DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Claim 10 is cancelled. Claims 1, 2, 6-9, 11-13, and 18 are amended. Claims 1-9, and 11-26 are pending and under examination.
Response to Arguments
Rejections Withdrawn
The rejection of claim 10 under 35 U.S.C. 103 as being unpatentable over Bathe et al. (WO 2017/189914 A1, published Nov. 2, 2017), as applied to claim 1 above and included here for reasons supra, in view of Cronin et al. (US 2003/0165830 A1, published Sep. 4, 2003) is withdrawn following the cancellation of the claim.
New Rejections/Objections
Claim Objections
Claims 2, 6-8, 12-13, 15-16, and 26 are objected to for inconsistent use of “oligonucleotide feature tags” versus “feature tags”. Claim 1 has been amended to consistently recite oligonucleotide feature tags.” The identified claims however, revert to the unsupported unmodified term “feature tags” (or in claims 13 and 16, “feature tag sequences”). It is unclear whether these terms are intended to refer to the same “oligonucleotide feature tags” recited in claim 1, or whether a broader or different class of feature tag is intended. If the same tags are intended, the terminology should be made consistent throughout the claim set. If a different or broader class is intended, written description and enablement support for that broader class would need to be identified. Clarification is required.
Claim 22 is objected to because of the following informalities: typographical error. Appropriate correction is required. Claim 22 recites step “(f) accessing the desired sequence-controlled polymers,” but no step “(e)” is recited anywhere.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 1-9, 11-26 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.
Throughout the specification, the relationship between a feature tag and its corresponding feature is consistently described using different language than “encoded by.” A “feature tag” is defined as “an oligonucleotide of a defined sequence that corresponds to a feature attributable to a sequence controlled polymer” (see [0122]), and a “feature attributable to a sequence-controlled polymer” is in turn defined as “a feature that the sequence-controlled polymer possess or embodies” (see [0123]). This same “attributable to” language is used throughout the Summary of the Invention (see [0021]) and every disclosed example of a “feature” is consistent with this attribution-type relationship rather than an encoding relationship, e.g., species identity, taxonomic rank, and collection date (see [0454], Example 1), properties extrinsically assigned to a sample and associated with, not information recoverable by decoding the sequence of the tagged sequence-controlled polymer itself.
The term “encoded by,” by contrast, appears in the specification in a materially different context, the general statement that “the sequence of any sequence-controlled polymer encodes the date represented by the sequence of the polymer” (see [0130] describing an intrinsic relationship in which a polymer’s own sequence is the encoded information. No portion of the specification describes, and no working example demonstrates, a feature tag correspond toa feature that is itself encoded within, and recoverable by decoding, the sequence of the sequence-controlled polymer to which the tag pertains. Accordingly, the specification fails to describe the claimed combination with sufficient specificity to establish possession. See Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010), MPEP 2163.
To the extent this limitation is construed to require that a feature be intrinsically encoded within, i.e., decoded from, the sequence of the sequence controlled polymer to which its corresponding feature tag pertains, claims 1 and 18 are further rejected as failing to enable their full scope. Claim 1 and 18 are not limited to nucleic acid embodiments as “sequence controlled polymer” is expressly defined to include non-nucleic acid biopolymers and synthetic polymers, including polypeptides, carbohydrates, and peptidomimetics (see [0136]-[0157]). The specification’s only disclosed mechanisms for encoding information within a sequences controlled polymer’s sequence, directed bit-to-base conversion, are described exclusively in nucleic acid terms (see [0131], [0143], [0260]-[0282]). No guidance is provided for encoding, or recovering a feature from the sequence of a non-nucleic acid sequence controlled polymer. As such the Applicant has not provided adequate written description to show possession across the full breadth of the claim. Claims 2-8, and 12-26 depend from either claim 1 or claim 18 and do not correct this deficiency and are likewise rejected under 35 U.S.C. 112(a).
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 1-9 and 11-26 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential elements, such omission amounting to a gap between the elements. See MPEP § 2172.01. Claim 1 has a broken clause “wherein the single feature to which each different oligonucleotide feature tag corresponds is a feature attributable to one or more of ___ “, missing the essential conclusion and one of ordinary skill in the art would not be able to fill in this gap to know the metes and bounds of the claim.
Claims 1, 2, and 6-8 recites the limitation "the sets". There is insufficient antecedent basis for this limitation in the claim. Claim 1 recites that each of the plurality of different oligonucleotide feature tags “is a member of a distinct set” (singular, introduced without preceding plural antecedent). Claims 2 and 6-8 subsequently refer to “the sets of oligonucleotide feature tags” or “the sets of feature tags” (plural), and claim 8 further refers to “all of the sets of digit tags.” None of these plural recitations has proper antecedent basis, because claim 1 establishes only a singular “distinct set” on a per-tag basis and never introduces a plural “sets” as a claim term. This ambiguity is compounded in claims 6 and 7, which depend directly from claim 1 (not claim 2) and therefore lack even the intervening “sets” language of claim 2 in their dependency chain, such that “the sets of feature tags” in claims 6 and 7 has no antecedent basis whatsoever. Clarification and correction of the claim dependencies and/or antecedent language is required.
Claims 1, 9, 11, 18, and 26 use two different relational terms, “encoding”/”encoded by” and “attributable to”, to describe what appears to be the same relationship between a feature and a sequence controlled polymer or nucleic acid, without indicating whether the terms are intended to be synonymous or to denote distinct relationships.
Specifically, claim 1 recites that feature tags collectively correspond to features “collectively encoded by” the sequence controlled polymers. Claim 9 recites nucleic acids “encoding” one or more features in element (a) but digit tags “encoding a range of numbers attributable to” the feature in element (b), using both terms within a single claim. Claim 11, which depends from claim 9, then recites “the feature attributable to one or more of the nucleic acids”, a phrase with no antecedent basis in claim 9, which recites only nucleic acids “encoding one or more features”, not features “attributable to” the nucleic acids. Claim 18 recites, within a single claim, that the sequence-controlled polymers “encod[e] two or more features” in element (i) while separately reciting, later in the same claim, that each feature tag corresponds to a feature “attributable to” the polymers, and that the plurality of feature tags collectively corresponds to features “collectively attributable to” the polymers. Claim 26(f) recites feature tags “attributable to” the sequence controlled polymer while expressly incorporating the sequence controlled storage object of claim 1, which recites features “encoded by” the polymer.
A person of ordinary skill in the art cannot determine with reasonable certainty whether “encoding”/”encoded by” and “attributable to” are intended as interchangeable terms describing the same feature/polymer relationship or whether they are intended to describe two distinct relationships (e.g. feature intrinsic to an recoverable from the polymer’s own sequence, as opposed to a feature extrinsically associated with, but not encoded within, the polymer). This ambiguity affects the scope of every claim in which either term appears and those dependent upon them. Clarification and consistent use of terminology throughout the claim set is required. See Nautilus, Inc. v. Biosig Instruments, Inc., 134 S. Ct. 2120, 110 USPQ2d 1688 (2014); MPEP 2173.02.
The term “more similar features” / “less similar features” in claim 3 is a relative term which renders the claim indefinite. The term “more similar” / “less similar” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The specification provides no standard, metric or method by which a person of ordinary skill in the art could determine the “similarity” between two arbitrary features, as the term “feature” is used throughout the claims. The specification’s disclosed examples of “features” span heterogeneous categories with no common basis for comparison, including, e.g., taxonomic classification, species identity, sample collection date (see [0454]) and in related disclosure incorporated by reference to the same inventive concept, categories such as literary work title, authorship, and date of composition. Nothing in claim 1 or claim 3 restrict the members of a given “set” of feature tags to features of a common type or category. The specification discloses quantitative similarity metrics only for feature spaces that are inherently homogenous and already quantifiable (e.g., pairwise genetic sequence identity among viral genomes, (see [0273]-[0274]), and provides no guidance, qualitative or quantitative, for determining the similarity between features of different kinds (e.g., a sample collection date as compares to a taxonomic classification, or a color label as compared to a literary work title.)
Because “feature” is not limited to any defined category and no metric for cross-category comparison is disclosed, a person of ordinary skill in the art cannot determine with reasonable certainty what is required to satisfy the “similarity” limitation across the full scope of the claim. This renders claim 3, and claims 4 and 5 depending therefrom, indefinite.
Furthermore, claims 4 and 5 depend indirectly on claim 1, a composition claim directed to “A sequence controlled storage object comprising…”. Claim 5 recites that the similarity encoded feature tags “are similarity encoded by (a) reducing the dimensionality of the features to which the feature tags correspond; and (b) mapping the dimensionality reduced features to an n-dimensional hypercube…” These are active, enumerated method steps performed by an actor, not structural or compositional limitations of the storage object itself. Because claim 1 is a composition, it is unclear whether infringement occurs upon the making, using, or sell of the claimed sequence-controlled storage object, or only upon a party actually performing the recited “reducing” and “mapping” steps. A single claim that covers both a composition and active method steps for using or making that composition is indefinite, because a party cannot readily determine when infringement occurs. See IPXL Holdings v. Amazon.com, Inc., 430 F.3d 1377, 1384, 77 USPQ2d 1140, 1145 (Fed. Cir. 2005).
Claim 4 recites similar step-like language (“similarity encoded by mapping the features…”; “prior to mapping the features…, the dimensionality… is reduced”) and is rejected for the same reasons as claim 5.
Claim 9 recites that “each of the plurality of different digit tags is a member of a different set of digit tags.” Read literally, this requires that any two digit tags among the plurality belong to different sets from one another, i.e., that no two digit tags are in the same set, such that each set contains only a single digit tag. This is inconsistent with the rest of claim 9, which requires that “each set of digit tags has a digit tag corresponding to each of the possible digit values of the place in the multidigit number to which the set of digit tags corresponds,” a limitation that requires multiple digit tags to share a single set. This internal inconsistency makes it impossible for one of ordinary skill in the art to reconcile the requirement that every digit tag belongs to “a different set” from every other digit tag with the requirement that tags correspond to the same digit place share a common set containing one tag per possible digit value.
Claim 11 recites the limitation “the feature attributable to one or more of the nucleic acids” in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 12 recites the limitation "encapsulating reagent" in line 4. There is insufficient antecedent basis for this limitation in the claim.
Claim 13 recites the limitation "the single stranded nucleic acid including bit-stream data" in lines 7-8, 9, and 16. There is insufficient antecedent basis for this limitation in the claim.
Claim 14 recites the limitation "a staple strand" in lines 1-2. There is insufficient antecedent basis for this limitation in the claim.
Claim 15 recites the limitations “staple strands” in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 20 recites the limitation "the isolated sequence-controlled storage object" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 24 recites the limitation " storing the sequence-controlled storage objects" (plural) in lines 1-2. There is insufficient antecedent basis for this limitation in the claim. Claims 18-23, from which claim 24 depends, are directed to a singular sequence controlled storage object. There is no antecedent basis for a plurality of storage objects.
Claim Interpretation
For purposes of examination, certain claim terms that are broad or otherwise require construction have been interpreted in accordance with their broadest reasonable interpretation consistent with the specification, as is required during prosecution. See MPEP 2111; In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1369, 70 USPQ2d 1827, 1834 (Fed. Cir. 2004). The following claim constructions have been applied in this office action. This construction section governs application of the art below. Where a rejection depends on a construction issue not addressed here, it is separately noted within that rejection.
Sequence-controlled polymer: Under the broadest reasonable interpretation, a “sequence-controlled polymer” is any polymer having an identifiable sequence or ordering of monomer units, regardless of whether the sequence is fully defined, partially defined, repeating, or informationally encoded. A sequence-controlled polymers encompasses, for example and without limitation, any nucleic acid (e.g., DNA, RNA, or combination thereof), amino acid sequence (e.g., peptide, proteins), polysaccharides (e.g., cellulose, glycosaminoglycans). This construction is maintained from the prior Office Action and is unaffected by the current amendments.
Sequence-controlled storage object: A “sequence-controlled storage object” is interpreted as any physical object that includes a sequence-controlled polymers and one or more tags or identifiers, without requiring a particular structure, geometry, function, or intended use beyond what is expressly recited. A sequence controlled storage object encompasses, for example without limitation, barcoded nucleic acid constructs, DNA origami structures, tagged protein or ligand complexes, bead-based multiplex tagging systems, or other tagged assemblies in which nucleic acid sequences are used to represent associated features.
Oligonucleotide feature tag: Under the BRI, and consistent with the amendment narrowing “feature tag” to “oligonucleotide feature tag,” this term refers to any nucleic acid sequence associated with a sequence-controlled storage object that represents or identifies a feature attributable to one or more sequence-controlled polymers (e.g., sample ID, position, treatment, molecule type, length, etc.).
Feature: the term “feature” is not separately defined by the specification independent of its own circular use in defining “feature tag” (see [0122]) and “feature attributable to a sequence controlled polymer (see [0123]). Under the broadest reasonable interpretation consistent with the specification’s illustrative (non-limiting) examples, e.g., sample type, source, collection date/time (see [0013]); species, taxonomic classification (see [0454]), feature is construed broadly to mean any property, characteristic, or attribute capable of being associated with a sequence-controlled polymer, without limitation as to category or type. It does not resolve, and is without prejudice to, the separate rejection of this term under 35 U.S.C. 112 as failing to provide a discernible boundary of scope, set forth above, or for providing a basis for comparison.
“Encoded by”/”encoding”: Claims 1, 9, and 18 use “encoded by,” “encoding,” and “attributable to” in reference to the relationship between a feature and a sequence-controlled polymer or nucleic acid. The specification uses these terms inconsistently and does not clearly distinguish them (see 35 U.S.C. 112(b) rejection above). For purposes of applying the prior art below, and absent a clear indication that a narrower, structurally-distinct meaning is intended (e.g., that a feature must be intrinsically recoverable by decoding the payload polymer), “encoded by”/”encoding” is construed under BRI as coextensive with “attributable to”, i.e., as requiring only that the feature corresponds to, and be identifiable in association with, the sequence-controlled polymer(s), consistent with the specification’s own interchangeable usage of these terms (compare [0021] and [0130]) and with claim 18’s use of both terms within a single claim to describe what appears to be a single relationship. This construction is applied without prejudice to the separate rejection of this claim language under 35 U.S.C. 112(a) for lack of written description, set forth above, which addresses whether the specification adequately supports this limitation (under either the broad or narrower construction) across the full scope of the claim.
Digit tag: The specification does not define “digit tag” structurally. Under the BRI, and absent an express limitation to any particular polymer class, a “digit tag” is construes as any tag capable of corresponding to the digit value of a place in a multidigit number and of being hybridizably distinguished from other digit tags, without requiring that the digit tag be an oligonucleotide, nucleic acid, or nucleic acid analog. This broad construction is applied without prejudice to the separate rejection of “digit tag” under 35 U.S.C. 112(b), set forth above.
Hybridizably distinguishable: Under the BRI “hybridizably distinguishable” means that two molecules are capable of being differentiated from one another under at least one set of hybridization or binding conditions, and does not require absolute specificity, quantitative thresholds, or the absence of all cross-hybridization. Applicant is advised that, because “hybridization” is not expressly limited in the claims or specification to nucleic acid base-pairing, this term is not construed as inherently limiting the tags to any particular polymer chemistry.
Relative Hybridizability / similarity: As construed in the prior Office Action, “relative hybridizability” refers to a comparative ability of feature tags to hybridize under at least one set of conditions, without requiring a particular thermodynamic model, numerical, threshold, or measurement protocol, and “similarity” of features encompasses categorical or informational relationships and is not limited to any particular quantitative metric. This construction does not resolve, and is without prejudice to, the sperate rejection of claims 3-5 under 35 U.S.C. 112(b) for failure to disclose an ascertainable method of comparing the similarity of features across the full scope of “feature,” set forth above.
Claim Rejections - 35 USC § 102
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Applicant’s arguments, filed 05/19/2026, with respect to the rejection of claim 1 under 35 U.S.C. 102(a)(1) as being anticipated by Bathe et al. (WO 2017/189914 A1) have been fully considered, however they are moot in light of the amended rejection. The prior rejection did not previously demonstrate how Bathe teaches the new limitations in light of the amendments to the claim. However, upon further consideration, Bathe teaches the added limitations and a new ground(s) of rejection is made for claim 1 under 35 U.S.C. 102(a)(1)/(a)(2).
Claim 1 is rejected under 35 U.S.C. 102(a)(1)/(a)(2) as being anticipated by Bathe et al. (WO 2017/189914 A1, of record).
As previously set forth, Bathe teaches a sequence-controlled storage object (“sequenced-controlled polymer memory object”, SMO) comprising one or more different sequence-controlled polymers, and a plurality of different oligonucleotide feature tags (“address tags”) present at the surface of the object, wherein each different feature tag corresponds to a single feature attributable to one or more of the different sequence-controlled polymers, wherein the plurality of feature tags collectively corresponds to a plurality of features collectively attributable to the sequence-controlled polymer(s), and wherein each of the different feature tags is hybridizably distinguishable from all of the other different feature tags (see pg. 46, 2nd para. – pg. 47 2nd para.; pg. 9 lines 5-18; and throughout).
Claim 1, as amended, further recites that each of the plurality of different oligonucleotide feature tags “is a member of a distinct set that corresponds to one or more related features.” Bathe teaches this limitation. Specifically, Bathe’s Example 1 discloses four nucleic acid memory objects, each tagged with multiple address tags drawn from recurring tag categories, wherein each category groups tags that are related to one another by virtue of correspond to the same type of feature across different objects. For example, memory objects #1-#4 are each labeled with a title tag (e.g., a tag corresponding to “Waiting for Godot”, “The Crucible,” or “Hamlet,”), an author tag (e.g., Samuel Beckett,” “Arthur Miller,” or “Shakespeare”), and an act/scene tag (e.g., “Act II”, “Act III,” or “Act I, Scene III”) among other tag categories (see Example 1, listing the message and “metadate used for tagging” for memory objects #1-#4). The set for all title tags used across Bathe’s pool of memory objects, e.g., the tag corresponding to “Waiting for Godot,” and the tag corresponding to “The Crucible”, is a distinct set of oligonucleotide feature tags that corresponds to one or more related features, namely, the related “title” feature category with each individual tag corresponding to a different value (title) within that category. The same is true of Bathe’s author tag category and act/scene tag category, among others. Bathe further confirms that these categorically-related tags must be mutually orthogonal (hybridizability distinguishable) in order for the disclosed Boolean AND/OR/NOT selection scheme to function, since selection and retrieval for a specific memory object or subset of objects is achieved by capture and release hybridization to a specific tag within a category (e.g., selecting for the “Hamlet” title tag, see discussion of NOT logic, Boolean AND logic and OR logic, and the accompanying figures). This is squarely consistent with the “hybridizably distinguishable” requirement of claim 1 as applied to tags within , and across a distinct set.
Claim 1’s remaining sub-limitation, that the members of at least one set be “similarity encoded feature tags” (limitation (i)) and/or “hybridization ordered” with “the same number nucleotides” (limitation (ii)), are recited in the alternative, following the introductory phrase “optionally wherein.” Under the broadest reasonable interpretation, such optional claim language does not further limit the claim, because the claim does not require that either sub-limitation be present. See MPEP 2111.04. Because limitations (i) and (ii) are not required by claim 1, Bathe need not separately disclose these optional sub-limitations in order for claim 1 to be anticipated. Accordingly, Bathe discloses each and every limitation required of claim 1, including the newly-added “distinct set” limitation and claim 1 is anticipated.
Rejections Maintained
The rejection of claims 1 and claims depending therefrom 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” is maintained.
Examiner acknowledges that claims 1, 9 and 18 have been amended to specify that the feature tags are oligonucleotide feature tags, narrowing the previously rejected genus to a single polymer class. Applicant’s remarks regarding “Hybridizably distinguishable” further direct attention to the specification’s disclosure of specific structural parameters for controlling melting temperature and cross-hybridization among oligonucleotide tag sequences (see pg. 45 lines 8-18 of the specification as filed), considered together with Xu et al. (PNAS 106 2289-2294 (2009), of record), which discloses a network-elimination algorithm and a working setoff 240,000 orthogonal nucleic acid barcode probes. This disclosure reasonably conveys adequate written description of the claims amended oligonucleotide feature tags, however, “hybridizably distinguishable” was not only used only to describe feature tags but also to describe digit tags, which are not currently restricted to nucleic acids, and not defined at all in the specification’s definition section. As such, the specification continues to fail to provide written description to support
Applicant’s remarks direct attention to passages listing peptides, polysaccharides, and other biopolymer classes as species falling withing the defined genus of “sequence-controlled polymer” (see e.g., page 36 lines 5-15; pg. 11 lines 17-23; pg. 67 lines 17-20), together with the general knowledge of the field reflected in Lutz et al., Science 341 1238149 (2013). This showing is insufficient to establish possession of the full claimed genus. Naming a polymer class as a species falling within a genus, without more, does not by itself demonstrate possession of that species as configured and functioning within the claimed invention. See Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010). The specification’s structural and functional examples, including every discloses working example of folding, tagging, hybridization-based selection, encapsulation, and super-structure assembly (e.g., Examples 1-8, Figs. 3-28), is directed exclusively to nucleic acid embodiments. No portion of the specification describes a polypeptide, polysaccharide, or other non-nucleic acid sequence-controlled polymer tagged with an oligonucleotide feature tag, as required by claim 1, much less folded into a storage object nanostructure or selected/retrieved from a pool by hybridization, or discussion on how non-nucleic acid sequence controlled polymers encode attributes as required by the claims.
Applicant’s remarks do not address the rejection based on lack of definition for the term “feature”. The term “feature” remains undefined by the specification, the only passages purporting to define related terms “feature tag” and “feature attributable to a sequence-controlled polymer” each define the term using the word “feature” itself without independently defining what qualifies as a feature (see [0122], [0123]). As “feature” is the term principally responsible for defining the scope of correspondence between a feature tag and the sequence-controlled polymer to which it pertains, and as no boundary is provided (by definition or by a closed or exemplary list) as to what does or does not constitute a “feature”, a person of ordinary skill I the art cannot ascertain the metes and bounds of this term with reasonable certainty.
The rejection of claims 1-9 and 11-26 under 35 U.S.C. 103 as being unpatentable over Bathe et al. (WO 2017/189914 A1, published Nov. 2, 2017), as applied to claim 1 above and included here for reasons supra, in view of Cronin et al. (US 2003/0165830 A1, published Sep. 4, 2003) is maintained.
Applicant's arguments filed 05/19/2026 have been fully considered but they are not persuasive. Applicant argues that the claimed composition and methods are “conceptually distinct from the cited art” because “the combined cited art does not teach or suggest the same functionality of the addressed tags for sorting/retrieval, as required by the claims,” and that Cronin in particular is “conceptually distinct” from the claims because Cronin’s probes are designed to hybridize to target nucleic acid of interest (for capture of that target), whereas the claimed feature tags “are not required to hybridize to the biopolymer itself.” This argument is not persuasive for two reasons.
First, Applicant’s argument is not commensurate with the scope of the claims. Claim 1 does not require that the feature tags refrain from hybridizing to the sequence-controlled polymer(s) to which they correspond. No such negative limitation is recited in claim 1 or in any claim. Arguments concerning limitations not actually present in the claims are not persuasive. See MPEP 2145(I). Accordingly, whether or not Cronin’s disclosed probes are also usable to hybridize to a target sequence of interest is not relevant to whether Cronin teaches or suggest the specific, narrower principle for which it is relied upon in the rejection, the design of sets of related oligonucleotide tags exhibiting controlled, graded, and predictable hybridization behavior through defined-position nucleotide substitutions.
Second, Cronin is not relied upon for its overall target-capture architecture. Cronin is cited specifically for its teaching of a design principle, that a set of oligonucleotide sequences can be engineered, through controlled nucleotide substitutions at defined positions (with defined length, mismatch count, and mismatch placement constraints), to exhibit predictable, graded, and mutually distinguishable hybridization behavior. This design principle is applicable to and combinable with, any hybridization-based oligonucleotide tagging system, including Bathe’s, regardless of what Cronin’s own disclosed probes are ultimately used for. Applicant’s argument that Cronin’s overall system is “conceptually distinct” from the claims attacks Cronin individually for lacking the full architecture of the claimed invention, rather than addressing what the Bathe-Cronin combination as a whole would have suggest to a person of ordinary skill in the art. In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Applicant further argues that “based on Cronin, the skilled person would understand that the barcode(s) associated with the sequence-controlled polymer must be or include a sequence of the polymer itself,” and that this represents “a different concept, a distinct design strategy and a distinct structure” from the claimed “user-defined feature address tags.” This argument is not persuasive for the same reason set for above, Cronin is not relied upon for the proposition that its tags must be sequences of the underlying target polymer, and the rejection does not require Bathe’s or Cronin’s tags to be incorporated bodily, structure-for-structure, into the claimed invention. It is the specific, narrower teaching identified above, controlled-substitution design of a related oligonucleotide tag set exhibiting predictable hybridization behavior, that is relied upon, and Applicant does not dispute that Cronin teaches this narrower principle.
Applicant additionally argues that the claimed aspects are directed to storage and retrieval of “specific discrete objects containing multiple biopolymers (including non-nucleic acid polymers),” implying that the scope of the claims extends meaningfully beyond nucleic acid embodiments in a manner not addressed by the cited art. This argument is not persuasive as applied to the rejection above, because the rejection is based on Bathe’s disclosed nucleic acid embodiments, which fall squarely within the scope of claim 1 as amended (which recites “oligonucleotide feature tags” and does not require that the underlying sequence-controlled polymer(s) be anything other than nucleic acid). To the extent Applicant intends to rely on non-nucleic acid embodiments to distinguish over the art, Applicant is remined that the full genus of “sequence controlled polymers” recited in claim 1remains separately rejected under 35 U.S.C. 112(a) for lack of written description to non-nucleic acid species, as set forth above. Applicant cannot rely on the breadth of a claim term to distinguish over the art while simultaneously failing to support that same breadth under 112.
The rejection of claim 1 on the ground of as being unpatentable over claims 1-6 of U.S. Patent No. 11,514,331 B2 is maintained, as modified below to reflect the current claim amendments.
Applicant argues that the ‘331 patent “does not render the instant claims obvious for at least the same reasons as set forth above with relation to Bathe,” relying on the prior Office Action’s statement that “Bathe does not expressly teach organizing such feature tags into defined sets correspond to related features, nor does Bathe teach designing feature tags which a set to exhibit graded or relative hybridizability based on feature similarity,” and further arguing that “the claims as amended require feature tags organized into defined sets corresponding to related features within a set that are associated with or encoded by a biopolymer.” This argument is not persuasive, for two independent reasons.
First, as set forth in the rejection of claim 1 under 35 U.S.C. 102 above, the ‘331 patent’s parent publication (Bathe) in fact discloses feature tags organized into defined sets corresponding to related features. Bathe’s Example 1 discloses multiple nucleic acid memory objects, each labeled with tags drawn from recurring categories, e.g., a title tag, an author tag, and an act/scene tag, such that the set of all title tags used across the discloses pool of memory objects constitute a distinct set of tags corresponding to the related “title” feature category, with the same true of the author-tag, and act/scene-tag categories. This disclosure is not limited to the WO publication; it forms part of the same specification underlying the ‘331 patent , and the ‘331 patent’s claims 1, 6, 18, and 30 (previously relied upon) are supported by this same disclosure. Accordingly, the premise underlying Applicant’s traversal, that organizing feature tags into defined sets corresponding to related features is not taught by the Bathe/’331 disclosure is incorrect, and claim 1’s “distinct set” limitation does not, by itself, distinguish the instant claims from the ‘331 patent’s disclosure.
Second, the obviousness-type double-patenting analysis is not confined to what is expressly recited in the claims of the ‘331 patent, but extend to what would have been obvious to a person of ordinary skill in the art in view of the ‘331 patent’s claims together with the knowledge generally available in the art at the relevant time. See In re Longi, 759 F.2d 887, 892 n.4, 225 USPQ 645, 648 n.4 (Fed. Cir. 1985), MPEP 804(II)(B)(1). To the extent Applicant maintains that the ‘331 patents claims do not expressly recite the “distinct set” and graded/relative-hybridizability limitations now present in claim 1 (as amended to incorporate former claim 2’s base “distinct sets” limitation), wit would nonetheless have been obvious to one of ordinary skill in the art, at the time of the instant application, to organize the ‘331 paten’s address tags into defined sets corresponding to related features and to design such sets to exhibit graded, relative hybridizability reflecting feature similarity, in view of Cronin’s teaching of engineering sets of related oligonucleotides tags through controlled, defined-position nucleotide substitutions to produce predictable, graded, and mutually distinguishable hybridization behavior (see Cronin, Abstract, Figs. 1-9, [0012]-[0014], [0017]-[0018], and throughout). One of ordinary skill would have been motivated to apply Cronin’s tag-set design principles to the ‘331 patent’s address-tag system for the same reasons articulated in the rejections above., which is incorporated herein by reference with a reasonable expectation of success given the well-understood, tunable nature of oligonucleotide hybridization specificity.
Accordingly, whether analyzed under the ‘331 patent’s disclosure alone (which itself teaches the distinct set” limitation, per the first ground above) or under the ‘331 patent’s claims in view of Cronin (per the second, independent ground above), claim 1 as amended is not patentably distinct from claims 1-6 of the ‘331 patent. The rejection is maintained. A terminal disclaimer, if filed, may obviate this rejection.
Conclusion
No claim is allowed.
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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/MATTHEW HAROLD RAYMONDA/ Examiner, Art Unit 1684
/AARON A PRIEST/ Primary Examiner, Art Unit 1681
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