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 .
Priority
This application No. 18/288,545 filed 10/26/2023 is a National Stage entry under 35 U.S.C. §371 of International Application No. PCT/EP2022/061630 filed 04/29/2022. Applicant’s claims to priority from PCT/EP2022/061630 filed 04/29/2022 and Foreign Application No. EP21382377.6 filed 04/29/2021 is hereby acknowledged.
Election/Restrictions
Applicant's election with traverse of Invention Group I, claims 1-11, 15 and 16 drawn to a linear double-stranded DNA product comprising a sense and antisense
strand, a complex comprising the linear double-stranded DNA product, a nanoparticle, a library or a vaccine comprising the linear double-stranded DNA product, in the reply filed on 07/20/2026 is acknowledged.
The traversal is on the ground(s) that “the claims of Groups I-IV, especially as
amended herein, relate to a single general inventive concept under PCT Rule 13.1”.
This is not found persuasive because the Restriction Requirement was based on
claims and Groups identified/defined within those claims before amendments filed 07/20/2026. Applicants’ arguments are therefore moot, since the Restriction Requirement dated 06/05/2026 was established on claims as presented and filed on 05/20/2024, and the amendments filed 07/20/2026 were not entered at the time.
The requirement is still deemed proper and is therefore made FINAL.
Claims 12-14 are withdrawn from further consideration pursuant to 37 CFR
1.142(b) as being drawn to nonelected Inventions, there being no allowable generic or
linking claim. Applicant timely traversed the restriction (election) requirement in the replay filed on 07/20/2026.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Application Status
Amendments to claims filed 07/20/2026 are hereby acknowledged. Claim 2 is cancelled. Claims 1 and 3 are currently amended. Claims 1 and 3-16 are currently pending. However, claims 12-14 are withdrawn since they are drawn to a non-elected invention.
Therefore, claims 1, 3-11 and 15-16 are under consideration in this office action.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on 10/26/2023, 03/06/2024, 09/11/2024, 03/06/2025, 06/04/2025, 06/12/2025, 08/19/2025, 10/29/2025, 01/08/2026, 03/25/2026, 04/23/2026, 05/19/2026, 08/12/2026 and 09/25/2026 are hereby acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
However, the listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892 or submitted on an IDS, they have not been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings (FIG. 1) are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
From the “Brief Description of the Drawings” in Specification (page 64) and “Examples” (page 76), it is not clear what SEQ ID NO correspond to the sequences shown in FIG.1.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Drawings
The drawings are objected to because "MAGNIPHI" , "T13-G" and Sp1 c" in
Figure 1 are not explained in Specification.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5)
because they do not include the following reference sign(s) mentioned in the
description: Sequences in Figure 1 do not have specifically listed SEQ ID NO in
Drawing description.
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.
Specification
The disclosure is objected to because of the following informalities: "T7-
FlashScribeTM" and "ScriptGuardTM RNase inhibitor: should be "T7-FlashScribe ™"
and "ScriptGuard ™" on page 83, second paragraph. Appropriate correction is required.
The use of the terms "Lipofectamine" (pages 38, 68, 81-83), "CutSmart" (pages
65-66, 68, 77-80), "PolyPlus" ( pages 68, 80-82), "jetOptimus" ( pages 68, 81-82),
"QualiPhi" ( pages 64-67, 76-80 ), "TruePrime" (pages 64, 76), "OptiMEM" (pages 81-
82), "ClarioSTAR" (page 82), "Pierce" and "BCA protein assay" (page 82), "ARCA Cap"
( pages 83-84), "Qubit" (pages 68, 83), "CellScript" (pages 83-84), "MAGNIPHI" (Figure
1) which are trade names or marks used in commerce, has been noted in this
application. The terms should be accompanied by the generic terminology; furthermore, the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as TM, SM , or® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks,
service marks, certification marks, and collective marks) are permissible in patent
applications, the proprietary nature of the marks should be respected and every effort
made to prevent their use in any manner which might adversely affect their validity as
commercial marks.
Claim Rejections - 35 USC § 101
35 U.S.C. § 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 10, 11 and 15 are rejected under 35 U.S.C. §101 because:
The claimed invention in claims 10, 11 and 15 are directed to non-statutory subject matter. The claims do not fall within at least one of the four categories of patent eligible subject matter because they are directed to the use of a product.
MPEP 2106.03 clearly specifies statutory categories for patentability eligibility as claims drawn to either a process with specific actions/steps, a machine, manufacture and composition of matter.
Claim Rejections - 35 USC § 112(b)
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 6, 7, 9-11 and 15 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.
Regarding claims 6, 7 and 10, the claims recite the term “optionally” before a narrower limitation in the same claim. MPEP §2173.05(h) provides guidance for the use of Alternative limitations. An acceptable format for the use of the term “optionally” in a definite way involves for example claims with language “containing A, B, and optionally C”. In this instances, in claims 6, 7 and 10, the term “optionally” is used as to signify “preferentially”.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claims 6, 7 and 10 recite broader recitations such as “a functional portion”, or “production of RNA”, and the claims also recite “optionally wherein the functional portion is a binding molecule or a probe” or “the RNA is mRNA”, which are narrower statements of the ranges/limitations. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Regarding claims 10, 11 and 15, the claims are drawn to a use of a claimed product. The claims are improper as they are drawn to two patentably distinct statutory classes, a process and a product. See MPEP §2173.05(q) and MPEP §2106.03. In addition, claims 10 and 11 are dependent upon claims 1, 6, 7 and 8, without requiring any active steps. Claim 15 depends on claims 1, 6 and 8 without requiring any active steps.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 9 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Regarding claim 9, it recites: “The linear double-stranded DNA product of claim 1, the complex molecule of claim 6, the nanoparticle of claim 7, or the library of claim 8 for use in therapy.”
The limitation “for use in therapy” does not further limit the structures claimed in claim 1, claim 6, claim 7 or claim 8. Claim 9 requires only the products of claims 1, 6, 7 or 8, without any steps. This limitation is an intended use recitation, which does not impart patentability upon the claims.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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.
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 1 is rejected under 35 U.S.C. §103 as being unpatentable over Zhu (Zhu, B. et al. “Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins”. Biotechnology and Bioengineering, Vol. 117 (2020), pp: 3849-3857; cited on IDS filed 03/25/2026), in view of Watzele (Watzele, M. et al. US 2004/0259081 A1, published December 23, 2004; cited on IDS filed 09/25/2026), Wang (Wang, L. et al. “DNA phosphorothioate modification – a new multi-functional epigenetic system in bacteria”. FEMS Microbiology Reviews, Vol 43, No. 2 (2019), pp:109-122), Ly (Ly, S. et al. “ Single-stranded phosphorothioated regions enhance cellular uptake of cholesterol-conjugated siRNA but not silencing efficacy”. Molecular Therapy: Nucleic Acids, Vol. 21 (2020), pp: 991-1005), and NEB-pdf1 (Phusion® Hot Start Flex DNA Polymerase, downloaded from URL: https://www.neb.com/en-us/products/m0535-phusion-hot-start-flex-dna-polmerase ; Phusion® Hot Start Flex DNA Polymerase | NEB; cited on IDS filed 03/25/2026).
Regarding claim 1, Zhu teaches DNA templates that are linear, i.e., Linear Expression Templates (LETs), for crude extract-based cell-free protein synthesis (CFPS) (see abstract). Zhu teaches that this LET contains a T7 promoter and a T7 terminator (see section 2.2., page 3851, right column).
A DNA expression template molecule, obtained by PCR and used for protein expression (see page 3850, “Introduction” section, left column, first paragraph), inherently comprises a sense and antisense strand, therefore Zhu teaches these elements; and the double strands are shown in drawings in Figure 1(a).
Zhu teaches stabilization of the LETs using different strategies for comparison:
Protection of LET via terminal protection using double strand DNA-binding protein, adding a scCro-binding site (ORC) at each end (see Figure 1); or
Protection using LET methylation with dam or CpG methyltransferases (see section 2.3, page 3851); or
Protection adding three phosphorothioate bonds modifications at the 5’ ends to prevent hydrolysis (see section 2.2., right column).
Zhu is silent on whether the end of the linear double-stranded DNA product comprises an overhang or a blunt end.
However, Zhu teaches that the DNA polymerase used to obtain the LET is a DNA polymerase (Phusion®) obtained from New England Biolabs (NEB) (see section 2.1, page 3851).
As evidenced by NEB-pdf1, the Phusion® DNA polymerase produces blunt ends (“Product Information” section, first paragraph).
Zhu does not teach three phosphorothioate nucleotides at each ends of the sense strand and the antisense strand.
Watzele teaches that combining methods/modalities to protect a double-stranded DNA templates for protein expression is acceptable (see title, abstract and [0001 ]-[0007]).
Watzele teaches that "the stability of the linear short DNA is improved by one or
several of the following measures to protect the double-stranded DNA from exonucleases:
a) Incorporation of exonuclease resistant nucleotides analogues or other
exonuclease-resistant molecules at the 3' end of the template,
b) Use of PCR primer pairs which contain exonuclease-resistant nucleotides to
produce a linear short DNA,
c) Protection of a template produces by a PCR reaction by connecting the 5' end
to the 3' end of the complementary strand,
d) Protecting the template by DNA sequence-specific binding molecules which
bind to both ends of the linear template,
e) Inactivation of the exonucleases by adding competitive or non-competitive
inhibitors,
f) Circularization of the template to for a ring-shaped closed template."
See [0001 ]-[0007]).
Watzele teaches that “Exonuclease-resistant nucleotide analogues can be incorporated at the 3’ end of the template according to measure a)” and Alternatively it is possible to incorporate 5’ phosphothioate- protected nucleoside triphosphates or deoxy-nucleoside triphosphates (see [0030]-[0031]; claim 4 on page 10).
However, Wang teaches that DNA phosphorothioate modification exist in bacteria as a multifunctional epigenetic system (see title and abstract).
Wang teaches that DNA phosphorothioate modification occurs naturally in bacteria and is a versatile player in the maintenance of cellular redox homeostasis, epigenetic regulation and environmental fitness (see abstract).
Wang teaches cassettes of multiple genes in bacterial genome, flanked with phosphorothioate modifications modulating gene expression, that exist naturally as a defence mechanism (see Figure 2). Wang teaches specific restriction enzyme recognition sites with Phosphorothioate modification on both strand of DNA (see Figure 3). Wang teaches epigenetic control of expression cassettes in presence of phosphorothioate modification upstream of promoter sequence (see Figure 4).
Therefore, Wang’s teachings suggest that it is possible to obtain modifications on both strand of a double-stranded DNA molecule.
Ly teaches that both termini of a nucleic acid molecule can be modified with phosphorothioate linkages (see title and abstract).
Ly teaches nucleic acid molecules with internucleoside phosphorothioate modifications between 3 or more nucleotides at each ends (see Figure 1A; page 992).
Ly teaches that there is an increase in intracellular internalization when the molecule is modified with phosphorothioate modifications at both ends (see Figure 2A).
In KSR Int 'l v. Teleflex, the Supreme Court, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. 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 variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention, to have modified the LET taught by Zhu and Watzele and add three or more phosphorothioate modifications on each terminal end of each strand as taught by Ly and Watzele, and at the 5’ end of the promoter sequence as taught by Wang. One with ordinary skills in the art motivated in increasing gene expression in crude cellular extract and cellular uptake in transfection as taught by Ly and Wang, could have performed these modifications with a reasonable expectation of success and would have arrived at the claimed invention.
Claim 3 is rejected under 35 U.S.C. §103 as being unpatentable over Zhu (Zhu, B. et al. “Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins”. Biotechnology and Bioengineering, Vol. 117 (2020), pp: 3849-3857; cited on IDS filed 03/25/2026), in view of Watzele (Watzele, M. et al. US 2004/0259081 A1, published December 23, 2004; cited on IDS filed 09/25/2026), Wang (Wang, L. et al. “DNA phosphorothioate modification – a new multi-functional epigenetic system in bacteria”. FEMS Microbiology Reviews, Vol 43, No. 2 (2019), pp:109-122), Ly (Ly, S. et al. “ Single-stranded phosphorothioated regions enhance cellular uptake of cholesterol-conjugated siRNA but not silencing efficacy”. Molecular Therapy: Nucleic Acids, Vol. 21 (2020), pp: 991-1005), and NEB-pdf1 (Phusion® Hot Start Flex DNA Polymerase, downloaded from URL: https://www.neb.com/en-us/products/m0535-phusion-hot-start-flex-dna-polmerase ; Phusion® Hot Start Flex DNA Polymerase | NEB; cited on IDS filed 03/25/2026), as applied to claim 1 above and in further view of NEB-pdf2 (“PCR Protocol for Taq DNA Polymerase with Standard Taq Buffer (NEB#M0273)”- downloaded from Internet from URL: https://www.neb.com/en-us/protocols/taq-dna-polymerase-with-standard-taq-buffer-m0273#; cited on IDS filed 03/25/2026).
The rejection of claim 1 is described above. The combination of references Zhu, Watzele, Wang, Ly and NEB-pdf1 renders elements of claim 1 obvious.
Regarding claim 3, Ly teaches a double-stranded molecule comprising a blunt end and a 3’ overhang (see Figure 1A).
However, the combination of references Zhu, Watzele, Wang, Ly and NEB-pdf1 does not render elements linear DNA product comprising a coding sequence and a promoter as required by claim 3 obvious, i.e. “The linear double-stranded DNA product of claim 1, wherein the linear double-stranded DNA product comprises an overhang, and wherein the linear double-stranded DNA product comprises:
A 5’ overhang and a blunt end;
Two 5’ overhangs;
A 3’ overhang and a blunt end;
Two 3’ overhangs; or
A 5’ overhang and a 3’ overhang.”
However, NEB-pdf2 provides for another type of DNA polymerase that is used since 1985, as taught in “References” section, page 2 of NEB-pdf2.
NEB-pdf2 teaches that Taq DNA polymerase leads to PCR products that contain dA overhangs (see page 2, paragraph 11, “PCR product” section).
NEB-pdf2 teaches that Taq polymerase is powerful and sensitive and widely used in PCR for routine applications (see page 1, “Overview” section).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention, to have substituted the DNA polymerase used by Zhu, a DNA polymerase that is used for cloning ideally, with a DNA polymerase that is widely known and used routinely for product that may not require a step of cloning, as taught by NEB-pdf2. One with ordinary skills in the art motivated in obtaining a product easily with a powerful and sensitive enzyme that is used routinely and readily available in any Molecular Biology laboratory, could have performed this substitution, and as a result obtained a PCR product comprising 3’ overhangs. One with ordinary skills in the art could have performed this modification with a reasonable expectation of success and arrived at the claimed invention.
Claims 6, 7, 9, 11 and 15-16 are rejected under 35 U.S.C. §103 as being unpatentable over Zhu (Zhu, B. et al. “Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins”. Biotechnology and Bioengineering, Vol. 117 (2020), pp: 3849-3857; cited on IDS filed 03/25/2026) , in view of Watzele (Watzele, M. et al. US 2004/0259081 A1, published December 23, 2004; cited on IDS filed 09/25/2026), Wang (Wang, L. et al. “DNA phosphorothioate modification – a new multi-functional epigenetic system in bacteria”. FEMS Microbiology Reviews, Vol 43, No. 2 (2019), pp:109-122), Ly (Ly, S. et al. “ Single-stranded phosphorothioated regions enhance cellular uptake of cholesterol-conjugated siRNA but not silencing efficacy”. Molecular Therapy: Nucleic Acids, Vol. 21 (2020), pp: 991-1005), and NEB-pdf1 (Phusion® Hot Start Flex DNA Polymerase, downloaded from URL: https://www.neb.com/en-us/products/m0535-phusion-hot-start-flex-dna-polmerase ; Phusion® Hot Start Flex DNA Polymerase | NEB; cited on IDS filed 03/25/2026), as applied to claim 1 above and in further view of Gaspar (Gaspar, R. et al. “Lipid-Nucleic Acid complexes: physicochemical aspects and prospects for cancer treatment”. Molecules, Vol. 25 (2020), p: 5006) and Gutierrez-Triana (Gutierrez-Triana, J.A. et al. “Efficient single-copy HDR by 5’ modified ling dsDNA donors”. eLife, Vol. 7 (2018), p: e39468; cited on IDS filed 08/19/2025).
The rejection of claim 1 is described above. The combination of references Zhu, Watzele, Wang, Ly and NEB-pdf1 renders elements of claim 1 obvious.
Regarding claims 6 and 7, the combination of references does not teach “a complex molecule comprising the linear double-stranded DNA product”, nor “a nanoparticle comprising the linear double-stranded DNA product”.
However, Gaspar teaches lipid-conjugated nucleic acids as complexes (lipoplexes) that can be nanosized, i.e., nanoparticles (see title and abstract, section 4 on page 8 of 39).
Gaspar teaches that these nucleic acid molecules can be conjugated with lipid to form lipid nanoparticles that are used for cancer treatment, gene therapy, as they offer the possibility to supplement, repair or silence faulty genes or to stimulate immune system to fight diseases (see Abstract; and Figure 1).
Gaspar teaches that cationic lipids can self-assemble and associate strongly with DNA (see section 4.1; page 8 of 39). Gaspar also teaches that adding polyethylene glycol to the assembly improves circulation lifetime, stabilizes the nanoparticle structure and increase cellular uptake and targeting of the nucleic acid molecule (see section 5.1, page 16 of 39; section 6.1, pages 19-20 of 39).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have modified the linear double-stranded DNA taught by the combination of Zhu, Watzele, Wang, Ly and NEB-pdf1, and conjugated with lipids, forming a complex molecule that can be of nano size, as taught by Gaspar. One with ordinary skills in the art motivated in formulating a stable and efficient complex for gene therapy would have performed these modifications with a reasonable expectation of success and would have arrived at the claimed invention.
Regarding “a functional portion” in claims 6 and 7, The Specification teaches that “the functional portion” can be a nucleic acid sequence, a linker molecule, a targeting sequence, a protein, a peptide, a polypeptide, a DNA, RNA or DNA/RNA chimera sequence, a label, a fluorophore, a radioactive compound or a barcode (see page 19, section 2 (“Complex molecules”) to page 21.
Therefore, the combination of references Zhu, Watzele, Wang, Ly and NEB-pdf1 teaches at least two types of “functional portions”, Zhu teaches a nucleic acid binding sequence to scCro, and Ly teaches a label, i.e., Cy3®, as explained below:
Zhu teaches stabilization of the LETs using different strategies for comparison:
Protection of LET via terminal protection using double strand DNA-binding protein, adding a scCro-binding site (ORC) at each end (LET2) (see Figure 1); or
Protection using LET methylation with dam or CpG methyltransferases (see section 2.3, page 3851); or
Protection adding three phosphorothioate bonds modifications at the 5’ ends to prevent hydrolysis (LET5) (see section 2.2., right column).
Therefore, Zhu teaches a linear double-stranded DNA product comprising a
functional portion wherein the functional portion binds to scCro protein for protection (see Figure 1).
Watzele teaches that "the stability of the linear short DNA is improved by one or
several of the following measures to protect the double-stranded DNA from exonucleases:
a) Incorporation of exonuclease resistant nucleotides analogues or other
exonuclease-resistant molecules at the 3' end of the template,
b) Use of PCR primer pairs which contain exonuclease-resistant nucleotide
to produce a linear short DNA,
c) Protection of a template produces by a PCR reaction by connecting the 5’
end to the 3' end of the complementary strand,
d) Protecting the template by DNA sequence-specific binding molecules
which bind to both ends of the linear template,
e) Inactivation of the exonucleases by adding competitive or non-competitive
inhibitors,
f) Circularization of the template to for a ring-shaped closed template."
See [0001 ]-[0007]).
Watzele teaches that “Exonuclease-resistant nucleotide analogues can be incorporated at the 3’ end of the template according to measure a)” and Alternatively it is possible to incorporate 5’ phosphothioate- protected nucleoside triphosphates or deoxy-nucleoside triphosphates (see [0030]-[0031]; claim 4 on page 10).
Therefore, Watzele teaches that combinations of strategies can be used to protect a sequence of interest.
Ly teaches a binding molecule that is a probe, a label for detection, i.e., Cy3® , conjugated at the 5’ end of the antisense strand, combined with phosphorothioate modifications at both 5’ and 3’ ends of the nucleic acid molecule (see page 992, Figure 1).
However, the combination of references Zhu, Watzele, Wang, Ly and NEB-pdf1 does not teach a specific example of combining a linear double-stranded DNA product comprising phosphorothioate modifications with a functional portion wherein the functional portion is a binding molecule.
The Specification teaches that “the functional portion may be a binding molecule that is any molecule that is capable or binding the linear double-stranded DNA product or that is capable of binding to a further molecule or target, a molecule that may be a protein, a polypeptide, or a peptide (see page 20, 4th paragraph).
However, Gutierrez-Triana teaches an example of a linear double-stranded DNA comprising five (5) nucleotides modified with phosphorothioate at each 5’ terminal end of the molecule, with a probe, i.e., a biotin moiety (see Figure 1A, page 3 of 15).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention, to have modified the linear double-stranded DNA taught by Zhu modified by Watzele (combination of LET2 and LET5), and added at least 3 phosphorothioate modifications at each end, and conjugated the nucleic acid with a probe of a binding molecule, as taught by Ly and Gutierrez-Triana. One with ordinary skills in the art, motivated in visualizing the molecules in situ, in cells or in tissues after delivery of the complex molecule or nanoparticle could have performed this modification with a reasonable expectation of success and would have arrived at the claimed invention.
Regarding claim 9, the combination of references Zhu, Watzele, Wang, Ly, NEB-pdf1, Gaspar and Gutierrez-Triana teaches the use of lipid-nucleic acid complex/nanoparticle for gene therapy in the treatment of cancer (see Gaspar, title, Abstract, Section 8 on page 25 of 39). The obviousness of the combination of references Zhu, Watzele, Wang, Ly, NEB-pdf1, Gaspar and Gutierrez-Triana is described above.
Regarding claim 11, Gaspar teaches the design and use of lipid nanoparticle comprising linear nucleic acids in the treatment of cancer (see sections 5, 7 and 8). The obviousness of the combination of references Zhu, Watzele, Wang, Ly, NEB-pdf1, Gaspar and Gutierrez-Triana is described above.
Regarding claims 15 and 16, Gaspar teaches that the lipid-nucleic acid complexes/nanoparticles can be administered in intra-tumoral vaccines (see page 2 of 39, line 10; page 27, third paragraph).
The obviousness of the combination of references Zhu, Watzele, Wang, Ly, NEB-pdf1, Gaspar and Gutierrez-Triana is described above.
Claim 8 is rejected under 35 U.S.C. §103 as being unpatentable over Zhu (Zhu, B. et al. “Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins”. Biotechnology and Bioengineering, Vol. 117 (2020), pp: 3849-3857; cited on IDS filed 03/25/2026) in view of Watzele (Watzele, M. et al. US 2004/0259081 A1, published December 23, 2004; cited on IDS filed 09/25/2026), Wang (Wang, L. et al. “DNA phosphorothioate modification – a new multi-functional epigenetic system in bacteria”. FEMS Microbiology Reviews, Vol 43, No. 2 (2019), pp:109-122), Ly (Ly, S. et al. “ Single-stranded phosphorothioated regions enhance cellular uptake of cholesterol-conjugated siRNA but not silencing efficacy”. Molecular Therapy: Nucleic Acids, Vol. 21 (2020), pp: 991-1005), and NEB-pdf1 (Phusion® Hot Start Flex DNA Polymerase, downloaded from URL: https://www.neb.com/en-us/products/m0535-phusion-hot-start-flex-dna-polmerase ; Phusion® Hot Start Flex DNA Polymerase | NEB; cited on IDS filed 03/25/2026), as applied to claim 1 above and in further view of Gaspar (Gaspar, R. et al. “Lipid-Nucleic Acid complexes: physicochemical aspects and prospects for cancer treatment”. Molecules, Vol. 25 (2020), p: 5006) and Ramishetti (Ramishetti, S. et al. “ A Combinatorial Library of lipid nanoparticles for RNA delivery to leukocytes”. Advanced Materials. Vol. 32 (2020), p: 1906128).
The rejection of claim 1 is described above. The combination of references Zhu, Watzele, Wang, Ly and NEB-pdf1 renders elements of claim 1 obvious.
The combination of references does not teach a library comprising at least two linear double-stranded DNA products, wherein each double-stranded DNA product is as defined in claim 1.
However, regarding claim 8, Gaspar teaches lipid-conjugated nucleic acids as complexes (lipoplexes) that can be nanosized, i.e., nanoparticles (see title and abstract, section 4 on page 8 of 39). Gaspar also teaches that a series of ionizable cationic lipids and lipid nanoparticles can be designed and developed (see section 7, 4th paragraph). Gaspar refers to reference # 209, i.e., Ramishetti.
Ramishetti teaches a combinatorial library of lipid nanoparticles for RNA delivery (see title and abstract).
Ramishetti teaches that multiple, a series of lipid nanoparticles can be obtained by using different combinations of lipids with the same nucleic acid targeting PLK1 mRNA (see Figure 1; see page 3 of 8, left column, lines 4-7).
It would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have combined the teachings of Zhu modified by Watzele, Wang, Ly and NEB-pdf1, with the teachings of Gaspar and Ramishetti, and modified the linear LET2/5 conjugating with lipids mixtures of different compositions as taught by Ramishetti. One with ordinary skills in the art, motivated in testing a library of lipid nanoparticles for efficiency, could have performed this modification with a reasonable expectation of success since the level of skills is high in the art, and arrived at the claimed invention.
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 1, 3-7 and 16 of provisionally rejected on the ground of non-statutory double patenting as being unpatentable over claims 17, 24-26, 35, 37 and 39 of co-pending Application No. 19/054,584 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding claim 1, claim 17 of co-pending application ‘584 also recite “a linear double-stranded DNA product comprising a sense strand and an antisense strand, wherein the linear double-stranded DNA product comprises a single cassette”, and “wherein the cassette comprises a promoter and a coding sequence”. Claim 17 also is drawn to “wherein the sense strand comprises at least two modified nucleotides in the 5’ end region of the cassette and at least two modified in the 3’ end of the cassette”, i.e. upstream and downstream of the cassette.
Regarding claim 1, claims 24 of the copending application ‘584 also claim phosphorothioated modified nucleotides .
Regarding claim 3, claim 37 of co-pending app. ‘584 also claims 5’ overhang, 3’ overhang, and/or blunt end comprised in the linear double-stranded DNA product.
Regarding claim 4, claim 17(b) of co-pending app. ‘584 claims a ratio, i.e. 0.01, of modified/phosphorothioated nucleotides to total nucleotides, and a range encompassing the range claimed, i.e., 0.0025-0.1.
Regarding claim 5, claim 39 of co-pending app. ‘584 also claims the same range for the ratio of modified/phosphorothioated nucleotides to total nucleotides, i.e. 0.01-0.1.
Regarding claim 6, claim 25 of co-pending application ‘584 also claims the same elements, i.e. “a complex molecule comprising the linear double-stranded DNA product” and “a functional portion, optionally wherein the functional portion is a binding molecule or a probe.”
Regarding claim 7, claim 26 of co-pending app. ‘584 also claims a nanoparticle comprising the linear double-stranded DNA product.
Regarding claim 16, claim 35 of co-pending app. ‘584 also claims a vaccine comprising the linear double-stranded DNA product.
This is a provisional non-statutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claim is allowed.
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/A.D./Examiner, Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636
