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 .
Status of the Applications, Amendments and/or Claims
This action is written in response to applicant's correspondence submitted 01/07/2026. In the paper of 01/07/2026, Applicant amended claim 1 and canceled withdrawn claims 9-18. Claims 1-5 and 7-18 are pending and still under review.
Response to Arguments
Withdrawn Rejection(s)
The rejection of claims 1-5 and 7-8 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite is withdrawn in view of claim amendments. A new rejection of claims 3 and 5 was necessitated by the claim amendments.
The rejection of claims 1-5 and 7 under 35 U.S.C. 102(a)(2) as being anticipated by Kamberov et al., (WO2015/074017, filed Nov. 18, 2014 and pub. 05/21/2015) is withdrawn based on claim amendments, particularly by newly reciting a step of assembling a dsDNA of desired sequence.
The rejection of claim 8 under 35 U.S.C. 103 as being unpatentable over Kamberov et al., (WO2015/074017, filed Nov. 18, 2014 and pub. 05/21/2015) in view of Loakes et al. (1995, Nucleic acids research, 23(13), pp.2361-2366) and Faure et al. (2005, Biochemical and biophysical research communications, 328(4), pp.1188-1195) is withdrawn for the same stated reasons above, for withdrawal of the rejection of claim 1 under 35 U.S.C. 102(a)(2).
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.
Claims 3, 4 and 5 are 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 3 and claim 5 each recites the limitations “specifically cleaves the first 3' and first 5' primer binding sequences” and “the first 3' and first 5' primer binding sequences”, respectively. The underlined phrases of each limitation renders claim 3 and claim 5 indefinite, as the claims each fail to indicate how to identify a first 3’ and 5’ primer binding sequences where a plurality of pairs of oligonucleotides comprising a 3’ or 5’ primer binding sequence at terminal ends are provided, said plurality of pairs are arranged in order. In the case of claim 3, it is not known if the limitation is directed to providing uracil DNA glycosylase enzyme for acting only on a first oligonucleotide pair in the arranged order, or if something else is intended.
Concerning the structure intended by first 3’ and first 5’ primer binding sequence at the terminal ends, the structure is unclear. As previously stated, if the two pairs of oligonucleotides are assumed for the dsDNA assembly and each of the two pairs are double stranded, it is unclear what ends of each hybridized pair are to be characterized as the first 3’ or the first 5’ end.
Claim 4 recites the limitation “the enzyme mixture”. There is a lack of antecedent basis for this limitation in the claim.
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 1-5 and 7 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Church et al. (US2007/0269870A1, pub. Nov. 22, 2007).
Regarding claim 1, Church et al. teach a method of assembling a double-stranded DNA molecule in a synthesis reaction of a dsDNA molecule of desired sequence (para [0008], [0123]), the method comprising:
providing a plurality of pairs of oligonucleotides, each oligonucleotide of a pair comprising a 3' or a 5' primer binding sequence at the terminal ends having at least one non-standard base (para [0117]-[0118], [0123], [0158], [0299]), and
the 3' or 5' primer binding sequences flank an internal sequence of the dsDNA molecule of a desired sequence to be synthesized, and
wherein each oligonucleotide of a pair comprises a portion of the dsDNA molecule of desired sequence, and when the plurality of pairs of oligonucleotides are arranged in order, adjacent to each other and according to their internal sequences they comprise at least a portion of the desired sequence, and the 3' or 5' primer binding sequences flank an internal sequence that overlaps and is complementary to an internal sequence of the other oligonucleotide of the pair;
amplifying the pairs of oligonucleotides in an amplification reaction using primers that bind to the 3' and 5' primer binding sequences (para [0123], [0158], [0299]);
removing the 3' and 5' primer binding sequences from the plurality of pairs of oligonucleotides using an enzyme that specifically cleaves the primer binding sequences at a non-standard base (para [0129], [0157], [0299]); and
assembling the double-stranded DNA molecule of desired sequence (para [0170], [0313]).
Regarding claim 2, Church et al. teach the non-standard base is deoxyuridine (para [0299]).
Regarding claim 3, Church et al. teach the enzyme that specifically cleaves the 3' and 5' primer binding sequences at a non-standard base is uracil DNA-glycosylase (UDG) (see para [0129], [0152], [0158]).
Regarding claim 4, Church et al. teach an enzyme mixture further comprises endonuclease VIII and exonuclease T (para [0061], [0155], [0157]-[0158], [0299]-[0300]).
Regarding claim 5, Church et al. teach the 3' and 5' primer binding sequences are 6-30 nucleotides in length (para [0159]).
Regarding claim 7, Church et al. do not teach an assembled dsDNA molecule comprising of an expressed sequence tag.
Accordingly, the instant claims 1-5 and 7 are anticipated by Church et al.
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.
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.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Church et al. (US2007/0269870A1, pub. Nov. 22, 2007) in view of Loakes et al. (1995, Nucleic acids research, 23(13), pp.2361-2366: previously cited) and Faure et al. (2005, Biochemical and biophysical research communications, 328(4), pp.1188-1195: previously cited).
The teachings of Church et al. as it relates to claim 1 are above but applied here.
Regarding claim 8, Church et al. do not teach the non-standard base is 3-nitropyrrole and 5-nitroindole as cleavable bases within primer binding sequences at each terminal end of a double stranded oligonucleotide.
Loakes et al. teach the conventional practice of incorporating 3-nitropyrrole and 5-nitroindole into primers as they constitute universal base analog capable of binding all four canonical or standard nucleotides.
Faure et al. suggests nitroindole may be a substrate of AP endonucleases to provide AP sites and/or DNA glycosylases with associated AP lyase activity can also efficiently cleave regular AP sites (abstract).
It would have been obvious before the effective filing date of the instant invention for one having ordinary skill in the art to modify the cleavable base of the adaptors provided in the cleaving method taught by Church et al. by substituting 3-nitropyrrole or 5-nitroindole for the deoxyuridine of the uracil containing primers taught by Church et al. as Loakes et al. teach the ability of 3-nitropyrrole or 5-nitroindole to be functionally equivalent substitute alternative for all nucleotides based on the ability of 3-nitropyrrole or 5-nitroindoleto base pair with any of the four standard nucleotides.
The ordinary skilled artisan would also have been motivated by Faure’s suggestion that abasic site may be generated from action of one or more base excision repair enzymes on nitroindole and therefore use nitroindole in the same capability as deoxyuridine.
In view of the teachings of all the cited references, the instant claim 8 is prima facie obvious.
Conclusion
No claims are presently allowed.
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.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OLAYINKA A OYEYEMI whose telephone number is (571)270-5956. The examiner can normally be reached Monday -Thursday: 9:00 am - 5:00 pm, EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, GARY Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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OLAYINKA A. OYEYEMI
Examiner
Art Unit 1681
/OLAYINKA A OYEYEMI/Examiner, Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681
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