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 reply to the February 09, 2026 Office Action, filed July 09, 2026 is acknowledged. 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 Claim 31 remains withdrawn as being drawn to a nonelected group.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Any objection or rejection of record in the previous Office Action, which is not addressed in this action has been withdrawn in light of Applicant’s amendments and/or arguments. This action is Final.
Claim Interpretation
The term “capture element” is being interpreted to include any element involved in the capture process, including solid supports and/or beads. Therefore, any component included in the capture process would fall within the scope of the definition.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 13 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 13 is considered vague and indefinite for the following reasons:
In claim 13, line 1, the term “substantially” is unclear and confusing. The term “substantially” is not defined in the specification, so one would not be able to tell how many of the solid supports must be arranged in single file. Is it all solid supports? Or are some allowed to be side by side in orientation? If so, how many?
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 Church et al. (U.S. Patent Application Publication US 2007/0269870 A1, published November 22, 2007. This is a new rejection as necessitated by amendments.
Regarding claim 1, Church teaches a method of assembling a DNA strand from oligonucleotide fragments (Title, Abstract, Page 1, [0007] and Figs. 2-7). Church teaches providing one or more solid supports primed with a plurality of oligonucleotide capture elements in a microfluidic device (Page 15, [0131]-[0135], Page 21, [0172] and Page 28, [0205]). Church 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 (Pages 12-13, [0122], Page 13, [0124], Page 15, [0131]-[0135], Page 17, [0145], Pages 19-20, [0161], Page 21, [0172], Page 23, [0184]-[0185], Page 28, [0205], Page 29, [0210], Page 32, [0226]-[0227], Page 38, [0265]-[0266]). Church teaches flowing the oligonucleotide fragment mixture comprises capturing one or more oligonucleotide fragments on one or more of the plurality of oligonucleotide capture elements and flowing additional oligonucleotide fragments across the captured oligonucleotide fragments (Pages 12-13, [0122], Page 13, [0124], Page 15, [0131]-[0135], Page 17, [0145], Pages 19-20, [0161], Page 21, [0172], Page 23, [0184]-[0185], Page 28, [0205], Page 29, [0210], Page 32, [0226]-[0227], Page 38, [0265]-[0266]). Church 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 (Page 7, [0079]-[0080], Page 16, [0138], Page 20, [0162]-[0163] and Figs. 2-3).
Regarding claim 2, Church teaches flowing an error correction enzyme across the plurality of assembled DNA strands to create cleaved DNA strands and whole DNA strands (Page 27, [0202], Page 4, [0043], Page 6, [0073], Page 7, [0075], Page 29, [0210]). Church 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 20, [0162] and [0167], Page 28, [0205] and Page 27, [0197]).
Regarding claims 6-8, Church teaches an oligonucleotide diffusion distance is 500, 200 or 100 microns or less (Page 33, [0234] and [0236]).
Regarding claims 9-12, Church teaches the DNA assembly method is completed in 1 hour, 20 minutes, 5 minutes, 1 minute or less (Example 4).
Regarding claim 13, Church teaches the one or more solid supports are arranged substantially in single file (Page 15, [0131]).
Regarding claim 20, Church teaches the one or more solid supports comprises one or more beads (Page 16, [0140]).
Regarding claim 21, Church teaches the one or more solid supports comprises a support matrix located in a chamber, or channel, of the microfluidic device (Page 16, [0140] and Page 15, [0135]).
Regarding claim 23, Church teaches the one or more solid supports comprises a chamber wall of the microfluidic device (Page 21, [0172], Page 16, [0140] and Page 15, [0135]).
Regarding claim 24, Church teaches the one or more solid supports comprises a channel wall of the microfluidic device (Page 21, [0172], Page 16, [0140] and Page 15, [0135]).
Regarding claim 25, Church teaches the one or more solid supports comprises a flat substrate (Page 16, [0140]).
Church teaches each and every limitation of claims 1-2, 6-13, 20-21 and 23-25, and therefore, Church 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 Church et al. (U.S. Patent Application Publication US 2007/0269870 A1, published November 22, 2007, 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 as necessitated by amendments.
Regarding claim 3, Church teaches sequencing (Page 32, [0227]-[0228] and Page 34, [0241]).
Regarding claim 4, Church teaches flowing amplification primer corresponding to DNA strand across the plurality of assembled DNA strands to create cloned strands of DNA strands (Page 20, [0167], Pages 21, [0170], Page 27, [0203], Page 41, [0291], Page 42, [0304] and Example 5). Church teaches creating perfect DNA strands (Page 31, [0220]).
Regarding claim 5, Church teaches mixing the amplification primer corresponding to DNA strands with the free double stranded DNA to create cloned strands (Page 20, [0167], Pages 21, [0170], Page 27, [0203], Page 41, [0291], Page 42, [0304], Page 20, [0162] and [0167], Page 28, [0205] and Page 27, [0197] and Example 5).
Church 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. Church 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. Church 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.
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 have 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 Church 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 Church et al. (U.S. Patent Application Publication US 2007/0269870 A1, published November 22, 2007, 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 as necessitated by amendments.
Regarding claim 14, Church teaches each oligonucleotide capture element comprises a unique molecular identifier (Page 37, [0260], Page 5, [0063], Page 16, [0138] and Page 26, [0199]).
Church 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 Church 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 July 09, 2026, with respect to the
rejections under 35 U.S.C. §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 made in view of Applicant’s amendments.
As discussed above newly cited Church discloses flowing the oligonucleotide fragment mixture comprises capturing one or more oligonucleotide fragments on one or more of the plurality of oligonucleotide capture elements and flowing additional oligonucleotide fragments across the captured oligonucleotide fragments as well as the oligonucleotide fragments are tethered to the one or more solid supports during and after assembly.
Therefore, for all these reasons, and those listed above, Church and Church in view of Eckhardt as well as Church in view of Fu are deemed to render the instant invention anticipated/obvious.
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
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.
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
