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 .
Status of the Application
Claim(s) 1-3, 9-12, 16, and 18 are pending and under examination
Claim(s) 19-23, 25-27, 29, 31, 34-36 are withdrawn from consideration.
Applicant's election with traverse of Group I (claims 1-3, 9-12, 16, and 18), concatenated molecular barcodes, in the reply filed on 07/14/2026 is acknowledged. The traversal is on the ground(s) that Mohammed et al. does not break unity because the reference does not disclose a “concatenated molecular barcode that includes at least one identimer, which identimer includes a detectable label and a scaffold portion, which scaffold portion includes a recognition moiety that is orthogonal to a recognition moiety of at least one other identimer in the set.” Applicant contested the claims remain directed to a single general inventive concept.
This is not found persuasive because Applicant’s argument relies on a narrower interpretation of the claims than is supported by the claim language. Under broadest reasonable interpretation consistent with the specification, then claimed terminology is not limited to Applicant’s preferred embodiments or specific implementation described in traversal argument. The cited reference discloses teaches the broadly recited linking feature (more details will be included below in the rejection and claim interpretation sections), and the restriction requirement was therefore proper and is maintained.
The requirement is still deemed proper and is therefore made FINAL.
Specification
The disclosure is objected to because of the following informalities: the drawing includes Fig. 27C, but the specification does not provide a corresponding brief description for the figure.
Appropriate correction is required.
Drawings
The drawings are objected to because:
Specific deficiency - Sequences appearing in the drawings for Figs. 18 is not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Claim Interpretation
The claims are examined under broadest reasonable interpretation consistent with the specification. It is noted that limitations from a particular embodiment , figure, or intended uses are not read into the claims where the claim langue does not require them.
For examination purposes only, the following interpretations apply:
“Molecular barcode” is interpreted as a molecular structure that represents/conveys information. The claims do not require any minimum information capacity, specific decoding scheme, a predetermined codebook, or a barcode having multiple distinguishable segments.
“Operatively connected” is not limited to direct covalent attachment. Consistent with the specification, it broadly covers direct or indirect chemical interaction or association sufficient for the recited components to function together.
“Recognition moiety” is interpreted as a chemical moiety reactive to a chemical or enzymatic cleaving agent. It is not limited to a unique barcode-decoding sequence or to specific nuclease, protease, or chemical cleavage embodiments in specification.
“Cleavage site” is interpreted as the point, where two molecules become disassociate upon cleavage. The specification expressly permits the cleavage site to locates within, outside of, or distant from the recognition moiety. [0092]
“Orthogonal” requires only that a component react to a specific reagent under specific conditions while at least one other reagent has limited or no reactivity with that agent. The term does not require absolute exclusivity, zero cross reactivity, or complete set of unique and independent recognition moiety.
“Concatenated to each other” is interpreted as linked together. The claims do not narrow to a specific linkage chemistry, require direct attachment, or require construction by sequential split-pool synthesis.
“Three-dimensional arrangement” is interpreted as spatial arrangement produced by concatenated components. The claim does not recite a geometry, orientation, folding pattern, spatial separation, or minimum complexity. A linked molecular arrangement extending through 3-D space is not excluded.
“To encode” means converting information, data, or classification instruction into another format, consistent with specification. The claim does not require the encode information arise only from the precise physical order of multiple identimers or that it can be decoded by sequential cleavage.
Hence, the phrase “concatenated to each other in a three-dimensional arrangement to encode and form the molecular barcode” of claim 1 does not require the particular linear, modular, sequentially cleavable visual barcode shown in Applicant’s preferred embodiment.
“Mutual information” is interpreted as information obtainable about first variable by observing second variable. Thus, the term broadly encompasses an information correlation and does not necessarily require a particular physical connection, encoding algorithm, or quantitative information-theory calculation.
Finally, the functional language in claim 2 describing what occurs upon applying a cleavage agent. This functional limitation does not further narrow scope of claim 1 since it does not recite a structural limitation. Hence claim 1 is interpreted based on expressly recited structural limitations, not limited to a specific cleavage/decoding procedure.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim(s) 1-3, 9-12, 16, and 18 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 indefinite because the claim allows the set to contain only one identimer while requiring recognition moiety of each identimer to be orthogonal to the recognition moiety of at least one identimer in the same set. It is unclear how one identimer can be orthogonal to itself. Hence the claim is indefinite and the metes and bounds of the claim are unascertainable. Additionally, it is unclear which claimed components are “concatenated to each other”. Due to placement of the phrase following “set of one or more detectable labels”, the language may refer to detectable labels, cleavage siteand detectable labels, the scaffold portions, or the identimers. The claim failed to clearly define components that form the “three-dimensional arrangement”. The phrase “three-dimensional arrangement” itself also lacks clear structural referent. The claim does not explain the specific arrangement or what spatial relationship among those components. In further view of ambiguity concerning what is “concatenated to each other”, the boundaries of “three-dimensional arrangement” cannot be determined.
Claim(s) 2--3, 9-12, 16, and 18 depend from claim 1 and is/are therefore similarly rejected.
Claim 2 recites “the recognition moiety” lacks proper antecedent basis because the molecular barcode described in claim 1 include one or multiple identimers corresponds to one or multiple recognition moieties.
Claim 3 recites “the scaffold portion comprises one or more of” followed by both material classes and multi-element combinations and conclude with “and/or” does not clearly define the permissible alternatives. It is not clear whether the listed materials constitute a separate alternative, whether each later combination must be selected as a whole, whether individual features from different alternatives may be combined. Hence the claim is indefinite and the metes and bounds of the claim are unascertainable.
Claim 10 recites “an identimer linker between each identimer in the set of identimers” does not clearly identify the required number or placement of linkers. Also claim 1 permit the set to comprise only one identimer, which means the location “between” does not exist. Hence the claim is indefinite and the metes and bounds of the claim are unascertainable.
Claim 12 recites “one or more of” for substantially different alternatives and later use “and/or”. It is unclear if any alternative is sufficient, any combination of alternative is permitted, the “and/or” only apply to the final two alternatives, or all preceding alternatives may be freely combined. Hence the claim is indefinite and the metes and bounds of the claim are unascertainable.
Claim 18 recites “a material having mutual information with the three-dimensional arrangement of the molecular barcode”, which does not define any required relationship between material and the molecular barcode. Although specification defined mutual information by reference to information obtainable about one variable through observing another variable, the claim does not identify relevant variable, the information encoded, or the degree or type of association required. It is unclear whether physical attachment, predetermined correspondence, statistical correlation, mere colocalization, or any other relationship satisfy the limitation.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-3, 9-12, 16, and 18 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Mohammed et al. (US20200190583A1, EFD: December 13th 2019, disclosed in IDS)
Regarding claim 1, Mohammed discloses molecular barcode comprising a set of one or more identimers, each identimer in the set of identimers comprising a set of one or more detectable labels operatively connected to a scaffold portion, the scaffold portion comprising: a recognition moiety that is orthogonal to the recognition moiety of at least one identimer in the set of identimers; and a cleavage site operatively connected to the set of one or more detectable labels, concatenated to each other in a three-dimensional arrangement to encode and form the molecular barcode. [Fig. 3A shown below with all parts labeled]
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Regarding claim 2, Mohammed discloses the cleavage site locate between detectable label and identimer(s) [shown above].
Regarding claim 3, Mohammed discloses scaffold portion comprises nucleic acid and peptides combination(e.g. target-specific binding partners, .i.e. recognition moiety 1 and recognition moiety 2, means a molecule (or complex of molecules) that both (1) binds selectively to a target and (2) binds selectively to a probe. They can comprise an antibody, an antibody fragment (e.g., Fab, Fab′, F(ab′)2, single heavy chain, diabody, and the like), an aptamer, a polypeptide, peptide (e.g., a ligand), a nucleic acid, or small molecule (e.g., a suicide substrate of an enzyme of interest). The target-binding functionality will generally be selected based on the character of the target. For example, when the target is a protein, an antibody can often provide the needed selective target-binding functionality. [¶0216-0129]).
Regarding claim 9, Mohammed discloses recognition moiety comprises the cleavage site (e.g. since the recognition moieties are polypeptide and/or nucleic acids, they can be digested/cleaved using endonuclease and protease)
Regarding claims 10 and 11, Mohammed discloses identimer linker between each identimer in the set of identimers [shown above], wherein the linker is native chemical ligation linker [¶0256].
Regarding claim 12, Mohammed discloses the recognition moiety of at least one identimer in the set of identimers comprises a chemical linker, peptide, or nucleic acid (e.g. peptide and/or nucleic acid as explained in claim 3 rejection [[¶0216-0129])
at least one or more of the detectable labels in the set of identimers comprises a fluorophore (e.g. probe, i.e. detectable label, can be fluorophore [¶0230])
each recognition moiety in the set of identimers comprises at least one moiety selected from a protease recognition moiety, an endonuclease recognition moiety, an epitope recognizable by an affinity reagent, a nucleic acid probe recognition moiety, a modified peptide side chain, and an unnatural peptide side chain; (e.g. since the recognition moieties are polypeptide and/or nucleic acids, they can be digested/cleaved using endonuclease and protease).; and/or
the molecular barcode is attached to a bead. (e.g. the molecule can be attached to a bead [¶0237])
Regarding claim 16, Mohammed discloses the bead is further attached to a test agent (e.g. the reference used Dynabeads M-270 Epoxy beads, which are coated by covalent binding to primary amino (-NH2) and sulfhydryl (-SH) groups [¶0270]).
Regarding claim 18, Mohammed discloses a material having mutual information with the three-dimensional arrangement of the molecular barcode. ( e.g. All three probes simultaneously produce detectable signal corresponding presence of target molecule [Abstract])
Conclusion
No claims are allowed
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Khai Quynh Tien Pham whose telephone number is (571)272-6998. The examiner can normally be reached M-T, 9-4 ET.
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/KHAI QUYNH TIEN PHAM/ Examiner, Art Unit 1684
/JEREMY C FLINDERS/ Primary Examiner, Art Unit 1684
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