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 Status
Claims 1-20 are pending an under examination.
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 - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is defective. See item 1) a) or 1) b) above.
The statement should include the complete file name “UCI013.txt.” and size in exact bytes “25460 bytes.”
***Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, 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.
Claim Rejections - 35 USC § 112 – Written Description
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.
Claims 1, 4-6, 7, 10-13, 14, and 17-20 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.
While providing sufficient description to demonstrate possession of compositions for gene silencing that comprise modified nucleotides (i.e. 2’-fluoroarabino (FANA)) within the catalytic domain (i.e. SEQ ID NO: 1) of a catalytic nucleic acid molecule (“XNAzyme”), the specification fails to reasonably demonstrate possession of the entire scope of XNAzymes as currently claimed.
Claim Breadth
The claimed invention (particularly claim 1) reasonably encompasses a broad range of
diverse XNAzyme structures. The claim is drafted to cover “one or more nucleic acids” of the catalytic domain and binding arms replaced by “xeno‑nucleic acids (XNA)” without restriction on:
which positions in the catalytic domain are substituted;
how many positions are substituted; or
which XNA chemistries are used (the specification lists FANA and TNA as exemplified, but also recites a broad set of other XNAs including HNA, CeNA, GNA, PNA, ANA, tPhoNA, LNA, pRNA, XNA, dXNA) (see [0053]).
The art exemplifies dozens of XNA variants (see e.g., Chaput et al. The XNA alphabet. Nucleic Acids Res. 2025 Jul 8;53(13). The claim therefore encompasses innumerable positional combinations and chemistries in both the catalytic domain and the substrate recognition domains.
Furthermore, the written description must support not only structural breadth but also the functional limitation that every claimed composition has “enhanced stability and enhanced catalytic activity” compared to the wild-type 10-23 catalyst.
Disclosure in Specification
The specification only describes and characterizes a very limited set of specific constructs:
The principal working composition, “X10‑23,” uses a precise pattern of FANA substitutions at positions G2 and T8 within the catalytic core, FANA in the substrate binding arms, and TNA residues at the 5′ and 3′ termini (see e.g., Fig 2, 4).
A structure–activity scan shows that when individual catalytic‑core residues are replaced by FANA, only a subset of positions (e.g., G2 and T8) tolerate substitution with near‑wild‑type activity; several positions yield only moderate activity; and “the remaining 8 positions are each inactive when the wild‑type DNA residue is replaced with FANA.” See e.g., Table 1 and related text.
The specification expressly recognizes that 10‑23 has an “evolutionary optimum” core where “almost any nucleotide change leads to a mutant enzyme with reduced catalytic activity,” underscoring narrow tolerance to modification (see e.g., [0077]).
Unpredictability of Structure–function Relationships
The field of RNA‑cleaving 10‑23 DNAzymes is characterized by significant unpredictability in how specific sequence and backbone modifications affect catalytic activity and stability. The present specification’s own FANA substitution map demonstrates that small changes in sugar chemistry at different positions in SEQ ID NO: 1 frequently abolish activity, showing that structure–function relationships are not straightforward.
Such findings are consistent with other reported results:
Schubert et al. (RNA cleaving '10-23' DNAzymes with enhanced stability and activity. Nucleic Acids Res. 2003 Oct 15;31(20):5982-92) reported that modified nucleotides in the catalytic core and arms must be “studied systematically” to obtain DNAzymes combining high activity and stability; prior phosphorothioate core modifications caused “substantial or almost complete loss of catalytic activity.” See pg. 5990, col. 2.
Zhang et al. (DNAzyme as a rising gene-silencing agent in theranostic settings. Neural Regen Res. 2022 Sep;17(9):1989-1990) emphasized that chemical modifications (e.g., phosphorothioate linkages, 2′‑O‑methyl, PNAs, LNA, FANA) “may unpredictably affect DNAzyme function,” and that modification strategies that enhance stability can also compromise catalysis. See pg. 1989, middle column.
Conclusion
Taken together, the evidence of record suggests that the specification does not demonstrate that the inventors were in possession of all (or even most) 10‑23 analogues in which “one or more” of the 15 catalytic‑core nucleotides are replaced by “XNA” (broadly defined), and all such analogues in which “one or more” nucleotides in the binding arms are replaced by XNA, that nonetheless retain both enhanced catalytic activity and enhanced stability relative to the wild‑type DNAzyme. Rather, the data shows that only a narrow subset of particular substitution patterns and chemistries meets this dual functional requirement, and that many allowed structural variations within the claim would not be expected to satisfy it.
Thus, based on a preponderance of the evidence, the disclosure does not reasonably convey to a person of ordinary skill that the inventors were in possession, as of the filing date, of the entire claimed genus of compositions.
Claim Rejections - 35 USC § 112 – Scope of Enablement
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.
Claims 1, 4-6, 14, and 17-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for making and using a narrow embodiment of the claimed XNAzyme structure, does not reasonably provide enablement for the entire scope of XNAzyme structures as claimed. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
The present disclosure, while providing sufficient description to demonstrate enablement for gene silencing compositions (and methods of validating gene mutations associated with disease) comprise modified nucleotides (i.e. 2’-fluoroarabino (FANA) or TNA) within the catalytic domain (i.e. SEQ ID NO: 1) of a XNAzyme, does not enable the full scope of XNAzymes as currently claimed without undue experimentation.
Evidence related to the Wands factors (e.g. state of the art, specification guidance, working examples, predictability) has been discussed above (see Written Description rejection) and is incorporated herein.
The specification does not provide working examples or predictive design rules for most of these XNA types in the catalytic core or binding arms, nor does it demonstrate that arbitrary substitution patterns in SEQ ID NO: 1 maintain sufficient catalytic activity and multiple‑turnover performance to achieve therapeutic gene silencing in cells, let alone in vivo. To the contrary, the structure–activity mapping presented for FANA demonstrates that activity is highly position‑dependent and often lost upon single substitutions.
Conclusion
The available evidence tend to show that a skilled artisan cannot reasonably extrapolate from the few disclosed FANA/TNA designs to the full genus of “one or more” substitutions of SEQ ID NO: 1 with any XNA in any positions and still obtain an enzyme with therapeutically relevant activity without engaging in substantial, open‑ended screening and optimization for each XNA chemistry and substitution pattern.
Thus, a preponderance of evidence tends to show that the exemplified embodiments and supporting disclosure do not enable a skilled artisan to practice the claimed invention beyond the narrow embodiments noted above without undue experimentation.
Claim Rejections - 35 USC § 112 – Full Enablement
Claims 7-13 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification does not reasonably provide enablement for the entire scope of treatment as claimed. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims. This is a full scope of enablement rejection.
The present disclosure, while prophetically describing methods of disease and symptom treatment with XNAzymes. does not enable any of such methods as currently claimed without undue experimentation.
Evidence related to the Wands factors (e.g. state of the art, specification guidance, working examples, predictability) has been discussed above (see Written Description rejection) and is incorporated herein.
In addition to the enormous breadth of XNAzyme structures, the claimed invention reasonably encompasses treatment (and prevention) of a wide array of diseases and related symptoms (including “genetic disease, viral or bacterial pathogen, cancer, inflammation, cardiovascular disease, immune deficiency or a neurological disorder”) in human and non-human subjects (see e.g., specification pg. 9 and 13).
The specification reports in vitro kinetics and cell‑culture knockdown for two targets (GFP and KRAS) in HEK293T, HeLa, and MDA‑MB‑231 cells (see e.g., FIGs. 10–16), but provides no disclosure for in vivo treatment, including:
No dosing ranges (e.g., mg/kg), dosing schedules, or routes of administration for subjects.
No formulations or delivery systems (e.g., lipid nanoparticles, conjugates) addressing biodistribution, cellular uptake, endosomal escape, and toxicity.
No pharmacokinetic/pharmacodynamic (PK/PD) or animal efficacy data demonstrating therapeutic potential for any disease or symptom.
In the unpredictable field of oligonucleotide therapeutics, such information is normally essential to enable therapeutic methods across the breadth recited. See MPEP 2164.01(b).
Relevant art emphasizes that the field of treating disease using catalytic oligonucleotides faces many unpredictable challenges. Yan et al. (Therapeutic DNAzymes: From Structure Design to Clinical Applications. Adv Mater. 2023 Jul;35(30):e2300374) explained that, despite research and high expectations, current enthusiasm is low:
“This is due to their low activity in vivo, which has led to stagnating clinical research Specifically, stability modification of DNAzymes lacks theoretical guidance. Without deep analysis of conformation and action mechanism of DNAzyme/RNA complex, the modification processes rely heavily on large-scale screening. Thus, the catalytic performance and stability of DNAzymes could not be enhanced simultaneously. Moreover, the concentration of metal cofactors in diseased tissues is insufficient, resulting in low catalytic efficiency. More importantly, although DNAzymes can recognize specific genes, they still induce off-target effects and cannot silence genes in specific diseased tissues.” (Page 2-3)
Regarding in vivo testing, Dass et al. (DNAzyme technology and cancer therapy: cleave and let die. Mol Cancer Ther. 2008 Feb;7(2):243-51) emphasized that:
“The journey from in vitro cleavage kinetics to cell culture assessment (down-regulation of the target gene, plus phenotypical changes) to evaluation in vivo (in clinically relevant models demonstrating efficacy and minimal toxicity) can be arduous and is usually accompanied by a large attrition rate of candidate molecules, … , Although in vitro assessment of DNAzyme efficiency helps establish gene and sequence specificity, and is an expedited form of screening, important issues such as delivery, pharmacokinetics, metabolism, toxicity, and efficacy can only be examined in vivo.” (Page 244, 247).
Taken together, the state of the art shows that achieving therapeutically effective, stable, tissue‑selective DNAzyme treatments requires resolving multiple interdependent, unpredictable variables (cofactor levels, structure–activity trade‑offs, delivery, and off‑target effects) through “large‑scale screening” in relevant models, i.e., extensive empirical experimentation, rather than routine optimization.
Conclusion
The available evidence suggests that designing functional catalytic oligonucleotides for treatment of disease (and symptoms) requires more effort than routine, predictable extrapolation of available in vitro data. To successfully determine if a catalytic oligonucleotide product may be used to treat a disease, one must, among other efforts, engage in extensive testing within a model disease environment. A preponderance of evidence tends to show that the supporting disclosure, which does not contain such evidence or guidance, does not enable a skilled artisan to practice the claimed invention.
Allowable Subject Matter
Claims 2, 3, 15, and 16 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.
All claims appear to be free of the prior art. While the prior art recognizes the claimed DNAzyme catalytic region (SEQ ID NO: 1) and base modifications (see e.g., Handel et al., US 2003/0148971; SEQ ID NO: 2, [0043], [0084]), such art does not teach or fairly the suggest the specific combination of XNA and TNA modifications as claimed.
The closest prior art found, Wang et al. (ChemBioChem 2020, 21, 1001; published online November 3, 2019), teaches modifying the catalytic core of a 12-7 RNA-cleaving catalytic nucleic acid with FANA nucleotides (see pg. 1002, Scheme 1; pg. 1002-04, Results). The reference fails to teach or fairly suggest modifying the catalytic core of a 10-23 catalytic nucleic acid (DNAzyme) with XNA nucleotides, nor use of TNA nucleotides at the terminal regions.
Conclusion
No claims are allowed.
Claims 2, 3, 15, and 16 are objected to.
Claims 1, 4-14, and 17-20 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTOPHER M BABIC whose telephone number is (571)272-8507. The examiner can normally be reached Mon - Fri, 8:30 AM - 5 PM.
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/CHRISTOPHER M BABIC/ Supervisory Patent Examiner, Art Unit 1633