Notice of Pre-AIA or AIA Status
1. 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
2. Applicant's election with traverse of group I, claims 1-4, 6, 8, 10-13, 17, and 19-20 in the reply filed on 13 May 2025 is acknowledged. The traversal is on the grounds that prior art Chu et al (WO2018144217A1) does not teach the fully single-stranded DNA adapters of claim 1. Upon further consideration, a more closely related reference was identified and applied herein. Schnable et al (US20150344947) teaches the technical feature linking groups I and II (as discussed herein) and therefore this feature is not a special technical feature.
Claim Objections
3. Claim 1 is objected to because of the following informalities: Applicant has amended claim 1 to include the phrase “wherein the buffer region comprises a nucleic acid sequence 4-8 base pairs in length.” Applicant is claiming a product of forward and reverse single-stranded DNA adapters, therefore it is believed that this should read ‘4-8 nucleotides in length.” Appropriate correction is required.
Claim Rejections - 35 USC § 102
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. Claims 1-2, 8, 10-12, and 19 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by NEB (NEB Catalog, Quick reference guide, published 1996).
Regarding claim 1, NEB teaches a composition of single-stranded DNA primers 24 nucleotides in length (catalog #1256). The composition comprises all possible 24mer oligonucleotides.
As the calculation below shows, about 9 molecules of every single 24-mer are present in each tube of the 24 nucleotide mixtures.
a. Molecular weight of 24-mer:
24 x 325 Daltons/nucleotide = 7,800 Daltons = 7,800 g/mol
b. Total number of possible 24-mers:
424 = 2.8 x 1014 molecules
c. How many molecules of 24-mer in a vial sold by NEB:
1 A260 unit = 33 µg = 3.3 x 10-5 g
3.3 x 10-5 g / 7,800 g/mol = 4.2 x 10-9 mol
(4.2 x 10-9 mol) x (6.02 x 1023 molecules/mol) = 2.5 x 1015 molecules
d. How many molecules of each 24-mer in a single vial:
2.5 x1015 molecules / 2.8 x 1014 molecules = 9 molecules/vial.
Without further claim limitations, any individual primer in this composition is inherently a forward ssDNA adapter and any other individual primer in this composition is inherently a reverse ssDNA adapter. These forward and reverse adapters are single stranded nucleic acids, and any region in each of the adapters inherently comprise regions that correspond to a probe binding region, a 4-8 nucleotide buffer region distal to the probe binding region, a barcode region distal to the buffer region, and a restriction enzyme overhang motif at the 3' end of the adapters (since these are random primers, there will inherently be a pair of primers with enzyme overhang motifs at the 3' end). Additionally, these random primers are inherently synthetic (i.e., non-naturally occurring) sequences consistent with applicant’s specification regarding non-native nucleic acid sequences (applicant’s specification, [0061]).
Regarding claim 2, NEB teaches the ssDNA adapter molecules of claim 1 as discussed fully above, wherein the restriction enzyme motif at the 3' end of the primers comprising a nucleotide sequence complementary to an overhang sequence produced upon cleavage by a restriction enzyme.
Regarding claim 8, without further limitations to the claim any region of the random primer that is 5 to 12 base pairs in length is called a barcode region.
Regarding claim 10, without further limitations to the claim the buffer region of the random primer is chosen to be directly adjacent to the barcode region.
Regarding claim 11, without further limitations to the claim the barcode region of the random primer is chosen to be directly adjacent to the restriction enzyme motif.
Regarding claim 12, without further limitations to the claim, since the probe binding region is comprised of single stranded nucleotides the probe binding region inherently facilitates to a probe (i.e., a separate nucleic acid molecule that is complementary to at least a portion of the nucleic acid sequence of the probe binding region).
Regarding claim 19, NEB teaches a composition of 24 nucleotide random nucleic acid primers (catalog # 1256). Without further claim limitations, this composition inherently comprises a plurality of cos-probes capable of integration into target regions of a genomic template (e.g., by hybridization to overhangs produced by restriction enzyme fragmentation), and the ssDNA adapters of claim 1 as discussed fully above and incorporated here.
Claim Rejections - 35 USC § 103
6. 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.
7. 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.
8. Claims 1-3, 8, 10-12, and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Schnable et al (United States Patent Application No. US 20150344947, published 03 December 2015) in view of Kongsbak (United States Patent Application No. US 20170017820, published 19 January 2017).
Regarding claim 1, Schnable teaches forward and reverse single-stranded DNA (ssDNA) adapter molecules, the adapter molecules comprising: a probe binding region at the 5' end of the adapters (FIG 4, [0012], and [0014]), a buffer region distal to the probe binding region ([0053], without additional limitations to the claims any region of this strand 5' of the barcode region is labeled the probe binding region and any region between the probe binding region and the barcode region is labeled as the buffer region), a barcode region distal to the buffer region (FIG 4, [0010] and [0053]) and that both of the adapter oligonucleotides comprise barcodes (FIG 4 and claim 22); The barcode is distal to the probe binding region, and when using a shortened primer (e.g., 15 nucleotides) as described in [0053] the region between the primer binding site and the barcode is considered a buffer region (i.e., the barcode is distal to the buffer region, and the buffer region comprises 5 nucleotides: GATCT; see table 1, SEQ ID NO: 1), and a restriction enzyme overhang motif at the 3' end of the adapters (FIG 4 and [0010]).
Schnable teaches that the barcode sequence is “unique” to every barcode oligonucleotide, but does not specifically teach that the barcode sequence comprising a non-naturally occurring sequence.
However, Kongsbak teaches that barcode sequences are made by generating sequences known to not be present in any naturally occurring nucleic acid ([0035]).
It would have been obvious to have modified the barcode sequence taught by Schnable with the non-naturally occurring barcode sequence taught by Kongsbak to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Kongsbak specifically teaches that barcodes comprising non-naturally occurring sequences are used to tag or identify a DNA fragment without being confused with any part of the fragment ([0035]). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in barcoding nucleic acids for sequencing experiments.
Regarding claim 2, Schnable teaches that the barcode oligonucleotides comprise a region complementary to “the overhang,” i.e., where the genomic DNA is fragmented by restriction enzymes (FIG 4, [0009] and [0010]).
Regarding claim 3, Schnable teaches that the adapters are bound to a genomic DNA fragment via a region on the adapter that is complementary to the overhangs produced by genomic DNA fragmentation (FIG 4, [0009] and [0010]).
Regarding claim 4, Schnable teaches the ssDNA adapters of claim 1 as discussed fully above and incorporated here. Schnable additionally teaches restriction enzymes that produce 3' overhangs (FIG 4 and [0012]). It is noted that although the claim states that the restriction enzyme produces 5' overhangs, this is being interpreted as a typographical error in light of the applicant’s specification, as applicant specifically discusses hybridization of the adapter to 3' overhangs produced by fragmentation of the genomic DNA in FIG 1A-D and [0045].
Regarding claim 8, Schnable teaches a barcode having a length of 6 nucleotides ([0047]).
Regarding claim 10, Schnable teaches a buffer region directly adjacent to a barcode region (SEQ ID NO: 1 and [0053]). Schnable additionally teaches that primers are barcodes can be of different lengths in the ssDNA adapter ([0053] and [0047]). Additionally, without further limitations in the claims any region between the probe binding region and the barcode region is a buffer region that is directly adjacent to the barcode region.
Regarding claim 11, Schnable teaches that the barcode region is directly adjacent to the restriction enzyme motif (FIG 4 and SEQ ID NO: 1; barcode region = TATATG, restriction enzyme motif = CATG).
Regarding claim 12, Schnable teaches a probe binding region as discussed fully above and incorporated here. Since the ssDNA adapter comprises single-stranded stretches of nucleotides, these adapters inherently comprise probe binding regions that facilitate binding to a probe (i.e., any nucleic acid complementary to a portion of the probe binding region).
Regarding claim 17, Schnable teaches a double-stranded genomic DNA fragment comprising the ssDNA adapters of claim 1 appended to each end of the genomic DNA fragment (FIG 4).
Response to Arguments
9. Previous rejections under U.S.C. 101, 112(a) and 112(b) have been overcome by amendments to the claims and/or cancellation of claims 4 and 20.
Applicant's arguments filed 16 October 2025 have been fully considered but they are not persuasive.
Applicant argues that the buffer region was ascribed to the primers (referenced in Schnable [0053]) rather than the adapters in in table 1 of Schnable, however, [0053] of Schnable was referenced regarding the length of the primers taught by Schnable (e.g., a 15 nucleotide primer) with respect to the barcoded adapters taught by Schnable in table 1. Schnable teaches a 20 nucleotide 5' region of the barcoded oligonucleotide, a barcode, and a restriction enzyme binding motif, when using a 15 nucleotide primer (i.e., a probe that binds the claimed probe binding region) the intervening 5 nucleotide region on the barcoded oligonucleotide taught by Schnable is considered the buffer region (i.e., a buffer region of 4-8 nucleotides). Therefore this argument is not persuasive.
Kongsbak has been used to modify this rejection in order to address applicant’s amendment wherein the barcode comprises a non-naturally occurring sequence.
10. Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Conclusion
11. No claims are allowed.
12. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-F 0730 - 1700.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682