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 Claims
It is acknowledged that Applicant amended claims 1-9, 11, and 14-22 and cancelled claims 10, 12, and 13 in the response filed June 24, 2026.
Claim(s) 1-9, 11, and 14-22 is/are currently pending.
Claim(s) 22 is/are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected invention(s), there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 2/09/26.
Claim(s) 1-9, 11, and 14-21 are herein examined.
Summary of Response to Applicant’s Arguments
This action is in response to the papers filed June 24, 2026. Applicant’s remarks and amendments have been fully and carefully considered but are not found to be persuasive. Any new grounds of rejection presented in this Office Action are necessitated by Applicant’s amendments. Any rejections or objections not reiterated herein have been withdrawn. This action is made FINAL.
The rejection of claim 16 under 35 U.S.C. 112(b) and the objection to the specification have been withdrawn due to corrective amendments. New and modified rejections under 35 U.S.C. 112(b) and 35 U.S.C. 102(a)(1) are set forth below. Responses to the arguments concerning Markarov as they apply to the rejections under 35 U.S.C. 102(a)(1), 35 U.S.C. 103, and Double Patenting are addressed on pg.10-12 of this office action.
Priority
It is acknowledged that the instant application is a 371 of International Application No. PCT/KR2022/003869, filed March 21, 2022, and that it claims foreign priority based on application KR 10-2021-0036727 filed in Korea on March 22, 2021. It is noted, however, that the foreign priority date is the effective filing date of the claimed invention if:
the foreign application supports the claimed invention under 112(a), and
the applicant has perfected the right of priority by providing
a certified copy of the priority application, and
a translation of the priority application (if not in English)
In the instant case, the applicant has submitted a certified copy of the priority application but it is not in English and the examiner cannot determine if it supports the claimed invention. The effective filing date of the application is considered to be March 21, 2022, which is the filing date of the International Application No. PCT/KR2022/003869.
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(s) 1-9, 11, and 14-21 is/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(s) 1-9, 11, and 14-21 are rejected for the recitation of “which differs by 1 to 10 bases” in line 14 of claim 1, as indefinite. It is unclear which elements of the invention are required to differ by 1 to 10 bases from each other. The ambiguous language of the claim allows for several possible and potentially contradictory interpretations of the limitation:
the clamping probe as a whole differing by 1-10 bp from the target nucleic acid or from the partial primer as a whole or both
the sequence complementary to the detection region of the target nucleic acid in either the partial primer, the clamping probe, or both is 1-10 bp different from the detection region itself in the target nucleic acid
the sequence complementary to the detection region of the target nucleic acid is comprised in both the clamping probe and the partial primer, save that it is 1-10 bp different between the two
As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter.
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 pre-AIA 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) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
Claims 1, 2, 5-9, 11, and 14-21 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Markarov et al. (published June 2, 2011; Patent Publication No. US 2011/0129832).
Markarov recites polynucleotide combinations used in detection and amplification of nucleic acids (par. 52).
Regarding claim 1, Markarov recites a method of amplifying a target nucleic acid, comprising amplifying an isolated nucleic acid by performing polymerase chain reaction (par. 100-104: “Methods of Use: PCR”) in the presence of: a guide probe (par. 9: the “second polynucleotide” or “F”) comprising a sequence capable of hybridizing with a region of a target nucleic acid other than a detection region (“Fb”) and a sequence not hybridizing with the target nucleic acid (“Fd”); a partial primer (par. 9: the “first polynucleotide” or “P”) comprising a sequence complementary to the sequence not hybridizing with the target nucleic acid in the guide probe (“Pc”) and a sequence complementary to the detection region of the target nucleic acid (“Pa”); a clamping probe (par. 9: the “blocker polynucleotide”) that inhibits amplification of other nucleic acids except the target nucleic acid (Figure 4); and a specific primer (par. 20; Fig. 8A) capable of amplifying the target nucleic acid by pairing with the partial primer. Markarov recites that the method comprises determining presence or absence of an amplicon (par. 40).
See annotated Fig. 4 below for reference.
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Markarov recites that the sequence in the partial primer which is complementary to the detection region of the target nucleic acid is a sequence of 5-15 base pairs (par. 10, 15). Note that in Markarov, this sequence is referred to as the ‘Pa’ region. This overlaps the range of 3-15 bases with sufficient specificity that the limitation is considered to be anticipated.
Markarov recites that the clamping probe inhibits amplification of the other nucleic acids except the target nucleic acid by preventing the partial primer from binding to the other nucleic acids except the target nucleic acid (par. 8, 63, 119). Note that the binding of the partial primer/Pa to the target is either partially or completely blocked by the clamping probe/blocker polynucleotide (i.e. par. 8: “In another aspect, the blocker polynucleotide has a sequence that overlaps Pa over the whole length of Pa”). Both scenarios are consistent with the language of the instant claim and the content of the instant specification (
Markarov recites that the sequence complementary to the detection region of the target nucleic acid is comprised in both the clamping probe and the partial primer, save that it is 2-10 bp different between the two (par. 64). This overlaps the claimed range of 1-10 bases with sufficient specificity that the limitation is considered to be anticipated.
Regarding claim 2, Markarov recites that the guide probe is configured such that the sequence hybridizing with the target nucleic acid is present at a 5' end or N-terminus and the sequence not hybridizing with the target nucleic acid is present at a 3' end or C-terminus (par. 30, Figure 4). If the partial primer overlaps with the clamping probe at its 3’ end (as recited in par. 30), Fig. 4b depicts the guide probe in the required orientation.
Regarding claims 5 and 17, Markarov recites that the guide probe, the partial primer, the clamping probe, the specific primer, OR the probe capable of binding to the amplicon comprise any one or a combination of two or more selected from among an oligonucleotide, LNA, and PNA (par. 71, 75, 81).
Regarding claims 6 and 7, Markarov in paragraph 0015 describes that a first half of the guide probe (“Fb”) can have a minimum length of 10 bases and a maximum length of 5000 bases, and that a second half (“Fd”) can have a minimum length of 5 bases and a maximum length of 200 bases. Markarov’s total length range for the guide probe is from 15-5,200 bases. Thus, Markarov anticipates guide probes that are 15 to 500 bases and guide probes that are 20 to 150 bases.
Regarding claim 8, Markarov recites that the guide probe and the clamping probe hybridize to a strand of the target nucleic acid opposite a strand to which the specific primer binds (par. 9, 20).
Regarding claim 9, Markarov teaches that the complementary regions of the partial primer are separated by 10 nucleotides or more (par. 56), and that the separation is accomplished with a single-stranded DNA linker (par. 152, Fig. 13A). Thus, Markarov anticipates a partial primer which further comprises a spacer, which is a single-stranded oligonucleotide with a length of 1 to 100 bases, between the sequence complementary to the sequence not hybridizing with the target nucleic acid in the guide probe and the sequence complementary to the detection region of the target nucleic acid.
Regarding claim 11, Markarov teaches a blocker polynucleotide which is from about 5 nucleotides in length to about 100 nucleotides in length (par. 92), which is a PNA (par. 75). Thus, Markarov anticipates that the clamping probe is PNA with a length of 5 to 100 bases. This overlaps the range of 5-500 bases with sufficient specificity that the limitations are considered to be anticipated.
Regarding claim 14, Markarov teaches a primer pair (SEQ ID NO: 18 and SEQ ID NO: 20 in Example 9) which generates an amplicon with a length of around 79 bp (in the annotated figure below, the binding site of the partial primer is underlined in red and the binding site of the specific primer is underlined in dark blue). Given that Markarov discloses a value within the claimed range, the limitation that the amplicon is 50 bp to 1 kbp in length is considered to be anticipated.
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Regarding claim 15, Markarov recites that determining the presence or absence of the amplicon in step (b) uses a nucleic acid-binding dye (par. 141; Example 3) or probe capable of binding to the amplicon (par. 9, 31).
Regarding claim 16, Markarov recites that the nucleic acid-binding dye may be ethidium bromide (par. 141).
Regarding claims 18-20, Markarov recites that the probe capable of binding to the amplicon has a reporter and a quencher connected to both ends thereof (par. 31, Fig. 5a). Markarov also recites that the reporter is at least one fluorescent material selected from the group consisting of fluorescein, fluorescein chlorotriazinyl, Rhodamine Green, Rhodamine Red, tetramethylrhodamine, FITC, Oregon Green, Alexa Fluor, FAM, JOE, ROX, HEX, Texas Red, TET, TRITC, TAMRA, cyanine-based dyes, and thiadicarbocyanine dyes (par. 141). Markarov also recites that the quencher is at least one selected from the group consisting of Dabcyl, TAMRA, Eclipse, DDQ, QSY, Blackberry Quencher, Black Hole Quencher, Qxl, Iowa Black FQ, Iowa Black RQ, and IRDye QC-1 (par. 143).
Regarding claim 21, Markarov recites that the isolated nucleic acid is isolated from a sample of a subject (par. 148).
Response to Arguments
In the response, Applicant argued that the structures of the reference and instant claims are distinct. Applicant asserted that Markarov’s blocker binds to the extension direction of the primer to prevent amplification while the clamping probe of the instant invention binds competitively with the partial primer to the target nucleic acid detection site to prevent amplification of non-target nucleic acids.
This argument has been fully considered but is not found persuasive. Markarov’s clamping probe (‘blocker’) and partial primer (‘first polynucleotide’/’P’) bind to overlapping regions of the target, leading to competition for binding over a portion or the entirety of the partial primer’s target binding region (par. 8, 119). For example, Markarov’s disclosure states: “In some embodiments, the blocker polynucleotide overlaps with the first domain of the first polynucleotide. In other words, the nucleotide(s) at the 3′ end of the first polynucleotide and the nucleotide(s) at the 5′ end of the blocker polynucleotide would be complementary to the same nucleotide(s) of the target polynucleotide” (par. 63) and “In another aspect, the blocker polynucleotide has a sequence that overlaps Pa over the whole length of Pa” (par. 8). Note that ‘Pa’ indicates the target-binding portion of the first polynucleotide/partial primer. Markarov further states: “In certain aspects of the method, the sequence in the first region (T1) in the target polynucleotide differs from the sequence in the first region (T1*) in the non-target polynucleotide at one base. In other aspect, the method further comprises the step of detecting the sequence extended from Pa, wherein detection indicates the presence of the target polynucleotide in the sample” (par. 22) and “In some embodiments, the overlapping sequences of the blocker polynucleotide and the first domain of the first polynucleotide (Pa) differ by at least 2 bases…” (par. 64).
Thus, sequences in the blocker/clamping probe and first oligonucleotide/partial primer which are either partially or entirely overlapping over the length of Pa and which differ in at least two bases would result in competitive binding, leading to preferential amplification of target vs. non-target nucleic acids. This anticipates the limitations of the clamping probe in the amended claim.
Applicant argued that the instant invention requires that “the clamping probe does not bind to the target nucleic acid (only the partial primer binds to the target nucleic acid), while the clamping probe binds exclusively to the non-target nucleic acid (the partial primer does not bind non-target nucleic acid).”
This argument has been fully considered but is not found persuasive. The amended claims do not require that the clamping probe does not bind to the target nucleic acid, and in fact allow that “the clamping probe comprises the sequence complementary to the detection region of the target nucleic acid in the partial primer, which differs by 1 to 10 bases,” which would allow the binding of the relevant nucleic acids, albeit at a lower level of complementarity than a competitor nucleic acid. The instant specification sets forth that “binding of the partial primer and the target nucleic acid is not hindered due to low complementarity between the clamping probe and the nucleotide sequence of the target nucleic acid” and “…in the presence of a non-target nucleic acid having a partial nucleotide sequence different from the target nucleic acid in (b), even when the guide probe hybridizes with a specific region of the non-target nucleic acid and thus the partial primer hybridizing with a portion of the guide probe is close to the non-target nucleic acid, complementarity between a portion of the 3′ end of the partial primer and the nucleotide sequence of the non-target nucleic acid is low and the clamping probe hybridizes to the non-target nucleic acid, so that binding of the partial primer and the non-target nucleic acid is hindered, resulting in inhibited extension amplification” (par. 18). Low complementarity of a primer or probe leading to it being outcompeted for binding in the target/non-target nucleic acid is the same principle espoused in Markarov (see the discussion above; Markarov: par. 8, 63). Therefore, Markarov’s invention is consistent with both the language of the amended claims and the content of the instant specification, which allow for embodiments where the clamping probe does bind or is capable of binding the target nucleic acid, but is outcompeted for the binding region by the partial primer.
Applicant claimed that the primer of Markarov overlaps with the target nucleic acid detection site by up to 1 bp, which is distinct from the length required by amended claim 1.
This argument has been fully considered but is not found persuasive. The portion of Markarov’s partial primer which binds or overlaps with the target nucleic acid detection site (’Pa’) is explicitly set forth as ranging from between 5-15 bases in length (par. 15), which is sufficiently overlapping with the claimed range of 3-15 bases that the limitation is considered to have been anticipated.
The rejections have been modified to address the newly amended limitations, and are set forth above.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 3 and 4 are rejected under 35 U.S.C. 103 as unpatentable over Markarov et al. (published June 2, 2011; Patent Publication No. US 2011/0129832), as applied to claim 1 above, and in view of Egholm et al. (published April 3, 2003; Patent Publication No. US 2003/0064402).
Markarov recites the limitations of claim 1, as discussed above.
Regarding claims 3 and 4, Markarov does not recite that the guide probe further comprises a linker between the sequence hybridizing with the target nucleic acid and the sequence not hybridizing with the target nucleic acid, wherein the linker is at least one selected from the group consisting of: beta-alanine (@-Ala-OH, C3), aminobutyric acid (C4), aminohexanoic acid (C6), aminolauric acid (C12), acetoacetoxyethyl acrylate (AAEA (O-linker)), 2-[2-[2-[2-(amino)ethoxy]ethoxy]ethoxy]acetic acid (AEEEA), AEEEEA, DL15, and L35.
Egholm et al. teaches probes for hybridizing to a target nucleic acid (Abstract).
Regarding claims 3 and 4, Egholm teaches a probe comprising a linker between the sequence hybridizing with the target nucleic acid and the sequence not hybridizing with the target nucleic acid (par. 9; Figure 1A), wherein the linker is at least one selected from the group consisting of: beta-alanine (@-Ala-OH, C3), aminobutyric acid (C4), aminohexanoic acid (C6), aminolauric acid (C12), acetoacetoxyethyl acrylate (AAEA (O-linker)), 2-[2-[2-[2-(amino)ethoxy]ethoxy]ethoxy]acetic acid (AEEEA), AEEEEA, DL15, and L35 (par. 58).
It would be obvious to a person with ordinary skill in the art to combine the teachings of Markarov and Egholm before the effective filing date of the instant invention. One would have been motivated to do so, with reasonable expectation of success, in order to alleviate the strain associated with the three-way junction structure (par. 78) and allow for the formation of more stable PNA:DNA duplexes (par. 128).
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 1-9, 11, and 14-21 are provisionally rejected on the ground of non-statutory double patenting as being unpatentable over claims 1-18 of co-pending Application No. 18/254,126) in view of Markarov et al. (published June 2, 2011; Patent Publication No. US 2011/0129832).
Although the claims at issue are not identical, they are not patentably distinct from one another. Both sets of claims are drawn to methods of amplifying a target nucleic acid (ref claim 1). Both sets of claims require: a guide probe comprising a sequence capable of hybridizing with a region of a target nucleic acid other than a detection region and a sequence not hybridizing with the target nucleic acid; a partial primer comprising a sequence complementary to the sequence not hybridizing with the target nucleic acid in the guide probe and a sequence complementary to the detection region of the target nucleic acid; and a specific primer capable of amplifying the target nucleic acid by pairing with the partial primer (ref claim 1). Both sets of claims require determining the presence or absence of an amplicon (ref claim 1).
The co-pending claims additionally recite the limitations of instant claims 2-4, 5 (except those concerning the clamping probe), 6, 7, 8 (except those concerning the clamping probe), 9, 10, and 14-19, as well as of withdrawn claim 22 (except those concerning the clamping probe). The co-pending claims do not recite the limitations of instant claims 11-13, which describe the clamping probe.
However, as discussed in the art rejections set forth above, Markarov teaches these limitations and it would have been obvious to modify the method of the co-pending claims in view of Markarov in order to improving selectivity for detection of a single mutant allele (par. 249).
This is a provisional non-statutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicants argued that “In the March 24, 2026 Office Action, claims 1-21 as then pending were provisionally rejected on the ground of nonstatutory double patenting as unpatentable over claims 1-18 of copending Application 18/254,126 in view of Markarov.
In view of the amendment of claim 1 herein, it is respectfully requested that the amended claims 1-9, 11, and 14-21 be reconsidered, and that the nonstatutory double patenting rejection be withdrawn”.
The arguments have been responded on pages 10-12 of this Final Office Action regarding maintained and updated rejection of claims 1, 2, 5-9, 11, and 14-21 under 35 U.S.C. 102(a)(1) as being anticipated by Markarov et al. (published June 2, 2011; Patent Publication No. US 2011/0129832).
Conclusion
No claims are 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Christine M Jones whose telephone number is (571)272-2585. The examiner can normally be reached Monday - Friday, 8AM - 4PM.
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/C.M.J./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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