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 .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on November 6th, 2023 is acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Election/Restrictions
Applicant’s election without traverse of Group III, claims 15-19 and new claims 21-27, in the reply filed on January 27th, 2026 is acknowledged.
Claim Status
Claims 1-14 and 20 have been canceled. Claims 21-27 have been added. Claims 15-19 and 21-27 are pending. Claims 15-19 and 21-27 are under examination and discussed in this Office action
Claim Objections
Claim 19 is objected to because of the following informalities: the listing of proteins lacks a comma before “and UvsX”. Appropriate correction is required.
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.
Claims 15-18, 21-24, and 26 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Chenchik et al (US 20210301329 A1, published September 30, 2021; cited on the IDS filed November 06th, 2023).
Regarding claim 15, Chenchik teaches a method of preparing barcoded nucleic acids that includes producing a plurality of partitioned cell/barcoded bead complexes from a cellular sample and a plurality of distinct barcoded beads comprising barcoded reverse gene-specific primers (claim 1-3; [0019; 0034]). Chenchik explains that barcoded beads are particles having barcoded oligonucleotides attached thereto, where the barcoded oligonucleotides may include temple-binding domains or gene-specific primer domains complementary to target nucleic acid sequence [0019].
Chenchik further teaches that the cell/barcoded bead complexes are partitioned such that nucleic acids from one complex do not interact with nucleic acids from another complex, and that partitioning may be performed using droplet-based methods or microwells (claims 2-3; [0034]). Chenchik further teaches hybridizing gene-specific temple binding domains of the barcoded reverse gene-specific primers to template nucleic acids of the cells to produce primed template nucleic acids (claim 1; [0061-0062]). Chenchik also teaches that the reaction mixtures used for primer extension may include additives such as single-stranded nucleic acid binding proteins, including RecA protein [0069].
Regarding claim 16, Chenchik teaches releasing the barcoded reverse gene-specific primers from the barcoded beads prior to hybridization, such as by cleavage of a photosensitive linker (e.g. via exposure to UV light), which allows the primers to hybridize with complementary RNA molecules (claim 7; [0061]).
Regarding claim 17, Chenchik teaches that oligonucleotides attached to a given bead share the same barcode domain, such that the majority of oligonucleotides on any given bead have identical sequences [0019]. Chenchik further teaches that different beads within a plurality of barcoded beads have different barcode sequences from one another [0039]. Accordingly, the barcode sequence present on the oligonucleotides of a given bead serves to distinguish those oligonucleotides from the oligonucleotides on a different bead, which carry a different barcode sequence.
Regarding claim 18, Chenchik teaches partitioning cell/barcoded bead complexes into physically separated compartments, including microwells (claim 3; [0034]).
Regarding claim 21, Chenchik teaches that the target nucleic acids released from cells include RNA molecules such as mRNA, which bind to barcoded reverse gene-specific primers following cell lysis [0061].
Regarding claim 22, Chenchik teaches that the nucleic acids present or released form a single cell may include RNA and DNA templates [0034]. Chenchik further teaches that the hybridization step may include treatment of DNA to make it more accessible for hybridization with the barcoded reverse gene-specific primers [0061].
Regarding claim 23, Chenchik teaches that single-cell analysis, each compartment/partition usually contains one cell and one bead, where the bead carries a unique barcode [0007].
Regarding claim 24, Chenchik teaches that the partitions can be droplets, where each droplet contains a cell and a barcoded bead (claim 2; [0034]).
Regarding claim 26, Chenchik teaches the method of claim 15. Chenchik teaches partitioning cell-barcoded bead complexes into water in oil microdroplets using a ddSeq droplet generator instrument with an oil-surfactant composition comprising EvaGreen [0132]. EvaGreen is a green fluorescent nucleic acid dye that is essentially non-fluorescent upon binding to double-stranded DNA, and is used in a wide variety of applications including digital PCR and real-time monitoring of nucleic and amplification reactions.
For the reasons given above, claims 15-18, 21-24 and 26 are anticipated by Chenchik.
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 15, 19, 25, and 27 are rejected under 35 U.S.C. 103 as being unpatentable over Chenchik et al (US 20210301329 A1, published September 30, 2021; cited on the IDS filed November 06th, 2023), in view of Kovalenko (A novel nucleic acid-binding protein that interacts with human Rad51 recombinase, Nucleic Acids Research, 1997, 25(24), 4946-4953).
Regarding claim 15, Chenchik teaches a method of preparing barcoded nucleic acids as discussed in the 35 U.S.C. 102 rejection above. However, Chenchik’s disclosure is limited to RecA and does not extend to the broader genus of recombination proteins or DNA repair proteins.
Kovalenko, in a reasonably pertinent field, teaches that human Rad51 is a recombination protein and DNA repair protein that binds both single-stranded and double-stranded DNA in a non-sequence specific manner, forming RecA-like nucleoprotein filament on DNA. Rad51 is the eukaryotic structural and functional homolog of RecA (p. 4946, left column, para 2; p. 4952, left column, para 5 – right column, para 1), thereby sharing the same class of non-sequence specific nucleic acid binding activity. RecA promotes DNA aggregation upon pairing of homologous sequences present on different DNA molecules by facilitating nucleic acid interactions in a reaction mixture, and describes a simple assay for this activity consisting of centrifugation of a reaction mixture containing DNA and analyzing the partitioning of DNA between pellet and supernatant, establishing that RecA-family proteins including Rad51 are known to facilitate nucleic acid interactions in reaction mixtures (p. 4952, left column, para 2).
It would have been obvious to one of ordinary skill in the art, before the effective filling date of the claimed invention, to have modified the method of Chenchik to use Rad51 or other RecA-family recombination proteins as the non-sequence specific nucleic acid binding protein in the claimed method. One of ordinary skill in the art would have been motivated to make this modification because Kovalenko teaches that Rad51 is the eukaryotic functional homolog of RecA with the same class of non-sequence specific nucleic acid binding and nucleoprotein filament forming activity and Chenchik did teach that RecA is a suitable additive in a nucleic acid reaction mixture, such that a skilled artisan would have had a reasonable expectation that other RecA-family proteins including Rad51 would function in the same capacity.
Regarding claim 19, Chenchik, as evidenced by Kovalenko, teaches the methods of claim 15. Chenchik as described above teaches a non-sequence specific nucleic acid binding protein that is a recombination protein, specifically RecA [0069]. Kovalenko teaches the human Rad51 is a recombination protein and DNA repair protein with non-sequence specific nucleic acid binding activity that is the eukaryotic functional homolog of RecA (p. 4946, left column, para 2).
Regarding claim 25, Chenchik, as evidenced by Kovalenko, teaches the method of claim 15. As described above, Chenchik teaches a reaction mixture comprising multiple non-sequence specific nucleic acid binding proteins, including RecA. RecA is listed as additives in the primer extension reaction mixture without suggesting mutual exclusivity [0069].
Kovalenko teaches both RecA and Rad51 as non-sequence specific nucleic acid binding proteins belonging to the same functional class of recombination proteins. Specifically, Kovalenko characterizes human Rad51 as the eukaryotic structural and functional homolog of RecA that shares the same class of non-sequence specific nucleic acid binding activity and forms nucleoprotein filaments of DNA (p. 4946, left column, para 2). Kovalenko further discusses RecA as a protein that promotes DNA aggregation upon pairing of homologous sequences by facilitating nucleic acid interactions (p. 4952, left column, para 2). Kovalenko therefore teaches that RecA and Rad51 are two different non-sequence specific nucleic acid binding proteins that are known to function in nucleic acid binding proteins and that a skilled artisan would recognize as member of the same functional class of recombination proteins.
It would have been obvious to one of ordinary kill in the art, before the effective date of the claimed invention, to have modified the method of Chenchik to include at least two different non-sequence specific nucleic acid binding proteins, specifically RecA and Rad51, in the same partitions. One of ordinary skill in the art would have been motivated to do so because Chenchik discloses multiple non-sequence specific nucleic acid binding proteins together in the reaction mixture without suggesting that only one may be used at a time [0069], and Kovalenko establishes that RecA and Rad51 are two well-characterized members of the same functional class of non-sequence specific nucleic acid binding proteins with nucleic acid binding activities.
Regarding claim 27, Chenchik, as evidenced by Kovalenko, teaches the methods of claim 15. The instant application identifies SEQ ID NO:4 directs UniProt accession number Q06609 as an exemplary Rad51 protein [0055]. Kovalenko’s article is listed as a publication associated with Uniport accession Q06609 for human Rad51. Kovalenko teaches that human Rad51 is a recombination protein with non-sequence specific nucleic acid binding activity that forms RecA-like nucleoprotein filaments on DNA [p. 4946, left column, para 2].
Conclusion
All claims are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Nura Choudhury whose telephone number is (571)272-6148. The examiner can normally be reached M-F, 9-5 ET.
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/NURA M. CHOUDHURY/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683