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 November 19, 2025 is acknowledged.
Claims 1-6 were pending. Claims 1, 3-4 and 6 are being examined on the merits. Claims 2 and 5 are canceled.
Response to Arguments
Applicant’s arguments filed November 19, 2025 have been fully considered.
The following objections and rejections are WITHDRAWN in view of Applicant’s arguments and claim amendments:
Objections to claims 1-6
Rejection of claims 1-6 under 35 USC § 112(b), indefiniteness
Rejection of claim 5 under 35 USC § 112(d)
The following rejections are MODIFIED in view of the instant claim amendments:
Prior art rejections
Response to arguments regarding prior art rejections
Applicant argues that the prior art rejections of record do not teach or suggest all the limitations of instantly amended claim 1 (Remarks, p. 8).
The Examiner agrees. The prior art rejections below are modified to account for the instant amendments. To the extent that Applicant’s arguments relate to the modified prior art rejections below, the Examiner notes the following.
Applicant argues that the instantly claimed primer has certain improved effects, including that incorporating the reporter and quencher into the primer molecule eliminates the need for an additional probe, and that when the RNA sequence in the primer is cleaved the quencher is released thus producing a signal (Remarks, p. 11).
The Examiner agrees that instantly claimed primer would have such capabilities when used in a LAMP assay, however, it is not clear that these advantages would be unexpected, and if so, why.
Applicant additionally notes that “[w]hen measuring the amount of light emission of fluorescence caused by unquenching, nonspecific binding and dimer formation during the amplification process can be suppressed, thereby increasing amplification efficiency and detection specificity”, and further and that such an improvement is unexpected. Thus, Applicant concludes that the instant primer modification “is not a merely obvious substitution” (Remarks, p. 11).
The Examiner agrees that use of the instantly claimed primer will result in a highly specific assay, as is recognized in the Du reference. Specifically, Du teaches that …
PNG
media_image1.png
230
380
media_image1.png
Greyscale
(p. 133, left col., para. 3). Thus, Du teaches that the high specificity of the reaction is due to the formation of the RNase H2 cleavable duplex of the primer to the template with no mismatches. Therefore, use of the instantly claimed primer would be expected to result in a highly specific reaction, due to the requirements of the RNase H2 activity. However, it is not clear if or how the instant modification to that primer (i.e., adding the dual FRET labels) would improve the specificity of the reaction further. Thus, it is not clear that the instant modification to the Du primer generates an unexpected property.
These arguments are not persuasive. The prior art rejections are modified in view of the instant claim amendments.
Claim Objections
Claims 1, 3 and 6 are objected to because of the following informalities:
In claim 1, the limitation “the blocker is a quencher and located …” in the penultimate
line should be “the blocker is a quencher and is located …”.
In claim 1, the Examiner suggests changing the limitation “an RNA sequence that is
complementary to a template … in a 3’ end direction” to “an RNA sequence that is complementary to a template … in a 3’ end region”, and changing the limitation “wherein the blocker is … located in a 3’-end direction of the RNA sequence” to “wherein the blocker is … located 3’ of the RNA sequence”.
In claim 3, the Examiner suggests changing the limitation “a DNA sequence that is complementary to the template … in a 3’ end direction” to “a DNA sequence that is complementary to the template … in a 3’ end region”.
In claim 6, the Examiner suggests changing the limitation “from 5’ to 3’-end direction of
the target nucleic acid sequence” in step (a) to “from 5’ to 3’ of the target nucleic acid sequence”.
Appropriate correction is required.
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 1, 3-4 and 6 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 1 has been amended, in part, to recite “in a 5’-end direction of the RNA sequence
and a region of F2 or B2”, the meaning of which is unclear. Specifically, “F2” and “B2” do not have a fixed meaning in the art, and thus it is unclear where the “F2” and “B2” parts of the primer are relative to one another and to the other primer parts. Since the ordinary artisan would not be able to determine the metes and bounds of the claim, it is indefinite.
Claims 3-4 and 6 depend from or otherwise incorporate the limitations of claim 1, and
consequently incorporate the indefiniteness issues of claim 1.
To overcome this rejection, the Examiner suggests amending claim 1 to add a clause which states “wherein the inner primer comprises from 5’ to 3’ the regions of F1c or B1c, F2 or B2, RNA sequence, DNA sequence, quencher and blocker” (as in Fig. 1B), or something equivalent that describes the order of the primer regions, and then to delete “in a 5’-end direction”.
Claim 6 recites the limitation “performing … (LAMP) … using the primer composition of claim 4 …”, the meaning of which is unclear. Specifically, claim 4 requires “the inner primer … of claim 1” and an F3 and a B3 primer. Claim 1, in turn, has been amended to recite that the inner primer is either “FIP” or “BIP”. Thus, claim 4 is now directed to a composition comprising three primers: FIP or BIP, plus F3 and B3. It is not clear if claim 6 is then intended to be directed to performing LAMP with only 3 primers, or if it is intended to require both an FIP and a BIP, with only one of those primers being modified according to the requirements in claim 1. If it is intended to be the former, it is not clear how LAMP could be performed with such a primer composition. To the extent that it is intended to be the latter, the claim is indefinite for omitting essential subject matter. See MPEP 2172.01. Since the ordinary artisan would not be able to determine the metes and bounds of the claim, it is indefinite.
To overcome this rejection, the Examiner suggests amending either claim 4 or 6 to require both an FIP and a BIP primer. For example, claim 4 could be amended to read “… and an additional BIP primer when the inner primer for the LAMP of claim 1 is the FIP primer, or an additional FIP primer when the inner primer for the LAMP of claim 1 is the BIP primer”.
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.
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 1, 3-4 and 6 are rejected under 35 U.S.C. 103 as being unpatentable over Du1 (Single-step, high-specificity detection of single nucleotide mutation by primer-activatable loop-mediated isothermal amplification (PA-LAMP), Analytica Chimica Acta, 1050, 132-138, 2018) in view of Hardinge2 (Reduced False Positives and Improved Reporting of Loop-Mediated Isothermal Amplification using Quenched Fluorescent Primers, Scientific Reports, 9:1, 1-13, 2019) and Ding (US Patent App. Pub. No. 2020/0150047 A1), as evidenced by Barany (WO 2014/160199 A1).
Regarding independent claim 1 and dependent claim 4, Du teaches …
An inner primer modified for looped-mediated isothermal amplification (LAMP) of a target nucleic acid sequence, wherein the inner primer is a backward inner primer (BIP), wherein the BIP includes an RNA sequence that is complementary to a template target nucleic acid sequence in a 3'-end direction and is capable of being cleaved by Ribonuclease (RNase) and a blocker that inhibits gene amplification (p. 134, Scheme 1: BIP primer with “r” (RNA sequence) and “C3 spacer” (blocker)). Du additionally teaches a forward outer primer (F3) and backward outer primer (B3) (p. 134, Scheme 1: F3 and B3 primers).
Regarding the detection chemistry, Hardinge teaches using a primer with an RNase cleavable RNA sequence and teaches labeling the primer with FRET dyes, and more specifically, teaches labeling the RNase cleavable primer with a reporter in the 5’-end direction (Fig. 1, BIP). In addition, Ding teaches a cleavable primer with a FRET reporter in the 5’ end region and a FRET quencher in the 3’ end region with the cleavage site being between reporter and the quencher (e.g., Fig. 1), and teaches that this eliminates the need for an additional probe, as in a Taqman assay (Table 1). Thus, the combination of Hardinge and Ding teach that the primer has “a reporter in a 5’-end direction of the RNA sequence and a region of F2 or B2” and “a quencher … located in a 3’-end direction of the RNA sequence”.
Finally, regarding the limitation “wherein the blocker is a quencher”, FRET quencher molecules are generally understood in the art to block polymerase extension, as evidenced by Barany (para. 95). Thus, the Ding quencher is also a “blocker”.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to modify the Du primer to incorporate the Ding detection chemistry. The ordinary artisan would have been motivated to do so to achieve the expected advantage of improving the detectability of an amplification product generated from such a primer, without increasing the number of oligonucleotides required (i.e., the primer is now capable of generating a real-time amplification signal when used in an amplification method, but an additional probe is not required). The ordinary artisan would have had an expectation of success as labeling oligonucleotides with detection agents is well-known in the art, and because Hardinge teaches that LAMP primers can be labeled with FRET labels.
Regarding dependent claim 3, Du additionally teaches that the BIP includes a sequence that is complementary to the template nucleic acid in the 3’ end directed and recognized by the RNase (p. 134, Scheme 1: sequence between “r” and “C3 spacer”).
Regarding claim 6, Du teaches …
A method for detecting a target nucleic acid sequence, the method comprising: (a) selecting a sequence of six regions of B3, B2, B1, F1c, F2c, and F3c from 5' to 3'-end direction of the target nucleic acid sequence; and (b) performing Looped-mediated isothermal amplification (LAMP) on a sample using a primer composition and a Ribonuclease (RNase) (p. 134, Scheme 1).
In addition, Du in view of Hardinge and Ding, as evidenced by Barany, teach the primer composition of claim 4 (see citations above).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to modify the Du primer to incorporate the Ding detection chemistry. The ordinary artisan would have been motivated to do so to achieve the expected advantage of improving the detectability of an amplification product generated from such a primer, without increasing the number of oligonucleotides required (i.e., the primer is now capable of generating a real-time amplification signal when used in an amplification method, but an additional probe is not required). The ordinary artisan would have had an expectation of success as labeling oligonucleotides with detection agents is well-known in the art, and because Hardinge teaches that LAMP primers can be labeled with FRET labels.
Conclusion
Claims 1, 3-4 and 6 are being examined, and are rejected. Claims 1, 3 and 6 are objected to. 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 CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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.
/CAROLYN L GREENE/Primary Examiner, Art Unit 1681
1 Du was cited in the Information Disclosure Statement submitted April 9, 2024.
2 Hardinge was cited in the Information Disclosure Statement submitted April 9, 2024.