurity, 2019], in view of Kulkarni et al. [The current landscape of nucleic acid therapeutics, Nature, May 2021].
For claim 1, Tikhomirov teaches every element except the triangular subunits forming a cylindrical shell. However, Tikhomirov et al. discloses DNA origami structures, i.e. triangular DNA nanostructures with edge programmable interactions, capable of self-assembly into higher-order shapes that could include a macromolecular cylindrical shell. In Fig. 2, discloses a three-dimensional globe-like structure showing that structures requiring curved structures is very possible. This concept is also shown in Fig. 4 parts a and c. Based on this, a person of ordinary skill would have been motivated to configure the triangular subunits disclosed in Tikhomirov et al. to self-assemble into a number of shapes, including a cylindrical shell given it would require routine adjustment of known geometric parameters of the subunits in order to form a cylindrical shell.
With respect to claim 2 where the triangular subunits require self-assembled lateral edge-to-edge stacking via base pair stacking, Tikhomirov et al. discloses base stacking along the edges of the three edges of the triangular tile, i.e. subunit, where the edge is complementary to itself as well as to the other two edges [pg. 17362, Left column, ¶ 1].
For claim 3 where each of the three edges “mate” with only one of the other two edges, Tikhomirov et al. discloses programmable edge sequences that hybridize to complementary edges of other subunits [pg. 17362, Left column, ¶ 1]. Additionally, Fig. 3 discloses a triangular subunit where one edge is capable of binding to two other edges as displayed in part “a”. Therefore, it would have been prima facie obvious to a person of ordinary skill in the art to combine the teachings of Tikhomirov et al. to create a cylindrical shell using triangular DNA nanoscale subunits where the subunits self-assembled via edge-to-edge stacking where one edge was capable of pairing or mating with the other two edges as disclosed in Fig. 3, part a. Because of this, there is a reasonable expectation of success for an artisan to modify the triangular DNA origami of Tikhomirov et al. to ensure that each of the three edges of the nanoscale triangular subunits mates with only one of the other two edges.
For claim 4 where the beveled edges contain specific angles, Tikhomirov et al. teaches DNA origami triangular subunits with programable designed edges that interact to assemble into higher-order structures [pg. 17361 Left column, ¶ 1]. Additionally, Fraden et la. teaches that triangular DNA origami building blocks with specific geometry and programmed edge interactions self-assemble into finite, self-closing shells such as octahedral or icosahedral structures. Fraden et al. further discloses beveled edges that are used to control curvature and ensures edges meet properly to form a shell [DNA origami shells]. Although Fraden et al. does not specifically cite specific degree angles of the edges, the concept of angling the beveled edges to specific degrees is present as a means of guiding self-assembly into specific geometric structures.
For claim 5 where one side of the triangular DNA subunit has a different bevel angle from the other two sides and also has a single-stranded DNA molecule self-assembled into the nanoscale triangular subunit along the one side, Rothemund, discussing bottom-up fabrication of folding DNA nanoscale shapes, discloses a single stranded scaffold used to hold the scaffold in place along with self-assembled staple strands [Abstract]. Tikhomirov et al. also discloses the use of single-stranded domains in bridge staples that could be used to program specific degrees of bending [pg. 17364, Left column, ¶ 1].
For claim 6 where the single-stranded DNA molecule is positioned along the base surface of the nanoscale triangular subunit, both Rothemund and Tikhomirov et al. disclose single-stranded DNA domains, along with bridge staples in some examples, along the edge [See previous paragraph].
For claim 7 where the DNA nanostructure includes a targeting moiety, Cao et al., discussing targeted cancer therapy using modified DNA origami, discloses the use of a targeting moiety [Abstract].
Here, it is prima facie obvious to a person of ordinary skill in the art prior to the filing of the claimed invention to modify the systems and methods of Tikhomirov et al. that discloses triangular DNA origami tilings with the teachings of Rothemund that discloses using single-stranded DNA scaffolding to help guide for the desired shape with the additional teachings of Cao et al. that specifically discloses the use of a targeting moiety associated with a modified DNA origami structure that is capable of targeting cancer cells where an aptamer served as a targeting ligand for binding with specific cancer cells [Introduction ¶ 3]. Given this, there is a reasonable expectation of success that a person of ordinary skill would combine the teachings of Tikhomirov et al. with the additional teachings of Rothemund and Cao et al. in order to create a nanoscale structure from triangular DNA origami that contained a targeting moiety, e.g. targeting ligand, for purposes of targeting specific cell types.
For claim 8 where the targeting moiety is a nucleic acid aptamer, Cao et al. discloses the use of a multivalent aptamers [Abstract].
For claim 9 where the targeting moiety binds to a viral capsid, although Cao et al. does not specifically disclose the use of a targeting moiety capable of targeting a viral capsid, Cao et al. does disclose the aptamer modifications enhance the specificity and binding affinity of DNA origami structures toward biological targets [Abstract]. Despite not disclosing specifically targeting a viral capsid, there is a reasonable expectation of success that a person of ordinary skill could modify a triangular DNA nanostructure with a targeting moiety that specifically targets a viral capsid. This is especially true given that there are known targeting ligands in the art that exhibit selective binding to different molecular targets including viral capsids.
For claim 12 where a macromolecular cylindrical shell is formed from a plurality of nanoscale triangular DNA structures, Tikhomirov teaches every element except the triangular subunits forming a cylindrical shell. However, Tikhomirov et al. discloses DNA origami structures, i.e. triangular DNA nanostructures with edge programmable interactions, capable of self-assembly into higher-order shapes that could include a macromolecular cylindrical shell. In Fig. 2, discloses a three-dimensional globe-like structure showing that structures requiring curved structures is very possible. This concept is also shown in Fig. 4 parts a and c. Based on this, a person of ordinary skill would have been motivated to configure the triangular subunits disclosed in Tikhomirov et al. to self-assemble into a number of shapes, including a cylindrical shell given it would require routine adjustment of known geometric parameters of the subunits in order to form a cylindrical shell.
For claim 13 where the three-dimensional structures are self-assembled by lateral edge-to-edge stacking via base-pair stacking, Tikhomirov et al. discloses base stacking along the edges of the three edges of the triangular tile, i.e. subunit, where the edge is complimentary to itself as well as to the other two edges [pg. 17362, Left column, ¶ 1].
With respect to claim 13 where the macromolecular cylindrical shell further comprises a linking agent that binds to two edge-to-edge stacked nanoscale triangular subunits, both Rothemund and Tikhomirov et al. disclose single-stranded DNA domains, along with bridge staples in some examples, along the edge [See previous paragraph].
For claim 15 where the lattice structure is in reference to lattice structure, Rice, describing nanotube edge structure, describes ‘zigzag’ and ‘armchair’ as basic configurations, i.e. 5,0 lattice structure, 5,3 lattice structure, and 5,5 lattice structure, also known as edge structures, for nanotubes or in the case of this application, cylindrical shells [¶ 1]. And given that Applicant’s drawings describe the respective lattice structures as zigzag, chiral, and armchair, a person of ordinary skill in the art would be aware of the different edge shapes of nanotube technology and their specific applications.
For claim 17 where a plurality of three-dimensional DNA molecular structures according to claim 1 are combined with a carrier, Kulkarni et al., discussing the known carriers for delivering nucleic acid constructs, discloses known and approved methods for delivering nucleic acid constructs [Fig. 1].
For claim 19 where the composition includes macromolecular cylindrical shells assembled from the plurality of three-dimensional DNA molecular structures, Kulkarni et al., again, discloses several carrier types that have been successfully used for carrying nucleic acids for in vivo gene therapy [Fig. 1]. Given the sensitive nature of nucleic acids, a person of ordinary skill would likely select with pre-approved, known methods for as a carrier for delivering both the three-dimensional DNA molecular structures for assembly in vivo or preconstructed macromolecular cylindrical shells that are assembled from the three-dimensional DNA molecular structures. Because of this, it is prima facie obvious to a person of ordinary skill in the art prior to the filing of the claimed invention to modify the systems and methods of Tikhomirov et al. with the additional teachings of Kulkarni when selecting carriers for administration of either the three-dimensional DNA molecular structures for assembly in vivo or for delivery of pre-assembled macromolecular cylindrical shells derived from the three-dimensional DNA molecular structures.
For claim 21 where the composition is combined with a pharmaceutical acceptable carrier, Kulkarni discloses multiple administration methods that would, including injections, that a person of ordinary skill would understand to include a pharmaceutical acceptable carrier. Therefore, it is prima facie obvious to a person of ordinary skill in the art that combining the three-dimensional DNA molecular structures or the macromolecular cylindrical shells assembled from the three-dimension DNA molecular structures would be combined with a pharmaceutical acceptable carrier in order for the composition to be successfully administered via injection, whether local or systemic.
The Supreme court has acknowledged:
When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable varition..103 likely bars its patentability…if a technique has been used to improve one device, and a person of ordinary skill in the art would recognize that it would improve similar devices in the same way, using the technique is obvious unless its actual application is beyond that person’s skill. A court must ask whether the improvement is more than the predictable use of prior-art elements according to their established functions…
…the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results (see KSR International Co. v. Teleflex Inc., 82 USPQ2d 1385 U.S. 2007) emphasis added.
In KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398 (2007), the Supreme Court reaffirmed "the conclusion that when a patent 'simply arranges old elements with each performing the same function it had been known to perform' and yields no more than one would expect from such an arrangement, the combination is obvious." Id. at 417 (quoting Sakraida v. Ag Pro, Inc., 425 U.S. 273,282 (1976)). The Supreme Court also emphasized a flexible approach to the obviousness question, stating that the analysis under 35 U.S.C. § 103 "need not seek out precise teachings directed to the specific subject matter of the challenged claim, for a court can take account of the inferences and creative steps that a person of ordinary skill in the art would employ." Id. at 418; see also id. at 421 ("A person of ordinary skill is... a person of ordinary creativity, not an automaton.").
From the teachings of the references, it is apparent that one of ordinary skill in the art would have had a reasonable expectation of success in producing the claimed invention. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made, as evidenced by the references, especially in the absence of evidence to the contrary.
Conclusion
No claims allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOHN DAVID MOORE whose telephone number is (703)756-1887. The examiner can normally be reached M-F 8-5.
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/JOHN DAVID MOORE/Examiner, Art Unit 1638
/Tracy Vivlemore/Supervisory Primary Examiner, Art Unit 1638