Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
This application claims priority to and benefit of U.S. Provisional Application No. 63/208,973, filed June 9, 2021, as such all claims will be awarded the earlier filing date for examination.
Claim Status
Claims 1-26 are pending and under examination. Claims 1, 9, 18, and 26 are independent claims.
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.
Claims 1-26 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Independent claims 1, 9, and 18 recite, inter alia, that “each feature tag is hybridizably distinguishable from every other feature tag” and the specification states that this means “orthogonal for hybridization” The written description of the application as filed does not reasonably convey to those skilled in the art that the inventors were in possession , at the time of filing, of the full scope of the genus “hybridizably distinguishable” feature tags required by the claim. While the specification mentions that feature tags can be orthogonal for hybridization and refers generally to “orthogonal barcodes” (see pg. 28, 2nd para., pg. 50 4th para.). It does not disclose any specific orthogonal sequence sets, numerical Hamming-distance thresholds, melting temperature differentials, mismatch tolerance levels, or hybridization conditions that would define or exemplify the claimed genus of “hybridizably distinguishable” sequences across the entire scope of the claim (which encompasses any sequence-controlled polymer and any environmental conditions). The disclosure provides only aspirational functional language, that the tags avoid cross-hybridization, without representative species or structural features that permit a skilled artisan to recognize members of the full genus. Absent such representative examples or explicit structural guidance, one of ordinary skill would not be able to conclude that the inventors were in possession of every embodiment falling within “hybridizably distinguishable,” particularly for non-nucleic-acid polymers or for extreme operating conditions.
Accordingly, claims 1, 9, and 18 and any claims depending therefrom, are rejected under 35 USC 112(a) for lack of written description. The specification, while describing feature tags in functional terms and providing general statements about orthogonality, does not reasonably convey to those skilled in the art that the inventors had possession of the claimed genus of “hybridizably distinguishable” feature tags at the time of filing.
Further, claim 1 recites “a sequence-controlled storage object comprising one or more different sequence-controlled polymers” while the term “sequence-controlled polymer” is defined in the specification to macro-molecule that is composed of two or more distinct monomer units sequentially arranged in a specific, non-random manner, as a polymer "chain." While describing exemplary sequence-controlled biopolymers include nucleic acids, polypeptides or proteins, linear or branched carbohydrate chains, or other sequence-controlled polymers.” However, the specification only provides detailed descriptions and exemplification for DNA-based nanostructures. The specification contains no description showing possession of sequence-controlled peptides folded into nanostructures, polysaccharide-based sequence-controlled objects, lipid sequence encoded polymers, or any non-nucleic acid polymer class capable of being folded, tagged, hybridized or assembled into storage objects. Thus, the genus of “sequence-controlled polymers” is vastly broader than the particular species disclosed. The disclosure of only DNA is insufficient to support the full scope of the genus recited in claim 1. See Ariad Pharm., Inc. v. Eli Lilly and Co., 598 F.3d 1336, 1341, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010).
Furthermore, claim 1 recites “a plurality of different feature tags wherein each different feature tag corresponds to a single feature” the specification mentions DNA oligonucleotide “tags” but provides no structural, mechanical, or algorithmic description for how a feature is defined or encoded. There is not description of feature definition rules, similarity metrics, digit-tag generation, or any mapping rationale beyond conceptual statements. The disclosure therefore does not support possession of the full functional scope of “feature tags” for arbitrary polymers. Functional claiming without commensurate structural support violates written description. See LizardTech Inc. v. Earth Resource Mapping Inc., 424 F.3d 1336, 1345, 76 USPQ2d 1724, 1732 (Fed. Cir. 2005). “Whether the flaw in the specification is regarded as a failure to demonstrate that the patentee [inventor] possessed the full scope of the invention recited in [the claim] or a failure to enable the full breadth of that claim, the specification provides inadequate support for the claim under [§ 112(a)]."
Accordingly, claim 1 and any claims depending therefrom, are rejected under 35 USC 112(a) for lack of written description.
In regards to claims 4 and 5, the claims recite “mapping the features to which the feature tags correspond to an n-dimensional hypercube based on the similarity of the features” however, the specification does not reasonably convey to a person of ordinary skill in the art that the inventors were in possession of the claimed method of similarity encoding feature tags by mapping features to a n-dimensional hypercube as recited.
The specification describes, in general terms, that features or barcodes may be associated with an n-dimensional hypercube to represent similarity relationships. However, the disclosure lacks a description of how the claimed mapping is performed, including but not limited to: how features are assigned to nodes or coordinates within the n-dimensional hypercube; how similarity between features determines adjacency, distance, or dimensional placement within the hypercube; how the dimensionality n is selected relative to the number or nature of features; or how the hypercube mapping results in specific nucleic acid sequences constituting the ”similarity encoded feature tags.”
The specification primarily discusses hypercubes in the context of abstract feature similarity metrics, visualization, or data analysis, rather than as a concrete encoding scheme that defines the structure or sequence composition of feature tags. The disclosure does not describe a complete algorithm, rule set, or representative examples demonstrating possession of the full scope of “similarity encoding” by hypercube mapping as claimed.
Moreover, the specification does not provide representative species or working examples illustrating feature tags generated by mapping features to an n-dimensional hypercube across varying values of n, nor does it disclose sufficient structural or sequence-level characteristics of such features tags to show possession of the claimed genus.
Accordingly, the disclosure fails to demonstrate that the inventors were in possession of the claimed similarity encoding method using an n-dimensional hypercube at the time of filing, and claim 4 therefore lacks adequate written description.
Claim Interpretation /Broadest Reasonable Interpretation of claim elements.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art.
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)
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.
Feature tag: Under the BRI, a “feature tag” 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.)
Hybridizably distinguishable: Under the BRI “hybridizably distinguishable” means that two nucleic acid sequence 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.
Claim 1 has been interpreted under the BRI consistent with the specification. Under this interpretation, the recited “sequence-controlled storage object” encompasses any physical object that comprises one or more sequence-controlled polymers and a plurality of nucleic acid tags associated therewith. The recited “feature tags” are interpreted broadly as nucleic acid sequences that are associated with, or represent, features attributable to one or more sequence-controlled polymers, without requiring any particular mechanism by which the feature is determined. The requirement that feature tags by “hybridizably distinguishable” is interpreted to mean that the feature tags are distinguishable from one another under at least one set of hybridization conditions without requiring complete specificity or the absence of all cross-hybridization.
Claim 3 has been interpreted such that “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 such that “similarity” of features encompasses categorical or informational relationships.
Claims 6 and 7 have been interpreted such that the recited mismatch numbers and positions define sequence design constraints without requiring a specific hybridization efficiency, specificity threshold, or exclusion of all unintended interactions.
Claim 11 has been interpreted such that “levels” or “intensities” encompass discrete, categorical, or symbolic representations of feature states and do not require continuous measurement or calibrated physical quantities.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim 1 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bathe et al. (WO 2017/189914 A1, published Nov. 2, 2017).
Bathe teaches a sequence-controlled storage object comprising one or more sequence-controlled polymers such as nucleic acids or polypeptides (see Abstract). Bathe further teaches a plurality of different oligonucleotide barcodes (feature tags) on their surfaces for indexing, sorting, and retrieval, wherein each different barcode corresponds to a single attribute of the stored sequence such as content, or origins, and the plurality of barcodes collectively represents multiple attributes of a particular sequence (see pg. 46, 2nd para. – pg. 47 2nd para., and throughout). Bathe further teaches that these barcodes are designed to be orthogonal to each other so that each barcode is hybridizably distinguishable from the other barcodes (see pg. 9, lines 5-18). Bathe therefore teaches the structural and functional limitations of claim 1, including surface-presented hybridizably distinguishable feature tags corresponding to features of sequence-controlled polymers.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-26 are rejected 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).
As recited above, Bathe teaches all of the limitations of claim 1. Claims 2-8 12-17 and 26 depend directly or indirectly from claim 1. Claims 2 and 3 further recite organizing feature tags into sets corresponding to related features, and designing feature tags within a set such that their relative hybridizability reflects similarity among the corresponding features.
Bathe teaches sequence-controlled storage objects comprising multiple surface-presented nucleic acid tags that are addressable by hybridization and attributable to properties of the underlying nucleic acid polymers (see pg. 46, 2nd para. – pg. 47 2nd para., and throughout). However, Bathe does not expressly teach organizing such feature tags into defined sets corresponding to related features, nor does Bathe teach designing feature tags within a set to exhibit graded or relative hybridizability based on feature similarity.
Cronin teaches designing libraries and sets of oligonucleotide tags that are intentionally related by controlled nucleotide substitutions at defined positions, such that tags within a set exhibit predictable and distinguishable relative hybridization behavior (see Abstract, Figs. 1-9, [0012]-[0014] and throughout). Cronin further teaches that relative hybridization behavior among tags in a set is engineered through controlled sequence variation and used to discriminate among closely related tagged entities (see [0017]-[0018], [0080], [0167], and throughout).
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing to organize Bathe’s feature tags into sets corresponding to related features and to design the tag sequences within a set to exhibit relative hybridizability. One would have been motivated to combine these since Bathe already relies on hybridization-based tagging to represent and act upon different attributes of sequence-controlled storage objects and organizing such tags into sets represents a predictable and routine approach for managing multiplexed feature representations. Since Bathe already teaches that feature tags represent features of sequence-controlled polymers, and Cronin teaches how to engineer relative hybridization behavior among related oligonucleotide tags, selecting tags sequences such that relative hybridizability reflects relationship among represented features represents a predictable design choice. Further, one of ordinary skill in the art would have a with a reasonable expectation of success, since hybridization strength is a well-understood and tunable property of nucleic acid sequences as demonstrated by Cronin.
Claims 4 and 5 depend on claim 3 and further recite encoding similarity relationships among features by mapping features to an n-dimensional hypercube based on similarity. Once feature tags are organized into sets corresponding to related features and designed to exhibit graded hybridizability reflecting feature similarity, it would have been further obvious to represent or index the similarity relationships among such features using a known mathematical or data-structural framework, such as an n-dimensional hypercube, optionally after dimensionality reduction, as a predictable organizational choice. The recited hypercube mapping defines only how similarity information among features is structured or indexed for purposes of assigning feature tags, and does not impose any new structural or functional limitations on the sequence-controlled storage object or the feature tags themselves. Selecting an n-dimensional hypercube, including selecting n as an integer related to the number of features, represents a routine design choice for organizing similarity relationships in a scalable manner once similarity-based tagging is desired and would have been expected to succeed because it affects only how features are mapped or represented, not how the feature tags physically hybridize.
Furthermore, reducing the dimensionality of features prior to similarity mapping represents a routine and predictable optimization when organizing or indexing similarity relationships among features, particularly where features are initially described by a large number of attributes. Dimensionality reduction is commonly employed to simplify similarity relationships while preserving relative distances or similarities, and its recitation in claim 5 does not impose any new structural or functional limitation on the sequence-controlled storage object or the feature tags themselves. Rather, dimensionality reduction affects only how feature information is represented prior to assignment of feature tags.
It would have been obvious to a person of ordinary skill in the art at the time of the invention to apply dimensionality reduction prior to similarity mapping to encode similarity relationships using proportional distances or edge counts within a hypercube representation , as a routine refinement of the similarity-encoding framework discussed with respect to claims 3 and 4. Such refinements represent predictable uses of known mathematical or organizational techniques to improve scalability and manageability of similarity-based tagging systems and one would have a reasonable expectation of success, because they affect only how similarity information is represented and indexed, not how the feature tags physically hybridize or function.
In regards to claims 6 and 7, as discussed above, Bathe and Cronin teach all of the limitations of claim 2 for which claims 6 and 7 depend. Claims 6 and 7 further recite specific sequence-level constraints on feature tags within a set, including uniform length, defined numbers of mismatched nucleotides, placement of mismatches away from tag termini and mismatch counts that scale with tag length. Bathe teaches the use of hybridizable feature tags but does not expressly teach specific mismatch counts, mismatch placement rules, or length-dependent mismatch constraints within tag sets.
Cronin, expressly teaches designing oligonucleotide tag sets in which tags are of uniform length and differ by controlled nucleotide substitutions at defined internal positions, and further teaches that the number and placement of mismatches are selected to modulate hybridization behavior and discrimination among related tags (see Figs 1-15, [0066]-[0067], [0284], and throughout).
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing to apply Cronin’s established tag-set design principles to Bathe’s feature tags in order to achieve predictable hybridization behavior. Such sequence level constraints represent routine optimization in oligonucleotide-based tagging systems and would therefore have a likelihood of success.
In regards to claim 8, Cronin teaches organizing oligonucleotide tags into discrete sets, with each tag within a set correspond to a distinct state or value and being hybridizably distinguishable from tags in other sets (see Abstract, Figs. 1-9, [0012]-[0014] and throughout). Encoding numeric values using digit-specific tag sets represents a straightforward application of known tag-set design principles.
In regards to claim 9, Bathe teaches a sequence-controlled storage object comprising one or more sequence-controlled polymers and a plurality of surface-presented nucleic acid tags that are attributable to information stored in the object and are hybridizably distinguishable, wherein the tags are used for hybridization-based identification, interaction, grouping, and selection of the storage object (see Fig. 20, pg. 19 ¶1, pg. 21 ¶2, and throughout). Bathe further teaches that multiple distinct tags may be present on the surface of a single storage object and that such tags may represent different informational attributes associated with the stored information (see pg. 46 ¶3, pg.49 ¶4, and throughout). However, Bathe does not expressly teach organizing presented tags into digit-position-specific sets for encoding a multidigit number.
Cronin teaches designing and using sets of oligonucleotide tags wherein each tag within a set corresponds to a distinct predefined state or value, and wherein tags in different sets are hybridizably distinguishable from one another (see Abstract, Figs. 1-15, [0012]-[0019], and throughout). Corning further teaches that such tag sets may be used to encode discrete symbolic or categorical information with each possible value represented by a unique oligonucleotide tag and hybridization serving as the readout mechanism (see [0135]-[0139], and throughout).
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing to implement Bathe’s surface-presented tag system using the tag-set encoding principles taught by Cronin, such that each digit place of a multidigit number is represented by a different set of digit tags, each set comprising tags corresponding to all possible digit values for that place, and one tag from each set being present on the storage object to encode the multidigit number. Assigning one tag per digit place and organizing tags into digit-specific sets constitutes a predictable and routine application of known symbolic encoding techniques to Bathe’s tag-based storage objects.
The optional limitation that each set of digit tags has the same number of members as the mathematical base in which the multidigit number is expressed merely reflects the conventional definition of positional number systems and does not impart patentable distinction.
In regards to claims 10 and 11, these claims depend directly or indirectly from claim 9 and further recited that the multidigit number encoded by the digit tags corresponds to a feature attributable to one or more of the sequence-controlled polymers, wherein the feature is a member of a set of related features, and wherein different numerical values are associated with members of the set to represent relative levels or intensities of the feature. Claim 10 and 11 further recite that the multidigit number is equal to, proportional to, or the same as a given number of digits of the numerical value of the feature, including optional variations such as proportional numerical spacing, arbitrary assignment, or use of the most significant digits.
As discussed with respect to claim 9, Bathe teaches associating tag-encoded information with features of sequence-controlled polymers, and Cronin teaches encoding discrete values using sets of oligonucleotide tags. It would have been obvious to a person of ordinary skill in the art to associated related features with numerical values representing relative levels or intensities and to encode all or part of such numerical values using the multidigit number encoded by the digit tags of claim 9, because doing so represents a predictable and routine information-representation choice once feature information is already being encoded using digit tags. The optional limitations recited in claim 11 merely describe alternative well-known ways of mapping feature information to numeric representations and do not impart patentable distinction.
In regards to claims 12, Bathe teaches encapsulating the sequence-controlled polymers, wherein the encapsulating reagent can be reversibly removed through chemical or mechanical treatment, optionally wherein (i) the feature tags are comprised in one or more of the encapsulating agents; and/or (ii) the one or more encapsulating agents are selected from the group consisting of natural polymers and synthetic polymers, or combinations thereof; and/or (iii) one or more encapsulating agents are selected from the group consisting of proteins, polysaccharides, lipids, nucleic acids, inorganic coordination polymers, metal- organic frameworks, covalent organic frameworks, inorganic coordination cages, covalent organic coordination cages, elastomers, thermoplasts, synthetic fibers, or any derivatives thereof (see Figs. 4, 19, 20 and 21, pg. 23 ¶3, pg. 37 ¶4 – pg. 41 ¶1, and throughout).
In regards to claim 13 and 17, Bathe teaches at least one of the sequence-controlled polymers is a single stranded nucleic acid, and wherein the nucleic acid is folded into a three-dimensional polyhedral nanostructure comprising two nucleic acid helices that are joined by either anti-parallel or parallel crossovers spanning each edge of the structure, wherein the three-dimensional polyhedral structure is formed from single stranded nucleic acid staple sequences hybridized to the single stranded nucleic acid including bit- stream data, wherein the single stranded nucleic acid including bit-stream data is routed through the Eulerian cycle of the network defined by the vertices and lines of the polyhedral structure, wherein the nanostructure comprises at least one edge including a double stranded or single-stranded crossover, wherein the location of the double strand crossover is determined by the spanning tree of the polyhedral structure, wherein the staple sequences are hybridized to the vertices, edges and double strand crossovers of the single stranded nucleic acid including bit-stream data to define the shape of the nanostructure, and wherein one or more of the staple sequences comprises one or more feature tag sequences. (see pg. 42 ¶3 – pg. 45 ¶1, Claim 31). Bathe further teaches these 3D storage objects having additional storage object bound thereto (see pg. 51 ¶4 – pg. 53 ¶2, Claim 41, and throughout), reading on the limitations of claim 17.
In regards to claim 14, Bathe teaches staple strands may comprise from 14 to 1,000 nucleotides, (see pg. 7 ¶2, claim 13, claim 36) inclusive, or wherein the single-stranded nucleic acid comprises approximately 100 to 1,000,000 nucleotides, inclusive, or combinations thereof (see pg. 7 ¶2, Claim 37).
In regards to claim 15, Bathe teaches that one or more staple strands include one or more feature tag sequences at the 5' end, at the 3' end, or at both the 5' end and at the 3' end (see pg. 47 ¶3, pg. 79 ¶3 - pg. 80 ¶1, Claim 15, Claim 38)
In regards to claim 16, Bathe teaches one or more feature tag sequences comprise one or more overhang oligonucleotide sequences, optionally wherein the one or more feature tag sequences comprise oligonucleotide sequences complementary to one or more feature tag sequences attached to a different sequence-controlled storage object (see pg. 6 ¶6, pg. 9 ¶2, pg. pg. 11 ¶2, Claim 39, and throughout).
In regards to claim 18, Bathe teaches assembling sequence-controlled storage objects comprising one or more sequence-controlled polymers and a plurality of surface-presented, hybridizably distinguishable feature tags attributable to features of the polymers. Cronin teaches designing and using sets of hybridizably distinguishable oligonucleotide tags to represent informational attributes as explained in respect to claim 1. It would have been obvious to assemble such as storage object using these teachings.
Performing the steps of assembling the storage object, storing the assembled object, and optionally retrieving the desired sequence-controlled polymers constitutes the inherent and intended use of the obvious storage object taught by Bathe, and therefore would have been obvious to a person of ordinary skill in the art. Bathe further teaches encapsulation (see pg. 73 ¶3 – pg. 78 ¶2), storage (see Title, and throughout), and retrieval (see pg. 6 ¶4 and throughout) of such storage objects, confirming the obviousness of the recited method steps.
In regards to claim 19, as discussed with claim 18, Bathe teaches hybridization-based identification and selection of sequence-controlled storage objects using surface-presented feature tags (see Abstract and throughout). Bathe further teaches that storage objects may be selected or isolated based on structural characteristics including shape, and based on affinity interactions mediated by function groups associated with the storage object (see pg. 10 ¶2-3, pg. 57 ¶4 – pg. 58 ¶1, and throughout)
Claim 20 depends on claim 18 and further recites modifying an isolated sequence-controlled storage object by the addition of one or more feature tags. As discussed with respect to claim 18, Bathe teaches assembling sequence-controlled storage objects with surface-presented feature tags and using oligonucleotide hybridization to attach, remove, or exchange such tags. Bathe further teaches dynamic modification of sequence-controlled storage objects, including reconfiguration, refolding, and reorganizing the storage object using additional oligonucleotides (pg.54 ¶3, pg. 57 ¶4 – pg. 58 ¶1, and throughout).
Claim 21 depends on claim 19 and further recites that one or more sequence-controlled storage objects are isolated from a pool of storage objects using Boolean logic, optionally including the use of Boolean NOT logic to delete one or more storage objects from the pool. Bathe expressly teaches performing selection operations on pools of sequence-controlled storage objects using logical operations including Boolean AND, OR, and NOT logic, to iteratively include or exclude storage objects based on the presence or absence of specific tags, structural features, or affinity markers (pg. 26 ¶1, pg. 30 ¶1, pg. 58 ¶2 – pg. 62 ¶2, and throughout). Further, Bathe teaches that Boolean NOT logic may be used to remove undesired storage objects from a pool by selectively depleting objects exhibiting specified characteristics, thereby refining the pool to isolate desired storage objects( pg. 61 ¶4 – pg. 62 ¶2, pg. 87 ¶2 – pg. 88 ¶1).
In regards to claim 22, Bathe teaches that sequence-controlled storage objects are assembled, stored, modified, and subsequently accessed in order to retrieve, read, or utilize the stored sequence-controlled polymers (see Abstract and throughout).
In regards to claims 23 and 24, Bathe teaches dehydrating, lyophilizing, or freezing the sequence-controlled storage object, optionally further comprising one or more of rehydrating or thawing the sequence-controlled storage object for processing (see Fig. 15, pg. 10 lines 9-14, pg. 19 lines 3-7, pg. 50 lines 20-25, and throughout). Bathe further teaches storing the sequence-controlled storage objects in a matrix selected from the group consisting of cellulose, paper, microfluidics, bulk 3D solution, on surfaces using electrical forces, on surfaces using magnetic forces, encapsulated in inorganic or organic salts, and combinations thereof (see pg. 8 ¶3, pg. 21 ¶3, pg. 77 ¶2, Claim 44, and throughout)
In regards to claim 25, Bathe teaches storing the sequence-controlled storage object and digitally processing droplets containing sequence- controlled storage objects (see Claim 45, pg. 10 ¶2, pg. 46 ¶1).
In regards to claim 26, this claim recites automating assembly of the sequence-controlled storage object using a flow-based device comprising means for flowing, mixing, annealing, purifying, tagging, encapsulating, selecting and de-encapsulating storage objects.
Bathe teaches the underlying assembly, tagging, and selection steps and teaches flow-based and microfluidic systems for automating nucleic acid assembly, annealing, purification, tagging, encapsulation, selections, and retrieval of sequence-controlled storage objects.
It would have been obvious to automate the assembly of Bathe’s storage objects using the flow-based system, because automation represents a predictable optimization that improves scalability and reproducibility without altering the underlying chemistry.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6 of U.S. Patent No. 11,514,331 B2. Although the claims at issue are not identical, they are not patentably distinct from each other.
In regards to claim 1, this claim is drawn to a sequence-controlled storage object with multiple hybridizably distinguishable feature tags on its surface. There limitation are taught in patent ‘331 through claims 1, 6, 18, and 30. In claim 1 of ‘331 the inventors claim a synonymous “sequence-controlled polymer memory object” comprising a sequence-controlled polymer and one or more address tags, wherein the address tags are present on the surface of the memory object. Claim 6 of ‘331 recites the limitation that the address tags are located on the surface of the storage object.
Conclusion
No claim is allowed.
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/MATTHEW HAROLD RAYMONDA/Examiner, Art Unit 1684
/AARON A PRIEST/ Primary Examiner, Art Unit 1681