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 arguments have been thoroughly reviewed and considered. Claims 2, 7, and 14-17 remain withdrawn. Claims 18 and 19 have been added. Claims 1, 3-6, 8-13, and 18-19 are pending and are examined on the merits herein.
Response to Applicant’s Amendments
Claim Objections
Claims 9 and 11-12 were objected to for various informalities. In light of Applicant’s amendments to the claims submitted 1/22/2026, these objections have been withdrawn, but see new ground of objection below.
35 USC 112(b) Rejections
Claims 5, 11, and 13 were rejected for various indefiniteness issues. In light of Applicant’s amendments to the claims submitted 1/22/2026, these rejections have been withdrawn, but see new grounds of rejection below.
35 USC 102 Rejections
Claims 1, 3-5, 8-9, and 12-13 were rejected under 35 U.S.C. 102(a)(1) as being anticipated by Deng et al. (WO 2019/226689 A1). In light of Applicant’s amendments to the claims submitted 1/22/2026, these rejections have been withdrawn, but see new grounds of rejection and “Response to Applicant’s Arguments” below.
35 USC 103 Rejections
Claims 6, 10, and 11 were rejected under 35 U.S.C. 103 as being unpatentable over Deng et al. (WO 2019/226689 A1) and various combinations of references. In light of Applicant’s amendments to the claims submitted 1/22/2026, these rejections have been withdrawn, but see new grounds of rejection and “Response to Applicant’s Arguments” below.
Response to Applicant’s Arguments
Regarding the 35 USC 102 Rejections, Applicant argues that the teachings of Deng provided in the Non-Final Rejection do not read on the newly amended portion of step (c) of claim 1, where the removed portion must be two or more bases in length (Remarks, page 11). Regarding the 35 USC 103 Rejections, Applicant argues that as Deng does not read on the current method of claim 1, these rejections are no longer proper. The Examiner agrees with this assessment with regard to the teachings of Deng brough forth in 35 USC 102 Rejections, and this is the basis for the withdrawal of these rejections.
In Deng, the nickase of their invention may be used to generate nicks of at least 10 or more nucleotides (para. 118). As 10 “or more” has no upper limit, this reads on the newly amended portion of claim 1, as well as newly added claims 18 and 19. This teaching is relevant to the embodiment of Deng originally described in the rejection of claims 5 and 12-13 in the Non-Final Rejection, which also inherently reads on instant claim 1. Specifically, this embodiment discusses using a nickase (i.e. not a USER enzyme) to generate a double-stranded circular nucleic acid with a gapped strand and a circular strand. Because the nickase teaching of para. 118 of Deng and its effects on the interpretation of the reference were not originally incorporated into the Non-Final Rejection, the rejections of claims 1, 5, 12-13, and 18-19 below are considered new grounds of rejection for all claims.
Additionally, in the embodiment of Deng originally described in the rejection of claims 1, 3-4, and 8-9, it is noted that Deng states that one or more uracil residues may be placed onto an adapter and one or more USER enzymes may be used to cleave the uracil (see paras. 200-201 of Deng). Though these teachings alone do not make explicit that the USER enzymes may remove more than a single uracil residue at once, these teachings are the basis for the new grounds of rejection below as related to these claims.
Applicant states in their arguments that a nicking site generate by a nickase is not the same as a gap (Remarks, page 12). However, Applicant does not define a “nicking site” in their instant specification, and the language “nicking site” is used in conjunction with the creation of “gapped circles” throughout the instant specification. See Example 1, where para. 103 refers to nicking sites and paras. 111-112 refer to created gapped circles. See also paras. 18-19, which refer to gapped circles created via nicking sites. Additionally, in the instant specification, “gapped circles” are referred to as “double-stranded circles with a short single stranded gap,” (para. 4). Thus, Applicant is using too narrow of a definition for a “gapped circle” according to their own instant specification. Further, Deng specifically states that a “nickase” can create a nick or a gap, and so the invention as a whole is not considered to be limited to solely either nicks or gaps (para. 118).
Thus, Applicant’s arguments against Deng are generally not persuasive, and the relevant portions of the previous prior art rejections are reiterated below. New grounds of rejection were required to fully address Applicant’s claim amendments.
Claim Objections
Claim 1 is objected to because of the following informalities: in line 4 of step (c), “on one of the strand” should read “on one of the strands.” Appropriate correction is required.
Claim Interpretation
Regarding step (c) of claim 1, the step states that a gapped circular nucleic acid is formed, where one of the strands is referred to as a “circular strand,” and the other strand is not referred to by any particular terminology. The gapped circular nucleic acid also must have a gapped portion of “one of the strand[s].” The term “circular strand” is not given a particular specific definition in the instant specification, and so has no structural requirements – meaning the circular strand could be the “one of the strand[s]” that contains the gapped portion. While this amendment does not necessarily render the claim unclear/indefinite, this amendment does not appear to align with Applicant’s intentions for the invention, and for a “circular strand” in the instant specification (e.g. see paras. 5 and 11-13, which refer to a circular strand and a gapped strand).
If Applicant wishes to better align claim 1 with the embodiments of the instant specification involving a “circular strand” and a “gapped strand,” it is recommended that the language of step (c) be amended to read “thereby forming a gapped circle nucleic acid template having a circular strand and a gapped strand, wherein the gapped strand contains the portion removed by the cleaving agent, and wherein the length of the portion removed is two or more bases in length” or similar/equivalent phrasing.
It is noted that such an amendment would affect the language of claim 11, which refers to “the gapped portion.”
Claim Rejections - 35 USC § 112(b)
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 11-13 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 11 is rejected because the method is not clear for all possible embodiments. As noted in the “Claim Interpretation” section above, claim 1 may be interpreted as though either strand of the double-stranded gapped circle nucleic acid template may contain the gapped portion. If the circular strand contains the gapped portion, then in claim 11, the primer-binding site must be in the portion removed from said circular strand. If the gapped portion is on the other strand (i.e. the strand not referred to as the “circular strand”) then the circular strand would not contain a gapped portion, and it is unclear how a primer-binding site would be in a location that does not exist on the circular strand. If Applicant decides to amend claim 1 according to the suggestion provided in the “Claim Interpretation” section above, it is recommended to amend this claim to state that the circular strand contains a primer-binding site in the portion of said circular strand that is opposite the gapped portion on the gapped circle nucleic acid template.
Claim 12 recites the limitation "the gapped strand" in line 1. There is insufficient antecedent basis for this limitation in the claim, as “a gapped strand” is not recited earlier in the claim or in claim 1, from which this claim depends. It will be interpreted as though this term is referring to the “gapped portion” of claim 1.
Claim 13 is rejected due to its dependence on rejection claim 12.
Claim 13 is also rejected because it recites the limitation “the one strand of the double-stranded nucleic acid.” Firstly, “the one strand” lacks antecedent basis, as “one strand” is not referred to earlier in the claim or in claims 1 and 12, from which this claim depends. It will be interpreted as though this is referring to the strand containing the gapped portion in claim 1, which is also being interpreted as containing the extendable 3’-end of claim 12 (as explained in the rejection of claim 12 above). However, this “one strand” is specifically stated to be part of the “double-stranded nucleic acid,” which no longer exists from step (a) onwards in claim 1. Thus, the entirety of the phrase “one strand of the double-stranded nucleic acid” is unclear. It will be interpreted as though the “double-stranded nucleic acid” in this claim is intended to be the “gapped circle nucleic acid template” of claims 1 and 12.
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.
Claims 1, 5, 12-13, and 18-19 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Deng et al. (WO 2019/226689 A1; cited in Applicant’s IDS), as evidenced by Shim et al. (Biomed Microdevices, 2016).
Deng teaches an embodiment of their invention in Figure 4b and para. 266. This embodiment involves ligating adapters to double-stranded DNA, circularizing the DNA, nicking a single strand of the DNA, and then amplifying and sequencing the DNA. The nicking can be done via the use of a nickase, and Deng states that the nickases of their invention may be nicking endonucleases (para. 118; instant claim 5). Deng also states that the nicking site may expose a 3’ free end that can serve as a template for a polymerase (para. 266), and this end is shown as being extended and sequenced in Figure 4b (instant claim 12). As the double-stranded circular DNA contains two strands complementary to one another, and the polymerase is shown attaching to both strands at the location of the extendable end in Figure 4B, this polymerase would then perform extension to create a strand at least partially complementary to the circular strand (instant claim 13). Furthermore, though para. 266 of Deng is not specific about the length of the nick generated by the nickase, para. 118 states that nicks may be 10 or more nucleotides long, with no upper limit provided. Thus, this embodiment also reads on instant claims 1, 18, and 19.
Claims 1, 3-4, and 8-9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Deng et al. (WO 2019/226689 A1; cited in Applicant’s IDS), as evidenced by Shim et al. (Biomed Microdevices, 2016).
Deng teaches methods and systems for processing or analyzing a nucleic acid molecule utilizing adapters, nicking, and circularization (Abstract). Paras. 200-201 and Figure 1D (process 170) show an example method in which a double-stranded nucleic acid is provided, and may be coupled with multiple adapters, where a single adapter contains one or more uracil nucleotides. Two adapters may be provided, one which does contain one or more uracils and one which does not. The adapters may be added via ligation (instant claim 3). The free ends of the two adapters are then ligated together, generating a circular molecule (instant claim 9). Then, the circular molecule may be treated with one or more uracil-specific enzymes which nick uracil residue on the adapter sequence. This results in a double-stranded molecule where one strand is fully circular and the other is gapped. Deng teaches that the adapters used for circularization may comprise one or more barcodes (para. 134; instant claim 4). After circularization, the mixture can be treated with an exonuclease to remove non-circularized polynucleotides (para. 306; instant claim 8).
In para. 201 it is stated that, “Following, the circular nucleic acid molecule may be treated with one or more uracil-specific enzymes (e.g., uracil-specific excision reagent or "USER") to generate a single nucleotide gap (i.e., nick) at the location of the uracil residue.” Here, the language of Deng does not make clear that USER enzymes may cleave multiple uracil residues, even if more than one USER enzyme is provided.
Shim teaches enzymatic reactions related to detaching DNA from particles (Abstract). To capture DNA, a DNA sequence was designed with a four uracil linker (page 2, column 1, para. 3). USER enzyme digestion was eventually performed to remove the entire uracil linker (i.e. more than one uracil residue; see Figure 1a). More than a single USER enzyme was provided (see the concentration illustration of Figure 1b, as well as page 2, column 2, para. 1).
Thus, Shim provides evidence that if more than a single USER enzyme is used, then said USER enzymes can cleave more than a single uracil residue. In the embodiment of Deng detailed above in paras. 200-201, it is explicitly stated that multiple uracil residues may be included on an adapter and that one or more USER enzymes may be used. Thus, this embodiment of Deng encompasses creating gaps of more than one base, and so reads on instant claim 1.
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 6 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Deng et al. (WO 2019/226689 A1; cited in Applicant’s IDS).
Regarding claim 6, Deng teaches the method of claims 1, 5, 12-13, and 18-19, as described above. In para. 159 of Deng, it states that amplification of double-stranded nucleic acids may occur before coupling to the double-stranded adapter, but then this would require the use of a number of adapters that is the same as or more than the number of amplification copies present. Such an amplification is also shown in Figure 4B. In paras. 221-222, Deng states that linear nucleic acids may generally be amplified before circularization via the use of ligated adapters (para. 221). However, it would be prima facie obvious to the ordinary artisan that by amplifying the adapter-ligated linear nucleic acids before circularization, this would prevent the need for creating adapters equal to the number of copies of the double-stranded nucleic acids. As the number of copies could easily be in the thousands or tens of thousands, by attaching the adapters before amplification, this would prevent the need for the time and resources required to create such a large number of adapters. This would likely also ensure a more accurate and effective circularization reaction, as there would be less un-ligated adapters present in the reaction mixture before circularization, which would lead to more accurate circularization processes, as there would be less interference from the smaller number of un-ligated adapters. There would be a reasonable expectation of success as this change would simply involving changing the order of known procedures (e.g. ligation and amplification) in the method of Deng, and the same result, namely a circularized double-stranded nucleic acid, would be produced.
Thus, claim 6 is prima facie obvious over Deng.
Regarding claim 11, Deng teaches that the nicking site of the double-stranded adapter is where sequencing can occur. Specifically, an extension reaction can occur from this nicking site to generate a growing strand (para. 9). This extension reaction can occur via the use of an oligonucleotide primer (paras. 74 and 156). Figure 4b also shows an example of extending the gapped strand, where a DNA polymerase can attach to the nicked site (para. 266). As Deng teaches that this extension can occur via the use of a primer, it would be prima facie obvious that the non-nicked strand (i.e. the fully circular strand) would need to contain a binding site for this primer to bind to, in order to guide the DNA polymerase to the correct position to begin extension (Figure 4B shows that the DNA polymerase is capable of such positioning, as it is shown as attached to both strands at the gapped location). This would simply require designing a primer that was similar to, or the same as, part of the sequence of the removed nucleotides on the gapped strand, which would correspond to a portion of the adapter sequence, as the adapter sequence is the nicked sequence in the teachings of Deng described above. Designing or obtaining such a primer would be possible for the ordinary artisan, as this process would be similar to designing or obtaining the initial adapter sequence.
Thus, claim 11 is prima facie obvious over Deng.
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Deng et al. (WO 2019/226689 A1; cited in Applicant’s IDS) in view of Weng et al. (US 2020/0010883 A1).
Deng teaches the methods of claims 1, 5, 12-13, and 18-19, as described above. Though Deng generally teaches methods involving heat denaturation (e.g. paras. 260 and 275), the reference does not teach denaturation to remove cleaved nucleic acids.
Weng teaches various sequencing, amplification, and enrichment methods (Abstract). In one such method, a single strand of a double-stranded bridge polynucleotide is cleaved, and is removed by denaturing (para. 103). Weng also teaches general denaturation methods (e.g. paras. 60, 93, and 114).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to combine the teachings of Weng with the methods described by Deng above. Specifically, this would involve using denaturation after the cleavage step to remove the gap nucleic acids from the double-stranded circularized nucleic acid molecule before further processing. By ensuring these gap nucleic acids are nowhere near the circularized nucleic acid, it would prevent inadvertent re-hybridization of the gap nucleic acids to the circular nucleic acid during steps such as amplification or sequencing, which might lead to inaccurate results. There would be a reasonable expectation of success in incorporating heat denaturation into the methods of Deng described above as Deng already teaches denaturation methods in procedures such as PCR (para. 304), providing evidence that they are compatible with other aspects of their invention.
Thus, claim 10 is prima facie obvious over Deng in view of Weng.
Conclusion
No claims are currently allowable.
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 FRANCESCA F GIAMMONA whose telephone number is (571)270-0595. The examiner can normally be reached M-Th, 7-5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/F.F.G./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681