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 previously canceled claims 15-19, 22, 26-30 and 32-54. Claims 1-14, 20-21, 23-25 and 31 are currently pending. Claim 31 remains withdrawn as being drawn to a nonelected group. Claims 1-14, 20-21 and 23-25 are under examination.
Any rejection of record in the previous office actions not addressed herein is withdrawn. New grounds of rejection are presented herein that were not necessitated by applicant’s amendment of the claims since the office action mailed May 23, 2025. Therefore, this action is not final.
Information Disclosure Statement
The Information Disclosure Statements filed November 03, 2025; and January 14, 2026, have been considered.
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 1-2, 6-13, 20-21 and 23-25 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Jacobson et al. (US 2012/0220497 A1, published August 30, 2012), cited on the IDS filed December 22, 2021. This is a new rejection.
Regarding claim 1, Jacobson teaches a method of assembling a DNA strand from oligonucleotide fragments (Page 5, [0057] and Page 23, [0140]). Jacobson teaches providing one or more solid supports primed with a plurality of oligonucleotide capture elements in a microfluidic device (Page 3, [0013], Page 20, [0126] and Fig. 15). Jacobson teaches flowing an oligonucleotide fragment mixture across the one or more solid supports to induce annealing based on the plurality of oligonucleotide capture elements and oligonucleotide fragments in the oligonucleotide fragment mixture (Page 2, [0008], Pages 2-3, [0011], Page 3, [0013]-[0014], Page 7, [0067] and Pages 21-22, [0129]). Jacobson teaches joining the annealed oligonucleotide fragments into a plurality of assembled DNA strands, each assembled DNA strand corresponding to a single capture element in the plurality of oligonucleotide capture elements (Pages 5-6, [0057]-[0059]).
Regarding claim 2, Jacobson teaches flowing an error correction enzyme across the plurality of assembled DNA strands to create cleaved DNA strands and whole DNA strands (Page 7, [0067], Page 17, [0116]-[0117], Page 21, [0128], Page 24, [0143] and Figure 19E). Jacobson teaches flowing amplification primers across the assembled DNA strands to create free double stranded DNA, wherein the amplification primers only match the whole DNA strands (Page 7, [0067], Pages 10-11, [0082], Page 17, [0116]-[0117], Page 21, [0128], Page 24, [0143] and Figure 19E).
Regarding claims 6-8, Jacobson teaches an oligonucleotide diffusion distance is 500, 200 or 100 microns or less (Page 6, [0062], Page 8, [0073], Page 12, [0091], Pages 18-19, [00120] and Page 19, [0123]).
Regarding claims 9-12, Jacobson teaches the DNA assembly method is completed in 1 hour, 20 minutes, 5 minutes, 1 minute or less (Page 13, [0094] and Pages 18-19, [0120]).
Regarding claim 13, Jacobson teaches the one or more solid supports are arranged substantially in single file (Figures 5 and 7B).
Regarding claim 20, Jacobson teaches the one or more solid supports comprises one or more beads (Page 6, [0062] and Page 7, [0069]).
Regarding claim 21, Jacobson teaches the one or more solid supports comprises a support matrix located in a chamber, or channel, of the microfluidic device (Page 24, [0144], Page 6, [0063], Page 7, [0067] and Pages 21-22, [0129]-[0130]).
Regarding claim 23, Jacobson teaches the one or more solid supports comprises a chamber wall of the microfluidic device (Page 24, [0144], Page 6, [0063], Page 7, [0067] and Pages 21-22, [0129]-[0130]).
Regarding claim 24, Jacobson teaches the one or more solid supports comprises a channel wall of the microfluidic device (Page 24, [0144], Page 6, [0063], Page 7, [0067] and Pages 21-22, [0129]-[0130]).
Regarding claim 25, Jacobson teaches the one or more solid supports comprises a flat substrate (Page 9, [0076] and Page 12, [0092]).
Jacobson teaches each and every limitation of claims 1-2, 6-13, 20-21 and 23-25, and therefore, Link anticipates claims 1-2, 6-13, 20-21 and 23-25.
Claim Rejections - 35 USC § 103
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 3-5 are rejected under 35 U.S.C. 103 as being unpatentable over Jacobson et al. (US 2012/0220497 A1, published August 30, 2012), cited on the IDS filed December 22, 2021, as applied to claims 1-2, 6-13, 20-21 and 23-25 above, in view of Eckhardt et al. (U.S. Patent Application Publication US 2016/0068901 A1, published March 10, 2016), cited on the IDS filed December 22, 2021. This is a new rejection.
Regarding claim 3, Jacobsen teaches sequencing double stranded DNA (Pages , [0144] Page 5, [0057], Page 13, [0097] and Page 14, [0099]).
Regarding claim 4, Jacobson teaches flowing amplification primer corresponding to DNA strand across the plurality of assembled DNA strands to create cloned strands of DNA strands (Pages 2-3, [0008], Page 3, [0011], Page 6, [0059], Page 7, [0067], Page 13, [0097], Page 14, [0100], Pages 15-16, [0106], Page 16, [0108]-[0109] and Page 24, [0144])
Regarding claim 5, Jacobson teaches mixing the amplification primer corresponding to DNA strands with the free double stranded DNA to create cloned strands (Pages 2-3, [0008], Page 3, [0011], Page 6, [0059], Page 7, [0067], Page 13, [0097], Page 14, [0100], Pages 15-16, [0106], Page 16, [0108]-[0109], Page 19, [0123] and Page 24, [0144]).
Jacobson does not teach or suggest selecting one of the sequenced free double stranded DNA as a perfect DNA strand and selecting an amplification primer corresponding to the perfect DNA strand. Jacobson does not explicitly teach or suggest flowing the amplification primer corresponding to the perfect DNA strand across the plurality of assembled DNA strands to create cloned strands of the perfect DNA strand. Jacobson does not teach or suggest mixing the amplification primer corresponding to specifically the perfect DNA strand with the free double stranded DNA to create cloned strands of specifically the perfect DNA strand. Jacobson does not teach or suggest each assembled DNA strand comprises a target DNA strand linked to a corresponding unique molecular identifier.
Eckhardt teaches sequencing methods for DNA error correction that may be used in droplet based microfluidic systems (Page 2, [0015], and Page 1, [0005]). Eckhardt teaches sequencing free double-stranded DNA (Page 17, [0150], Page 11, [0076] and Figure 4). Eckhardt teaches using a bead as a solid support (Page 1, [0005]). Eckhardt teaches free double stranded DNA (Page 7, [0027]). Eckhardt teaches amplifying perfect DNA strands which has 100% sequence identity to a template nucleic acid after error-correction by pyrosequencing (Page 10, [0070]. Eckhardt teaches bead free perfect strand DNA that may be flanked with primer sequences for use in amplification (Page 10, [0070]). Eckhardt teaches using the amplification primers corresponding to the perfect DNA strand with the free double stranded DNA to create cloned strands of the perfect DNA strand (i.e., amplifying the perfect DNA in the sample to increase the quantity if perfect DNA (cloning), Page 10, [0070] and Page 11, [0076]-[0080]). Eckhardt teaches as the length of the oligonucleotide sequences are increased, the probability of the oligonucleotides containing errors is also increased and because the oligonucleotides used to construct a DNA sequence may contain errors, the resulting pool of synthesized DNA strands may also contain errors (Page 16, [0142]). Eckhardt teaches using this pyrosequencing method allows one to eliminate imperfect DNA strands and resulting in a sample that is error free, which may be used for diagnosing or screening nucleotide repeat disorders (Pages 9-10, [0050]-[0053]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to have modified the teachings of Jacobson with the teachings of Eckhardt, to select one of the sequenced free double stranded DNA as a perfect DNA strand and selecting an amplification primer corresponding to the perfect DNA strand as well as flowing the amplification primer corresponding to the perfect DNA strand across the plurality of assembled DNA strands to create cloned strands of the perfect DNA strand. This would allow one to create an error free sample which may be used for diagnosing or screening nucleotide repeat disorders, as taught by Eckhardt (Pages 9-10, [0050]-[0053]).
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Jacobson et al. (US 2012/0220497 A1, published August 30, 2012), cited on the IDS filed December 22, 2021, as applied to claims 1-2, 6-13, 20-21 and 23-25 above, in view of Fu et al. (U.S. Patent Application Publication US 2016/0257993 A1, published September 08, 2016), cited on the IDS filed December 22, 2021. This is a new rejection.
Regarding claim 14, Jacobsen teaches each oligonucleotide capture element comprises a unique molecular identifier (Pages 21-22, [0129], Page 18, [0117] and Page 7, [0069]).
Jacobson does not expressly teach or suggest each assembled DNA strand comprises a target DNA strand linked to a corresponding unique molecular identifier.
Fu teaches labeling nucleic acids in a sample with barcode (Abstract). Fu teaches that the nucleic acids target may be double stranded DNA (Page 3, [0011], Page 9, [0083] and Page 24, [0191]). Fu teaches the oligonucleotides are attached to a solid support, (Page 2, [0009] and Page 5, [0016]). Fu teaches the oligonucleotide attached to the solid support is also attached to target that is labeled with a distinct stochastic barcode (Page 3, [0011]). Fu teaches the solid support may be a bead, a matrix, a chamber wall or flat substrate (Page 5, [0016], Page 9, [0077], Page 17, [0136] and Page 18, [0141]-[0142]). Fu teaches using a first and second amplification primer on the oligonucleotide with the target that is labeled with a distinct barcode (Page 3, [0011]). Fu teaches that the sample used may be analyzed with a microfluidic device, cell sorting device as well as in a droplet in an emulsion (Page 9, [0075] and Pages 20-21, [0164]). Fu teaches using the uniquely labeled targets can allow one to create a high resolution three dimensional spatial map showing the location multiple targets (Page 38, [0234]-[0236]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to modify the teachings of Jacobson with the teachings of Fu, using each oligonucleotide capture element comprises a unique molecular identifier and each assembled DNA strand comprises a target DNA strand linked to a corresponding unique molecular identifier. This would allow one to create a high resolution three dimensional spatial map showing the location multiple targets, as taught by Fu (Page 38, [0234]-[0236]).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-2, 21 and 23-24 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 72 of copending Application No. 17/420,988 (reference application). This rejection is maintained.
Although the claims at issue are not identical, they are not patentably distinct from each other because the preambles are slightly different, it appears that the steps of the claims are identical, so it would be obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to perform a method of DNA assembly or a method of assembling a DNA strand using those same steps. Therefore, the claims are not deemed to be patentably distinct.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant’s arguments and amendments filed June 03, 2024, with respect to the
rejections under 35 U.S.C. § 112, 102 and § 103 have been fully considered and are persuasive.
Therefore, these rejections have been withdrawn.
However, upon further consideration, new rejections under 35 U.S.C. § 102 and 103 are set forth above.
Additionally, applicant asserts that the double patenting rejection “will be addressed once it becomes the only remaining rejection”. Therefore, the nonstatutory double patenting rejection is maintained as set forth above.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684