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 Application
The Amendment filed January 13, 2026 is acknowledged.
Claims 1-13 were pending. Claims 1-12 and new claims 14-19 are being examined on the merits. Claim 13 remains withdrawn.
Response to Arguments
Applicant’s arguments filed January 13, 2026 have been fully considered.
The following objections and rejections are WITHDRAWN in view of Applicant’s arguments and claim amendments:
Objection to the Specification
Rejection of claim 2 under 35 USC § 112(b), indefiniteness
Prior art rejection of claim 6, and claims 3 and 7
Response to arguments regarding prior art rejection of claim 6, and claims 3 and 7
Applicant argues that the prior art rejection of claim 6 should be withdrawn, in part, because Nelson does not teach performing RCA with primers comprising the sequences of SEQ ID NOs: 1 or 2, and, even if the ordinary artisan modified the Nelson method with the Ito primer, they would fail to arrive at the claimed method steps (Remarks, p. 9).
While Applicant’s remarks are apparently focused more on the teachings of Nelson as to the RCA method steps rather than the sequences of the primers, per se, the Examiner has re-considered the rejection of claim 6 based on the combined teachings of Nelson and Ito for the reasons discussed below in the Prior Art section.
The rejection of claim 6 is withdrawn.
Applicant argues that the rejection of claims 3 and 7 should be withdrawn, in part, because it would not be obvious to modify Nelson to substitute the recombination protein with a restriction enzyme, such as BamHI, nor would it be obvious to modify the Nelson method to add an additional digestion step. Further, even if the Nelson method was modified in such a way, it would not work for its intended purpose (Remarks, pp. 9-11).
The Examiner has reconsidered the rejection and agrees with Applicant’s arguments.
The rejections of claims 3 and 7 are withdrawn.
The following rejections are MAINTAINED:
Prior art rejections of claims 1-2, 4-5 and 8-12
Response to arguments regarding prior art rejections
Applicant argues that the prior art rejections of, in particular, independent claim 1 should be withdrawn because the cited art does not teach all of the claim limitations. Specifically, Applicant argues that Nelson does not teach the step of adding an endonuclease to produce a linear double-stranded DNA fragment or the subsequent step of converting the linear double-stranded DNA fragment to a circular DNA molecule (Remarks, p. 7). Applicant additionally argues that Nelson, in para. 54, teaches using an endonuclease as “a mutation detection enzyme by incubating generated circular nucleic acids with the endonuclease to eliminate mismatched nucleotides” (Remarks, pp. 7-8).
The Examiner disagrees. Nelson teaches performing RCA to produce a double-stranded DNA product comprising tandem repeat sequences flanked by loxP sites, and then teaches adding a recombination protein (e.g., Cre recombinase, which is an endonuclease1) to “loop out” the expression cassette (i.e., excise the loxP sites and join the ends together) to form a circular DNA (e.g., para. 48). Thus, when the recombination protein excises the loxP sites that creates a linear double-stranded DNA fragment, as recited in the instant claim 1 “adding an endonuclease” clause, and when the ends of the excised fragments are joined together (i.e., “loop[ed]”) that creates a relaxed circular double-stranded DNA molecule, as recited in the instant claim 1 “converting the linear double-stranded DNA” clause.
Applicant additionally argues that the secondary references do not cure the deficiencies of Nelson (Remarks, p. 9).
The Examiner disagrees with Applicant’s characterization of the teachings of Nelson, for the reasons noted above, and consequently disagrees as to Applicant’s characterization of the teachings of the secondary references.
These arguments are not persuasive. The rejections are maintained.
Claim Rejections - 35 USC § 102
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.
Claims 1-2, 4-5 and 8-12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Nelson2 (US Patent Application Pub. No. 2010/0055744 A1).
Regarding independent claim 1, Nelson teaches …
A method for synthesizing a circular double-stranded DNA molecule, the method comprising: providing a nicked circular DNA template comprising two sequence-specific recombination sites (Fig. 1; paras. 5, 27, 30, 33, 34, 35, 39, 40, 41, 48, 50);
performing rolling circle amplification (RCA) to produce a double-stranded DNA product comprising the two sequence-specific recombination sites (Fig. 1; paras. 5, 27, 30, 33, 34, 35, 39, 40, 41, 48, 50);
adding an endonuclease to the double-stranded DNA product to produce a linear double-stranded DNA fragment comprising the two sequence-specific recombination sites (Fig. 1; paras. 5, 27, 30, 33, 34, 35, 39, 40, 41, 48, 50);
converting the linear double-stranded DNA fragment to a relaxed circular double-stranded DNA molecule (Fig. 1; paras. 5, 27, 30, 33, 34, 35, 39, 40, 41, 48, 50);
and converting the relaxed circular double-stranded DNA molecule to a supercoiled double-stranded DNA molecule (para. 69).
Regarding dependent claim 2, Nelson additionally teaches that the recombination sites are loxP sites (paras. 28-30).
Regarding dependent claims 4-5, Nelson additionally teaches that the RCA is performed in the presence of a DNA polymerase, dNTPs and primers (paras. 8, 36), as recited in claim 4, and that the DNA polymerase is phi29 polymerase (para. 8), as recited in claim 5.
Regarding dependent claims 8-10, Nelson additionally teaches that the recombination reaction occurs in the presence of a recombination and an exonuclease (paras. 34, 52), as recited in claim 8, specifically a Cre recombinase (para. 34) and a T5 exonuclease (para. 52), as recited in claims 9-10, respectively.
Regarding dependent claims 11-12, Nelson additionally teaches adding a DNA topoisomerase, optionally a DNA gyrase or DNA topoisomerase (para. 69), as recited in claims 11 and 12, respectively.
Prior Art
Regarding claims 6 and 17-19, SEQ ID NOs: 1 and 2 are free of the art. Regarding SEQ ID NO: 1, the closest prior art is La Rosa (US Patent App. Pub. No. 2004/0214272 A1), which is directed to nucleic acid polynucleotide sequences from plant sources that may be useful in production of transgenic plants with improved properties. La Rosa teaches the oligonucleotide SEQ ID NO: 174,213 which is 306 nucleotides in length. Nucleotides 120 through 138 of SEQ ID NO: 174,213 match instant SEQ ID NO: 1 nucleotides 1 through 19 with 87% homology. Regarding SEQ ID NO: 2, the closest prior art is Ito3 (US Patent No. 2020/0248231) which teaches SEQ ID NO: 84, which is 60 nucleotides in length. Ito teaches that SEQ ID NO: 84 is useful for creating double-stranded DNA. Nucleotides 24-43 of Ito SEQ ID NO: 84 correspond to instant SEQ ID NO: 2 with 100% homology. Thus, Ito SEQ ID NO: 84 comprises instant SEQ ID NO: 2. In addition, Wang Li (CN101525627A, 2009; English machine translation) teaches the oligonucleotide P11 (p. 6 of the English translation) which has 100% homology to instant SEQ ID NO: 2. Wang Li teaches that P11 is used as a primer to prepare a subclone of genetically engineered bacterium.
Thus, while the nucleotide sequences of SEQ ID NOs: 1 and 2, or sequences with a high degree of homology, are generally known in the art, they are either comprised within much larger sequences (as in La Rosa and Ito), or they are used in completely unrelated methods (as in Wang Li). Thus, the ordinary artisan would not have had an expectation of success in using such prior art sequences in the Nelson method. The ordinary artisan also would not be motivated to modify, in particular, the larger prior art sequences to arrive at the primers of SEQ ID NOs: 1 and 2, as nothing in the art would direct the ordinary artisan to the subportions of the larger sequences that correspond to SEQ ID NOs: 1 and 2. Therefore, SEQ ID NOs: 1 and 2 are free of the art.
Regarding claims 3 and 7, the claims are free of the art for the reasons noted above in the Response to Arguments section. Claims 14-16 are free of the art for the same reasons.
Claims 3, 6-7 and 14-19 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
Claims 1-12 and 14-19 are being examined on the merits. Claims 1-2, 4-5 and 8-12 are rejected. Claims 3, 6-7 and 14-19 are objected to. No claims are allowed.
THIS ACTION IS MADE FINAL. 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 CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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/CAROLYN L GREENE/Primary Examiner, Art Unit 1681
1 Cre recombinase is generally understood in the art to be an endonuclease. See Steele, General Genetic Strategies, Methods in Enzymology, Vol. 602, 2018, p. 128, section 4.2.2.2 “[t]he lox sites can be recognized by an endonuclease, Cre recombinase, which removes DNA at those positions”. Further, the instant specification does not define the term “endonuclease”, nor does it provide examples of embodiments of endonucleases that would exclude Cre recombinase from being considered an “endonuclease”.
2 Nelson was cited in the PTO-892 Notice of References Cited mailed October 22, 2025.
3 Ito was cited in the Information Disclosure Statement submitted June 27, 2025.