DETAILED ACTION
Applicant’s response, filed 18 Dec. 2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 1-15, 20, and 23 are cancelled.
Claims 32-34 are newly added.
Claims 16-19, 21-22, and 24-34 are pending.
Claims 16-19, 21-22, and 24-34 are rejected.
Claim 30 is objected to.
Priority
Applicant’s claim for the benefit of a prior-filed application, PCT/EP2020/077497 filed 01 Oct. 2020 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority to EP19306247.8 filed 01 Oct. 2019 under 35 U.S.C. 119 (a)-(d). Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Accordingly, the effective filing date of the claimed invention is 01 Oct. 2019.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 20 Nov. 2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the list of cited references was considered in full by the examiner.
Specification
The amendments to the specification filed 18 Dec. 2025 have been entered.
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 missing or incomplete. See item 1) a) or 1) b) above.
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.
Response to Arguments
Applicant's arguments filed 18 Dec. 2025 regarding sequence compliance at pg. 9, para. 2-3 have been fully considered and are persuasive. The specific deficiency because the application does not contain a statement that the CRF is identical to the "Sequence Listing" part of the disclosure, as described above in item 1), as required by 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) has been withdrawn.
Applicant's arguments filed 18 Dec. 2025 regarding sequence compliance at pg. 9, para. 5-6 have been fully considered but they are not persuasive.
Applicant remarks a new paragraph subtitled “REFERENCE TO A SEQUENCE LISTING” is added to page 1 of the substitute specification to overcome the deficiency (Applicant’s remarks at pg. 9, para. 5-6).
This argument is not persuasive. The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) incomplete because the paragraph does not identify i) the date of creation.
Claim Objections
The objection to claims 16, 21, and 28 in the Office action mailed 19 May 2025 has been withdrawn in view of claim amendments received 18 Dec. 2025.
Claims 30 is objected to because of the following informalities. This objection is newly recited and necessitated by claim amendment.
Claim 30 recites “SUP and SDO correspond to nucleic acid sequences of the [UP] and [DO]” in the last two lines of step a), which should be amended to recite “SUP and SDO correspond to nucleic acid sequences of the [UP] and [DO], respectively” to increase clarity.
Appropriate correction is required.
Claim Interpretation
Claim 24 recites “wherein each of the [UP] and [DO] nucleic acids contains at least one barcode-encoding nucleic acid and/or at least one meta-data encoding nucleic acid”. The information encoded by the nucleic acids, a nucleic acid encoding a barcode and/or metadata is simply an intended use of the device comprising the composite nucleic acid (e.g. nucleotides intended to represent certain information). See MPEP 2111.04 I.
Claim 25 recites “…storing at least one pool comprising…composite nucleic acid molecule(s)…into a storage cell” in the last limitation. Applicant’s specification at pg. 23, lines 24-28 discloses a storage cell may be a living organism, a glass-based recipient, a metal-based recipient, a silica-based recipient, a polymer-based recipient, or a paper-based recipient. Therefore, in light of Applicant’s specification the term “storage cell” is interpreted to mean any medium capable of storing nucleic acid molecules and is not limited to a literal “cell” (i.e. living organism) used for storage.
Claim 30 recites “A method for retrieving the digital data stored by the device according to claim 16, said method comprising the steps of:…”. The limitation “stored by a device according to claim 16” is interpreted to be a product by process limitation that merely defines the process in which the digital data was previously stored, but claim 30 does not require storing the digital data.
Claim 31 recites “A method for retrieving a digital data stored by the method according to claim 25, said method comprising the steps of:…”. The limitation “stored by the method according to claim 25” is interpreted to be a product by process limitation that merely defines the process in which the digital data was previously stored, but claim 31 does not require storing the digital data according to claim 25.
Applicant’s specification at pg. 5, line 11 through pg. 7, line 20 define various terminology. The definitions of terms currently included in the claims are provided below:
Applicant’s specification at pg. 5, lines 13-15 defines the term “about” to mean plus or minus 10% or less of the value of the figure. Therefore, any claim defining a value with the term “about” will be interpreted accordingly.
Applicant’s specification at pg. 6, lines 5-12 defines the term “replicative” to mean the ability to be replicated in vivo by a polymerase, and a “replicative nucleic acid molecule” refers to a nucleic acid molecule that can be copied at least once.
Applicant’s specification at pg. 6, lines 13-16 defines the term “composite” to mean an item made up of distinct parts or elements, and a “composite nucleic acid molecule” refers to a nucleic acid molecule that originates from fragments of nucleic acids.
Applicant’s specification at pg. 7, lines 4-5 defines the term “array” to refer to a solid support containing a set of nucleic acid molecules.
Claim Rejections - 35 USC § 112(b)
The rejection of claims 20 and 23 under 35 U.S.C. 112(b) in the Office action mailed 19 Sept. 2025 has been withdrawn in view of the cancellation of these claims received 18 Dec. 2025.
The rejection of claims 16-19, 21-22, and 24-30 under 35 U.S.C. 112(b) in the Office action mailed 19 Sept. 2025 has been withdrawn in view of claim amendments received 18 Dec. 2025.
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.
Claims 30, 32, and 34 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, regards as the invention. This rejection is newly recited and necessitated by claim amendment.
Claim 30, and dependent claim 32, are indefinite for recitation of “b) converting the SDB into digital data”. Claim 30 previously recites “a) sequencing at least one nucleic acid of formula…(Ia)…so as to obtain at least one nucleic acid sequence SUP-SDB-SDO), wherein SDB corresponds to a nucleic acid sequence of the [DB]”. Therefore, claim 30 recites obtaining at least one nucleic acid sequence of SUP-SDB-SDO, each which contains a SDB. As a result it is unclear if “the SDB” in b) intends to require converting each SDB of the one or more nucleic acid sequences SUP-SDB-SDO, or if b) intends to require converting only one SDB. If Applicant intends for the later, only converting one SDB of the at least one SDB, it is further unclear which SDB is being referenced. For purpose of examination, claim 30 is interpreted to mean converting at least one of the at least one nucleic acid sequence SDB.
Claim 34 is indefinite for recitation of “the [DB] nucleic acid”. Claim 25, from which claim 34 depends, recites “a) assigning….at least one double stranded digital data-encoding nucleic acid [DB]”. Therefore, in embodiments in which there are more than one [DB] nucleic acid, it is unclear which [DB] nucleic acid, “the [DB] nucleic acid” is referring to. Alternately, it is unclear if “the [DB] nucleic acid” is referring to the at least one [DB] nucleic acid, such that each nucleotide of each [DB] nucleic acid encodes for 1 or 2 bits of data.
Response to Arguments
Applicant's arguments filed 18 Dec. 2025 regarding 35 U.S.C. 112(b) have been fully considered but they are not persuasive because they do not pertain to the new grounds of rejection set forth above.
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 16-19, 21-22, 24, and 30-33 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. Any newly recited portion is necessitated by claim amendment.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 16, 30, and 31 being representative) is directed to a product for storing information and a method of retrieving data. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Law of Nature or Natural Phenomenon:
Claim 16 recites a product of nature of a naturally occurring double-stranded, in vivo replicative, composite nucleic acid molecule, or fragment, of the recited length and not comprising initiation codons or stop codons per 200 nucleotides in all 6 reading frames. There is nothing in the claims, other than the intended use of the nucleic acid in being “data-encoding” that preclude a naturally occurring DNA or RNA fragment from reading on the claim. Noncoding DNA without initiation codons are naturally occurring (e.g. noncoding DNA in humans). For example, Dagher et al. (Data storage in cellular DNA: contextualizing diverse encoding schemes, Feb. 2019, Evolutionary Intelligence, 14, pg. 331-434; previously cited) discusses noncoding DNA in cells having no biological function (i.e. no RNA transcription) and not including start codons (pg. 334, col. 2, para. 1-2).
Claim 17 further limits the length of the composite nucleic acid molecule to be from 500 to 1011 nucleotides, and thus also reads on a natural DNA or RNA fragment as discussed for claim 16.
Dependent claim 18 further limits the GC percentage to range from 35% to 65%. Piovesan et al. (On the length, weight and GC content of the human genome, Feb. 2019, BMC Res Notes, 12:106, pg. 1-17; previously cited) overviews DNA of the human genome, and discloses various chromosomes of the human genome have GC contents in the recited range, as well as in the recited length range (Table 2).
Dependent claim 19 further limits the nucleic acid to not encode RNA (i.e. noncoding DNA). However, as discussed above for claim 1, noncoding DNA of “about 8 nucleotides” without initiation codons are naturally occurring (e.g. noncoding DNA in humans).
Dependent claim 21 further limits the nucleic acid to not have one or more restriction sites for the recited enzymes. Dependent claim 22 further limits the nucleic acid to not have repeats. Dependent claim 23 recites an intended use of the nucleic acid to encode information, and thus is part of the law of nature of claim 16. However, similarly DNA of “about 8 nucleotides”, as encompassed by claim 1 naturally may not comprise restriction sites for the recited enzymes or repeats of 4 identical nucleotides.
Claim 24 requires each of [UP] and [DO] to encode particular information, but does not recite any particular sequence and thus still encompasses a naturally occurring nucleic acid molecule encoding the information.
Therefore, claims 17-19, 21-22, and 24 generally further limit the particular nucleotides of the nucleic acid sequence, but still encompass a product of nature of a naturally occurring nucleic acid molecule, and claims 16-19, 21-22, and 24 recite a law of nature. See MPEP 2106.04(b).
Abstract Ideas:
Claims 30-31 recite the following steps which fall under the mental processes groupings of abstract ideas:
b) converting the SDB into digital data/ converting the at least one nucleic acid sequence SDB into digital data.
The identified claim limitation falls into one of the groups of abstract ideas of mental processes because the limitation amounts to a mere analysis of the sequence SDB to decode the various nucleotides into binary information (e.g. A = 01, G = 10, etc.), thus obtaining digital data (e.g. 0110…). Therefore, claims 30-31, and dependent claims 32-33, recite a mental process. See MPEP 2106.04(a)(2) III.
In summary, claims 16-19, 21-22, and 24 recite the judicial exception of a product of nature and claims 30-33 recite the judicial exception of an abstract idea. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Claims 16-19, 21-22, and 24 recite a naturally occurring product as currently claimed, but do not recite any elements in addition to the law of nature. As discussed above, claims 16-19, 21-22, and 24 encompass a naturally occurring double-stranded DNA molecule. If the nature-based product limitation is naturally occurring, there is no need to perform the markedly different characteristics analysis because the limitation is by definition directed to a naturally occurring product and thus falls under the product of nature exception. See MPEP 2106.04(c)
The additional elements of claims 30-31 include:
a) sequencing at least one nucleic acid of formula 5’-([UP]-[DB]-[DO]-3’(Ia) comprised in the double stranded, replicative, and in vivo replicative composite nucleic acid molecule comprising a nucleic acid of formula (I), so as to obtain at least one nucleic acid sequence SUP-SDB-SDO, wherein SDB corresponds to a nucleic acid sequence of the [DB], SUP and SDO correspond to nucleic acid sequences of the [UP] and [DO] (Claim 30); and
a) sequencing the at least one nucleic acid of formula 5’-([UP]-[DB]-[DO]-3’(Ia) comprised in the double stranded, replicative, and in vivo replicative composite nucleic acid molecule comprising a nucleic acid of formula (I).
The additional elements of dependent claims 32-33 include:
a0) amplifying the at least one nucleic acid of formula (Ia).
The limitation of amplifying the at least one nucleic acid of formula (a) and sequencing at least one nucleic acid molecule only serves to collect information for use by the abstract idea, which amounts to insignificant extra-solution activity that does not integrate the judicial exception into a practical application. See MPEP 2106.05(g).
Therefore, the additionally recited element amounts to insignificant extra-solution activity and, as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 16-19, 21-22, 24, and 30-31 are directed to a law of nature and abstract idea, respectively. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception.
Claims 16-19, 21-22, and 24 recite a naturally occurring product as currently claimed, but do not recite any elements in addition to the law of nature, as discussed above.
The additional elements of claims 30-31 include:
a) sequencing at least one nucleic acid of formula 5’-([UP]-[DB]-[DO]-3’(Ia) comprised in the double stranded, replicative, and in vivo replicative composite nucleic acid molecule comprising a nucleic acid of formula (I), so as to obtain at least one nucleic acid sequence SUP-SDB-SDO, wherein SDB corresponds to a nucleic acid sequence of the [DB], SUP and SDO correspond to nucleic acid sequences of the [UP] and [DO] (Claim 30); and
a) sequencing the at least one nucleic acid of formula 5’-([UP]-[DB]-[DO]-3’(Ia) comprised in the double stranded, replicative, and in vivo replicative composite nucleic acid molecule comprising a nucleic acid of formula (I).
The additional elements of dependent claims 32-33 include:
a0) amplifying the at least one nucleic acid of formula (Ia).
The limitation of sequencing at least one nucleic acid molecule is well-understood, routine, and conventional, as evidenced by Applicant’s specification. Applicant’s specification at pg. 28, lines 8-12 discloses that sequencing a nucleic acid molecule may be performed by any suitable technique known from one skilled in the art, and non-limiting examples include sanger sequencing and next-generation sequencing. Applicant’s specification at pg. 28, lines 13-15 further discloses that amplifying nucleic acid molecules comprising formula (i) may be performed in vivo or in vitro by any suitable techniques known from the state of the art, and an example includes PCR.
Therefore, the additional element does not amount to significantly more than the above-identified judicial exception(s). Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea and/or law of nature without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Response to Arguments
Applicant's arguments filed 18 Dec. 2025 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Law of Nature or Natural Phenomenon
Applicant remarks that claim 16 is directed to the invention of “storing or editing digital data within a nucleic acid molecule” and has been amended to specify that the nucleic acid [DB] of the claimed molecule encodes all or part of said digital data, where the digital data may be program files, text files, etc., and therefore, the nucleic acid molecule is readily distinguishable to a skilled person from any naturally occurring nucleic acid molecule because, for a nucleic acid molecule according to claim 16, decoding provides digital data while decoding an arbitrary natural nucleic acid molecule would only provide random data without semantic structure (Applicant’s remarks at pg. 13, para. 3 to pg. 14, para. 2 and 5).
This argument is not persuasive. Claim 16 recites “A device for storage and/or editing of digital data, wherein the device comprises at least one double stranded and in vivo replicative, composite nucleic acid molecule”.
MPEP 2111.02 II states statements in the preamble reciting the purpose or intended use of the claimed invention must be evaluated to determine whether or not the recited purpose or intended use results in a structural difference (or, in the case of process claims, manipulative difference) between the claimed invention and the prior art. If so, the recitation serves to limit the claim. See, e.g., In re Otto, 312 F.2d 937, 938, 136 USPQ 458, 459 (CCPA 1963).
In the instant case, the preamble recites the intended use “for storage and/or editing of digital data”, but the device itself only comprises a double stranded and in vivo replicative composite nucleic acid molecule (e.g. DNA or RNA). While it is acknowledged that claim 16 recites that the nucleic acid of [DB] is nucleic acid encoding all or part of said digital data, claim 16 does not recite any details about a particular encoding scheme that imparts any physical or structural limitations, such as a particular sequence, on the actual nucleic acid of the device of claim 16. For example, an encoding scheme from a natural nucleic acid may be derived to specifically encode a piece of digital information. Therefore, as presently recited, the claims encompass a naturally occurring DNA or nucleic acid molecule that encodes information, as explained in the above rejection.
Abstract Ideas:
Applicant remarks that the conclusion of the Office action appears to rest on the assumption that the method of the claims rely solely on sequencing that could theoretically be performed mentally, using information occurring nature (Applicant’s remarks at pg. 14, para. 3-4).
This argument is not persuasive. The Office action does not state that sequencing can be performed mentally. Instead, the steps of sequencing in claims 30-31 were identified as an additional element, rather than as a judicial exception, as set forth in the previous and above rejection. However, the step of sequencing was found to recite insignificant extra-solution activity that is well-understood, routine, and conventional, and thus does not provide integration under Step 2A, Prong 2 or significantly more under Step 2B, as explained in the above rejection.
Applicant remarks that the claimed method expressly requires the use of a nucleic acid encoding digital data, which constitutes a specific technical means because retrieving digital data stored in a living organism necessarily requires a specific technical means that goes beyond a purely mental act, and thus the method cannot be performed mentally (Applicant’s remarks at pg. 14, para. 6-7).
This argument is not persuasive. As discussed above, the step of sequencing, which retrieves a sequence (i.e. information) from a nucleic acid was not considered a mental process. However, the steps of converting the determined sequence into digital data does recite a mental process as explained above, and Applicant does not appear to argue this characterization beyond arguing that sequencing cannot be performed mentally.
It is notable that mere physicality or tangibility of an additional element or elements is not a relevant consideration in Step 2A Prong Two. As the Supreme Court explained in Alice Corp., mere physical or tangible implementation of an exception does not guarantee eligibility. Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. 208, 224, 110 USPQ2d 1976, 1983-84 (2014) See also Genetic Technologies Ltd. v. Merial LLC, 818 F.3d 1369, 1377, 118 USPQ2d 1541, 1547 (Fed. Cir. 2016) (steps of DNA amplification and analysis are not "sufficient" to render claim 1 patent eligible merely because they are physical steps). Therefore, simply because claims 30-31 include a tangible step of sequencing is not sufficient to guarantee eligibility.
Applicant remarks the claims improve the field of data storage within living organisms, citing pg. 7-8 and 12 of the specification, and therefore, the claims produce a discernible physical effect and is not limited to an abstract data-processing scheme because the ability to retrieve stored digital data is a key issue in the field (Applicant’s remarks at pg. 14, para. 7 to pg. 14, para. 3).
This argument is not persuasive. First, the argument is not commensurate with the scope of the claims. Claims 30-31 do not require a step of storing data within living organisms. In contrast, it is noted that claim 25 does require “d) storing…” the synthesized nucleic acid molecules into a storage cell, and thus integrate the recited judicial exception into a practical application. In contrast, claims 30-31 only utilize sequencing to generate information for use by the abstract idea of decoding the sequence information into digital data, which does not provide integration. See MPEP 2106.05(g).
Claim Rejections - 35 USC § 102
The rejection of claims 16-18, 21, 23-24, and 30-31 under 35 U.S.C. 102(a)(1) as being anticipated by Ahn (2018) in the Office action mailed 19 Sept. 2025 has been withdrawn in view of claim amendments received 18 Dec. 2025.
Claim Rejections - 35 USC § 103
The rejection of claims 25-29 under 35 U.S.C. 103 as being unpatentable over Ahn (2018) in view of Ceze (2019) in the Office action mailed 19 Sept. 2025 has been withdrawn in view of claim amendments received 18 Dec. 2025.
The rejection of claims 19-20 and 22 under 35 U.S.C. 103 as being unpatentable over Ahn (2018) in view of Dagher (2019) in view of Ceze (2019) in the Office action mailed 19 Sept. 2025 has been withdrawn in view of claim amendments received 18 Dec. 2025.
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.
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.
Claims 16-19, 21-22, and 24-34 are rejected under 35 U.S.C. 103 as being unpatentable over Ahn (2018) in view of Dagher (2019) and Ceze (2019). This rejection is newly recited and necessitated by claim amendment.
Ahn et al., Storing Digital Information in Long-Read DNA, 2018, Genomics Inform, 16(4):e30, pg. 1-6; cited in IDS filed 28 Sept. 2022 (previously cited);
Dagher et al., Data storage in cellular DNA: contextualizing diverse encoding schemes, Feb. 2019, Evolutionary Intelligence, 14, pg. 331-434 (previously cited); and
Ceze et al., Molecular digital data storage using DNA, Aug. 2019., Nature Reviews, 20, pg. 458-466 (previously cited).
Regarding claim 16, Ahn discloses a method of storing digital information in Long-Read DNA, and discloses DNA encoding information (i.e. A device comprising nucleic acid)(Abstract). Ahn discloses the DNA comprises the following:
Ahn discloses the DNA is double stranded and is a composite nucleic acid molecule (Fig. 6). Ahn discloses the DNA can be used in polymerase chain reaction (Fig. 4), demonstrating the DNA is replicative (i.e. at least one double stranded, replicative, composite nucleic acid molecule).
Ahn discloses the DNA comprises a nucleic acid formula comprising a [Start]-[Data Block]-[End] (Fig. 3).
Ahn discloses the “Data Block” ([DB]) encodes data and has a length of approximately 800 base pairs (i.e. having a length from about 0 nucleotides to about 106 nucleotides; pg. 1, col. 2, para. 2).
Ahn discloses the “Start” and “End” DNA mark the start and end of the data block (i.e. a pair of non-digital data-encoding nucleic acids), and each have a length of 51 base pairs (i.e. having a length from about 1 nucleotides to about 104) (Fig. 3; pg. 1, col. 2, para. 2).
Regarding claim 17, Ahn discloses an embodiment in which the composite nucleic acid has a length of 945 base pairs (Fig. 3), which anticipated the claimed range of 500 to 1011 nucleotides. Ahn also discloses the length can range from 780 to 800 base pairs (pg. 2, col. 2, para. 3), which also anticipates the claimed range. See MPEP 2131.03 I.
Regarding claim 18, Ahn discloses the GC content of the DNA is from 50% to 54% (i.e. from about 35% to 65%) (pg. 2, col. 2, para. 3).
Regarding claim 21¸ Ahn discloses the “Start”, “Data Block” and “End” blocks (i.e. the nucleic acid of formula (I) do not comprise restriction sites for EcoRI (Fig. 3).
Regarding claim 24¸ Ahn discloses the “Start” and “End” blocks (i.e. [UP] and [DO] nucleic acids) each contain metadata encoding nucleic acid representing the start and end of the data block (i.e. data about where the data block starts and ends) (pg. 2, col. 2, para. 2; Figure 3), consistent with Applicant’s definition of “Metadata” meaning to relate to basic information about the digital data they are referring to. Here, the “basic information” is the start and end of the digital data.
Regarding claim 25, Ahn discloses a method of storing information in, and retrieving information from, Long-Read DNA (Abstract), comprising the following steps:
Ahn discloses encoding digital data into (i.e. assigning to the digital data to) a nucleic acid sequence including a data block encoding data (i.e. digital data-encoding [DB] nucleic acid sequence SDB) and a pair of non-digital-data encoding Start and End nucleic acid sequences (i.e. Sup and SDO) (pg. 2, col. 1, para. 1-2, e.g. 1 and 0 recorded in a specific sequence called the “signal”; Figure 3).
Ahn discloses synthesizing multiple nucleic acid sequences, each in the formula [Start]-[Data Block]-[End] (pg. 2, col. 2, para. 2-3; FIG. 1, e.g. “DNA fragment storing digital information can [be] synthesized; Fig. 3, e.g. see formula).
Ahn discloses ligating (i.e. assembling) each synthesized DNA fragment with the form [Start]-[Data Block]-[End] to form a longer DNA fragment (i.e. a nucleic acid molecule according to formula (I), wherein x = 2) (pg. 2, col. 2, para. 4; pg. 3, col. 1, para. 3 to col. 2, para. 1; Fig. 2; Fig. 3, e.g. restriction sites used for ligating are outside the Start-Data Block-End structure; FIG. 5). A ligation of two synthesized DNA fragments of Ahn corresponds to ([Start]-[Data Block-[End])2. Although it is noted that claim 25 does not require x=2, and thus does not require assembling multiple nucleic acids of formula (Ia), as discussed above under 35 U.S.C. 112(b). Ahn also discloses assembling a synthesized DNA fragment into a plasmid (FIG. 4; pg. 2, col. 2, para. 3).
Ahn discloses storing the assembled DNA fragment as long DNA fragments (pg. 2, col. 2, para. 3, e.g. DNA synthesized ; pg. 3, col. 1, para. 2; Fig. 4). Given the “pool” can require only one composite nucleic acid molecule, the assembled DNA fragment is considered to read on a “pool”.
Regarding claim 27, Ahn discloses the composite molecule obtained at step c) is a plasmid (pg. 2, col. 2, para. 3; FIG. 4, see top of figure).
Regarding claim 28, Ahn further discloses amplifying the at least one composite molecule (pg. 3, col. 1, para. 2, e.g. vector primer for DNA fragment amplification).
Ahn further discloses extracting and purifying the at least one composite molecule (pg. 3, col. 1, para. 2; e.g. PCR product was purified).
Regarding claim 29, claim 29 fails to further limit the subject matter of claim 28, as discussed above, and therefore claim 29 is rejected for the same reasons discussed above and below for claim 28.
Regarding claims 30-31, Ahn discloses a method for retrieving information stored by DNA (Abstract), comprising the following:
Ahn discloses sequencing a nucleic acid molecule of formula [Start]-[Data Block]-[End] (i.e. formula Ia or I, ([UP]-[DB]-DO])) (pg. 3, col. 2, para. 3 to pg. 4, col. 1, para. 1; FIG. 1; FIG. 3, e.g. see structure storing information).
Ahn discloses restoring binary information from the data block of the sequenced nucleic acid molecule (i.e. converting the nucleic acid sequence into digital data) (pg. 4, col. 1, para. 2; FIG. 2-3, e.g. data block stores the signal).
Regarding claims 32-33, Ahn further discloses amplifying the at least one composite molecule (pg. 3, col. 1, para. 2, e.g. vector primer for DNA fragment amplification).
Ahn does not disclose the following limitations:
Regarding claims 16 and 25, Ahn does not disclose the nucleic acid of formula (I) does not comprise one or more initiation codons or comprises one or more stop codons per about 200 nucleotides in all reading frames.
Regarding claim 19¸ Ahn does not disclose the nucleic acid of formula (I) does not encode one or more RNA(s).
Regarding claim 22, Ahn does not disclose the nucleic acid of formula (I) does not comprise one or more repeats of at least 4 identical nucleotides.
However, regarding claims 16, 19, 22, and 25, Dagher overviews DNA storage and DNA encoding schemes for storing information (Abstract), and discloses data can be embedded into noncoding regions of DNA in cells if the following constraints are met: truly nonfunctional region, no start codons, and no homopolymers (pg. 334, col. 2, para. 1-4). Dagher discloses it is imperative that the individual insert their message into ncDNA that is verified to have no biological use and is truly nonfunctional (i.e. the DNA does not encode RNA) (pg. 334, col. 1, para. 2). Dagher discloses to prevent the unwanted transcription from happening in ncDNA with embedded data, it is important to make sure the encoded nucleotides do not create a start (i.e. initiation) codon in any of the six reading frames (pg. 334, col. 2, para. 3). Dagher further discloses that homopolymers, where the same nucleotide is repeated multiple times, can cause errors during DNA replication through DNA polymerase slippage, which can distort the inserted message, and therefore, any ncDNA scheme should not include homopolymers greater than length (3) (pg. 334, col. 2, para. 4).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the nucleic acid composite of Ahn to have not encoded one or more RNA(s), to not have comprised one or more initiation codons in all 6 reading frames and to not comprise one or more repeats of 4 or more nucleotides, as shown by Dagher above. One of ordinary skill in the art would have been motivated to combine the method of Ahn and Dagher in order to not disrupt cell functionality, to prevent unwanted transcription from happening, and to prevent DNA replication errors distorting the inserted message, as shown by Dagher (pg. 334, col. 2, para. 2-4), thus creating a nucleic acid that could be stored in-vivo. This modification would have had a reasonable expectation of success given Dagher discloses considerations in DNA encoding schemes, which is applicable to the DNA encoding scheme of Ahn.
Further regarding independent claims 16, 25, and 30-31, Ahn in view of Dagher does not explicitly disclose the data-encoding nucleic acid molecule is in-vivo replicative.
Regarding claims 25 and 28-29, Ahn in view of Dagher does not disclose storing the at least one pool of nucleic acid molecule(s) into a storage cell, as recited in claim 25. Ahn further does not disclose the amplifying is performed in vivo by a microorganism, and therefore, that the extracting and purifying are from in-vivo nucleic acid, as recited in claims 28-29
However, regarding claims 16, 25, 28-31, Ceze discloses methods of molecular data storage using DNA (Abstract), and discloses encoding bits into DNA sequences, synthesizing the DNA sequences, and then storing the synthesized DNA either in-vivo or in-vivo within a biological cell (Fig. 2) by including the DNA within genomic or plasmid DNA (i.e. making the DNA in-vivo replicative), which is then propagated within the living organism (i.e. amplifying in-vivo) (pg. 463, col. 2, para. 3 to pg. 464, col. 1, para. 1). Ceze further discloses a variety of ways in which DNA can be stored in-vivo, including known techniques such as recombinases such as Cas9 or Cas-Cas2 (pg. 464, col. 2, para. 2 to pg. 465, col. 2, para. 1). Ceze further discloses digital data may be encoded into DNA into a population of bacteria using the Cas1-Cas2 system (pg. 465, col. 1, para. 3 to col. 2, para. 1, e.g. short movie stored in bacteria). Ceze further discloses that DNA-based data stored within a cell shares many of the features that make in vitro DNA storage attractive, and furthermore are naturally copied with high fidelity during cellular replication and are preserved after cell death (pg. 464, col. 1, para. 2 to col. 2, para. 1).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the method of Ahn in view of Ceze to have made the DNA in-vivo replicative by incorporating the DNA into bacteria using Cas1-Cas2 methods or plasmids, and then stored and amplified the DNA in vivo, as shown by Ceze, discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Ahn and Ceze in order to provide a DNA-based storage system with many of the same advantages of storing information in in-vitro DNA, in addition to the ability of naturally copying the stored DNA with high fidelity, as shown by Ceze (pg. 464, col. 1, para. 2 to col. 2, para. 1). This modification would have had a reasonable expectation of success because Ceze discloses a plurality of methods of incorporating DNA in vivo which are applicable to the DNA of Ahn.
Regarding claim 26, Ahn does not disclose organizing and grouping the pools obtained at step d) into at least one array.
However, as discussed above, Ceze discloses methods of molecular data storage using DNA (Abstract). Ceze further discloses synthesized DNA encoding digital data can be stored in-vitro (Fig. 2), and once synthesized the resulting DNA can be stored in library of DNA pools to scale out large storage systems, with each DNA pool storing on the order of 1012 bytes(pg. 458, col. 2, para. 2; pg. 463, col. 1, para. 3). Ceze further discloses these pools may be organized by data item and physically isolated (pg. 458, col. 1, para. 3; pg. 463, col. 1, para. 1-2), as well as stored in plastic well plates (i.e. an array) (pg. 463, col. 2, para. 2). Ceze discloses storing DNA separately in pools allows for retrieving a specific data item out of a larger set (pg. 458, col. 2, para. 3).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the method of Ahn to have organized and grouped pools of DNA encoding information into at least one array including pools of DNA, as shown by Ceze, discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Ahn and Ceze in order to allow for retrieving specific data items out of a larger set, as shown by Ceze (pg. 458, col. 2, para. 3). This modification would have had a reasonable expectation of success given both Ahn and Ceze relate to encoding information in DNA, such that the storage methods of Ceze are applicable to the DNA of Ahn.
Regarding claim 34, Ahn further does not disclose each nucleotide of the [DB] nucleic acid encodes 1 or 2 bits of the digital data. Instead, Ahn encodes one bit to a nucleic acid fragment of multiple nucleotides.
However, Ceze overviews methods of molecular digital data storage using DNA, and discloses DNA data storage starts with mapping strings of bits into DNA sequences (pg. 458, col. 1, para. 3), and that important aspects of data storage are the density, or bits per unit of physical volume (Abstract; pg. 456, col. 1, para. 1). Ceze discloses that the maximum theoretical logical density achievable with natural bases of DNA is 2, as the four bases that are possible at a single position can represent at most 2 bits (i.e. each nucleotide encoding 2 bits) (pg. 461, col. 1, para. 4; pg. 464, col. 1, para. 1). Ceze further discloses various DNA data storage that uses logical densities of the payload only (e.g. the data storing sequencing) with an average of between 1 to 2 bits per nucleotide (Table 1). Ceze further discloses using as few atoms as possible to store one bit of information leads to higher density, making molecular data storage attractive (pg. 456, col. 1, para. 2).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the encoding of Ahn to have utilized each nucleotide encoding 1 or 2 bits of digital data, as shown by Ceze, discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Ahn and Ceze in order to increase the logical storage density of the encoded information, as shown by Ceze (pg. 456, col. 1, para. 1). This modification would have had a reasonable expectation of success given Ahn and Ceze both encode DNA sequences into bits, and thus the encoding of Ceze is applicable to the method of Ahn.
Therefore, the invention is prima facie obvious.
Response to Arguments
Applicant's arguments filed 18 Dec. 2025 regarding 35 U.S.C. 102/103 have been fully considered but they are not persuasive.
Applicant remarks that Ahn does not disclose “wherein the nucleic acid…does not comprise one or more initiation codons…” or that the device comprises a “in vivo replicative composite nucleic acid molecule” (Applicant’s remarks at pg. 15, para. 4 to pg. 16, para. 1).
This argument is not persuasive because the Ahn is not relied upon to disclose these features. Instead, Dagher and Ceze are relied upon to disclose these respective features as applied in the new grounds of rejection under 35 U.S.C. 103.
Applicant remarks that the amendments made for listed distinguishing features allow collectively to improve the handling of nucleic acid molecules encoding digital data in a living organism, in particular their amplification and editing in a living organism, and Dagher explicitly recommends using protein-coding DNA to encode data, and thus such a skilled person in the art would have arrived at a different solution from the claimed invention because it would induce more undesirable effects resulting from the storage of data in protein coding DNA in a living organism, and Ceze would not have remedied such deficiencies (Applicant’s remarks at pg. 16, para. 4 to pg. 17, para. 1).
This argument is not persuasive. Dagher is not relied upon in the above rejection to teach the nucleic acid molecule being in-vivo replicative. Instead, Ceze was used to disclose this feature in claim 28 in the previous Office action, and now in the independent claims in the above new grounds of rejection under 35 U.S.C. 103. Dagher is instead used to disclose that the individual insert their message into ncDNA that is verified to have no biological use and is truly nonfunctional (i.e. the DNA does not encode RNA) (pg. 334, col. 1, para. 2). Dagher discloses to prevent the unwanted transcription from happening in ncDNA with embedded data, it is important to make sure the encoded nucleotides do not create a start (i.e. initiation) codon in any of the six reading frames (pg. 334, col. 2, para. 3). Therefore, Applicant’s argument regarding using “protein-coding DNA” is not persuasive because this was not relied upon in the above rejection, Dagher discloses the DNA used for storage should not encode a protein. Last, Applicant only states that “Ceze similarly, would not have remedie[d] such deficiencies”, referring to Dagher, but does not provide any arguments regarding why the teachings of Ceze as previously applied to claim 28 is deficient.
Applicant remarks that therefore, the combination of Ahn and Dagher and/or Ceze fails to teach every element of the claimed invention, and the attempt to bring the isolated teaching of Ahn and Dagher and/or Ceze would amount to improperly picking and choosing features from different references without regard to the teachings of the references as a whole, and that the evidence of motivation must come from somewhere within the record, and there is nothing in the record supporting the Office Action’s proposed combination of Ahn and Dagher and/or Ceze (Applicant’s remarks at pg. 17, para. 3-4).
This argument is not persuasive for the reasons discussed above. Furthermore, in response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). Applicant has not pointed out where in the above and/or previous rejection, information gleaned only from the applicant’s disclosure was used to make the rejection. Last, the previous Office action and the new grounds of rejection set forth above cite motivations from each of Ceze and Dagher to support their combinations with Ahn, and Applicant has not explained why the cited motivations were deficient.
Conclusion
No claims are allowed.
Claims 25-29 and 34 are patent eligible for the reasons discussed in the Office action mailed 19 Sept. 2025 at para. [047].
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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