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 . Applicant’s amendment filed 12/9/2025 is acknowledged. Claims 1-17 and 25-29 have been canceled. Claims 18-24 are pending. All of the amendment and arguments have been thoroughly reviewed and considered. Applicant’s arguments were found persuasive to obviate the rejections of the prior Office action.
This action is made non-final as the new grounds of rejections presented in this Office action are necessitated by Applicant’s amendment of the claims.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Previous Rejection
2. The prior art rejection under 35 USC 102(a)(2) as being anticipated by Gary et al is withdrawn in view of Applicant’s arguments. The prior art rejection under 35 USC 103 as being unpatentable over Drmanac
NEW GROUNDS OF REJECTIONS
Claim Rejections - 35 USC § 102
3. 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.
4. 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.
5. Claim(s) 18-24 is/are rejected under 35 U.S.C. 102(a)(1) and/or alternatively 35 USC 102(a)(2) as being anticipated by Jiang et al (US 20180044668, published 2/15/2018, effective filing date 10/13/2015).
The claims are drawn to a barcoded solid support comprising a concatemer disposed on a solid support, wherein the concatemer comprises a plurality of linked units, each unit comprising a barcode and a stem loop structure and wherein a plurality of the stem-loop structures extend from the surface of the solid support.
Regarding claims 18-24, Jiang et al teach concatemers that can be disposed on a surface ([0036] –{0037]) wherein said surface comprises paramagnetic beads [0047], [0200]., [0212]. Jiang et al further teach circular mate-pair polynucleotide construct comprising a mate pair of polynucleotide arms, a first adapter, and a second adapter are used to generate concatemers of the circular construct. These concatemers are also referred to herein as “nucleic acid nanoballs,” “DNA nanoballs,” and “DNB” [00196]. At the following paragraphs, Jiang teaches:
[0197] The concatemers comprise multiple copies, in tandem, of the mate-pair polynucleotide construct comprising the mate-pair polynucleotide arms, first adapter, and second adapter. In some embodiments, the concatemer comprises tens to hundreds of copies of the mate-pair polynucleotide construct, e.g., about 100 to about 500 copies, about 100 to about 400 copies, about 150 to about 400 copies, about 150 to about 300 copies, or about 150 to about 250 copies.
[0198] Concatemers of the mate-pair constructs may be produced by any of a variety of methods, including but not limited to, Rolling Circle Replication (RCR) and Circle Dependent Amplification (CDA).
[0202] RCR is used to generate concatemers of the mate-pair constructs as described herein. The RCR process relies upon the desired target polynucleotide being in a circular form. RCR uses the original circular polynucleotide, not copies of a copy, which ensures fidelity of sequence. Furthermore, as a circular entity, the circular mate-pair construct acts as an endless template for a strand-displacing polymerase that extends a primer complementary to a portion of the circle (e.g., in an adapter region). The continuous strand extension creates a long, single-stranded polynucleotide consisting of multiple (e.g., tens or hundreds) of concatemers comprising multiple copies of sequences complementary to the circular polynucleotide. The single-stranded polynucleotide comprising the concatemers can fold upon itself to form a three-dimensional ball (the DNB), which can subsequently be disposed on a surface or making DNB arrays.
[0206] Linear single-stranded polynucleotides (e.g., linear single-stranded polynucleotide constructs comprising a mate-pair of polynucleotide arms, a first adapter, and a second adapter) are circularized in the presence of both the 3′ end-blocked splint and the strand-specific amplification primer using a suitable ligase (e.g., T4 DNA ligase). The ligation products are then treated with an exonuclease (e.g., Exonuclease I) to remove non-circularized linear strands and excess non-annealed splint oligonucleotides. Single-stranded DNA circles are then purified from the free oligonucleotides and nuclease(s) using magnetic beads. The RCR reaction components are then combined with the purified ligation products under conditions that permit a DNA polymerase to extend the pre-annealed strand-specific primer to form concatemers of sequences complementary to the circular polynucleotide. Jiang et al teaches at paragraphs wherein the one or more tags or barcodes may be added to the adapter [0119]. Jiang et al teach the use of biotin/streptavidin labeling ([0165] and [0168[).
Thus, Jiang meets the limitations of the claims as recited above.
Conclusion
6. No claims are allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681