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 .
Election/Restrictions
Applicant’s election of Group I (claims 1-24) in the reply filed on 07/22/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claim Rejections - 35 USC § 102
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) 1-14, 16, 18-24 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by O’Connell et al. WO2020/236526
O’Connell et al. discloses a method for determining a sequence of a target polynucleotide with a nanopore-based sequencing system, the method comprising:
providing a target polynucleotide comprising nucleotides, wherein each
nucleotide comprises a modification, wherein the modification comprises a
construct configured to control translocation of the target polynucleotide through
a nanopore; [0094]; [0097]-[0098]; [0107]; applying a driving voltage to translocate one or more portions of the target polynucleotide through a nanopore; measuring a current of the nanopore continuously during translocation; and identifying the sequence of the target polynucleotide by correlating the measured current to an identity of one or more nucleotides ([0051-0059]; [0106];[00128]; figures 13A, 13B).
O’Connell et al. teaches nucleotides comprising arresting construct attached to a cycling loop, a reporter element and spacer (page 4, [0100]-[0105], Figures 7, 8A-8B, claims). O’Connell et al. discloses a compound comprising a Reporter Construct. The Reporter Construct can comprise a hydrophilic polymer (PEG), polyphosphate or combinations thereof, branched polymer, [0035]-[0045]; [0100], (Figs 6-8) (see claims also). The Reporter Construct can comprise an arresting construct (In some aspects, the reporter constructs for parsing the genetic information comprise a reporter code and a translocation control element, wherein the translocation control element provides translocation control by steric hindrance and pauses translocation of the Xpandomer when passed through a nanopore [0052]). Linker A and Linker B can comprise azide-alkyne conjugating moiety and further comprise a first linker between the conjugating moiety and X, and a second linker between the conjugating moiety and SP (see Figure 2). The reporter construct can comprise polymers comprising two or more repeat units [0046]. (This viewed to be inclusive of claims 11-14, 16, 18-22). The reporter construct can comprise elements that are designed for controlling the rate of Xpandomer translocation by the TCE through a combination of sterics and/or electrorepulsion. (This is viewed to be inclusive of claims 23-24).
O’Connell et al. teaches synthesizing a daughter strand and cleaving the daughter strand to generate the target polynucleotide having an elongated polynucleotide strand [0051].
O’Connell et al. teaches “A representative trace illustrating the level discrimination and translocation time of each code is shown in Fig. 13A (control - old codes) and 13B (test - new, PEG-based controls)” (this viewed as the dwell time of claims 7-8) .
O’Connell et al. teaches a baseline voltage [0052-0057]; which is viewed to be inclusive of claim 9.
Claim(s) 1-24 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Salam et al. US 20230357307.
The applied reference has a common inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Salam et al. teaches nanopore sequencing with a polynucleotide comprising a plurality of nucleotides, wherein each nucleotide comprises a linker construct between two positions of the nucleotide, wherein the linker construct optionally comprises a reporter moiety corresponding to the identity of the nucleotide, and wherein the linker construct is a part of the cleavable cyclic loop nucleotide comprising a cleavable site. In some embodiments, the nucleotides further comprise arresting constructs for slowing or halting the polynucleotide translocation through a nanopore (abstract).
Salam et al. teaches a method for determining a sequence of a polynucleotide in a nanopore-based sequencing system, the method comprising: providing a polynucleotide comprising a plurality of nucleotides, wherein each nucleotide comprises a linker construct, the linker construct having a first end attached to the first position of the nucleotide and a second end attached to the second position of the nucleotide; cleaving a cleavable bond on each of the plurality of nucleotide between the first and the second positions, thereby elongating the polynucleotide to form an elongated polynucleotide; applying a voltage to cause the elongated polynucleotide to insert into and translocate through a nanopore; and (i) detecting and identifying a reporter moiety when the linker construct passes through the nanopore; or (ii) detecting and identifying a base on the nucleotide when the nucleotide passes through the nanopore (claims). The signal from that change in current can be measured using any of a variety of methods. Each signal is unique to the species of nucleotide(s) (or linker constructs with a reporter moiety region) in the nanopore, such that the resultant signal can be used to determine a characteristic of the polynucleotide. For example, the identity of one or more species of nucleotide(s) (or probe) that produces a characteristic signal can be determined [0158].
Salam et al. teaches nucleotides comprising arresting construct attached to a cycling loop, a reporter element and spacer (pages 1-7).
Salam et al. provides a method that instead of directly sequencing the sample DNA, a daughter strand is synthesized using cyclic loop nucleotides. In some embodiments, each cyclic loop nucleotide contains a unique barcoding/reporter region that is specific to the original bases (e.g., A, T, C, or G) and a cleavable site. The daughter strand is then “elongated” by cutting the cleavable sites. Consequently, when sequencing the daughter strand, the nanopore can “read” the barcoding/reporter region to identify the base that it is coding for [0005].
Salam et al. teaches the arresting construct is a linear, a branched or a cyclic polymer [0022]. Salam et al. teaches arresting construct comprising one or more of the following moieties: (1) alkyl chains having 5 to 50 carbons, (2) oligonucleotides or modified oligonucleotides having 1 to 100 repeating units, (3) polypeptides having 1 to 100 repeating units, (4) hydrophilic polymers having 1 to 100 repeating units selected from the group consisting of polyethyleneglycol, polyvinyl alcohol, polyacrylamide, polyvinylpyrrolidone, polystyrenesulfonate, and polyethyleneimine, and (5) hydrophobic polymers having 1 to 100 repeating units selected from the group consisting of polylactic acid, polymethylmethacrylate, and polystyrene (pages 8-9). (This viewed to be inclusive of claims 11-22).
Salam et al. teaches “A modification may provide a resistance (in the form of a “holding force”) that slows and/or stops a polynucleotide to translocate through the nanopore unless the resistance due to the modification is overcome by a “driving force.” The resistance provided by the modification is due to a property of the modification (e.g., size, geometry, and/or non-covalent interaction with the nanopore). Modifications can operate as a ratchet or a brake for the polypeptide translocation through a nanopore. A modification can be attached to any part of the nucleotide and can also be attached to the nucleotide at two locations forming a loop. The modification may also be referred to as an arresting construct” [0165]… “the interactions of the spacer with the nanopore—a spacer monomer that is capable of forming stronger interactions (e.g., electrostatic interactions, H-bonding) with nanopore residues is likely to experience slower translocation speed as compared to a monomer that forms weaker interactions (e.g., non-polar interactions); .. the charge of the selected modifications—a loop with higher net negative charge would experience a higher translocation rate (compared to a lower net negative charged loop) in the presence of an applied voltage” [0191]. (This viewed to be inclusive of claims 23-24).
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/JEZIA RILEY/ Primary Examiner, Art Unit 1681 7 August 2026
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