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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-8, 10, 11, 14, 17, 18, and 27 in the reply filed on August 8, 2025 is acknowledged.
Claims 19 and 22-26 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on August 8, 2025.
Information Disclosure Statement
The IDS received on November 10, 2022, and two IDS received on February 14, 2023 are acceptable.
Drawings
The drawings received on November 10, 2022 are acceptable.
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, 4-8, 10, 11, 14, 17, and 18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liu et al. (Talanta, 2018, vol. 176, pages 422-427).
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With regard to claim 1, Liu et al. teach a method of utilizing a hairpin-quadruplex forming structure to detect a target nucleic acid, as reproduced below (from Scheme 1, page 424):
As seen, target DNA is provided, and is contacted with an oligonucleotide comprising a first nucleotide sequence comprising a quadruplex-forming sequence (see purple region of H1) and a second nucleotide sequence operably linked to the first nucleotide sequence (see red region of H1), the second nucleotide sequence being sufficiently complementary to the target sequence to hybridize therewith (see red region binding to target DNA); bound to the target sequence to the second nucleotide sequence, thereby inducing the quadruplex-forming sequence to take a quadruplex confirmation (see quadruplex conformation form when target DNA is bound to the “red region” (i.e., second nucleotide sequence); and detecting the oligonucleotide in the quadruplex conformation (“a fluorescent dye, NMM”, page 423, 2nd column, section 3.1; “[i]n the absence of the target DNA, the H1 … remained locked in the hairpin structures, which avoided the association of the fluorescent dye NMM … When the target DNA was present, the red part of H1 completely hybridized with the target DNA, and unfolded the hairpin structure of H1 … active G-quadruplex associated with NMM, and exhibited significantly enhanced fluorescent signal for sensitive monitoring of the target DNA”, page 423, 2nd column, section 3.1).
With regard to claim 2, the H1 oligonucleotide comprises the below sequence (from Table 1, page 423, H1 oligonucleotide):
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As seen, the underlined bases represent G contents and the toplined bases represent N and X bases, respectively. The above region results in G3+N2G3+N2G3+X2G3, which fits the formula represented by claim 2.
With regard to claim 4, the hairpin conformation is formed prior to binding the target sequence, wherein forming a hairpin conformation comprise hybridizing stem sequence of the second nucleotide quadruplex-forming sequence of the first nucleotide sequence (i.e., purple region that forms a stem with the red region).
With regard to claim 5, the assay involves the use of magnesium ions (“H1, H2, and DNAs were dissolved in 1x TE buffer … (500 nM, pH 7.5, 125 mM Tris and 20 mM MgSO4)”, page 423, 2st column, section 2.2).
With regard to claim 6, the red region (i.e., a region on second nucleotide sequence) comprises a “toehold” region (extra bases that form overhang) that is complementary to the target DNA (see Scheme 1).
With regard to claim 7, the binding of the target sequence to the second nucleotide sequence further comprises binding the target sequence to the stem sequence while the quadruplex-forming sequence dissociates from the stem sequence (see the entire red region that was previously a stem region annealing completely to the target DNA, while the first nucleotide sequence (i.e., quadruplex forming sequence) dissociates from the previous stem configuration by dissociation and forms a quadruplex conformation (see Scheme 1).
With regard to claim 8, the stem sequence (i.e., stem forming region of the second nucleotide sequence (red region) is encompassed by the formula C3+N1-7 (see below):
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As seen, the bolded sequence represents the target-binding sequence (i.e., the second nucleotide sequence), wherein the stem region comprises CCCAT.
With regard to claim 10, the assay involves heating the sample that involves the cycling of the hairpin-to-quadruplex conformations (see “10 mL target DNA of different concentrations were added … After the mixture was incubated at 40oC 80 min.”, page 423, 1st column, section 2.2).
With regard to claim 11, the assay also involves the use of potassium ions (“100 mL of H1, 100 mL of H2, 10 mL of KCl solution (2M), 10 mL NMM … and 10 mL of target DNA of different concentrations were added”, page 423, 1st column, section 2.2).
With regard to claim 14, the detection involves fluorescence (thus change in optically detectable property (see “exhibited significantly enhanced fluorescent signal for sensitive monitoring of the target DNA”, page 423, 2nd column, section 3.1).
With regard to claim 17, the assay does not involve an enzyme (see Fluorescent DNA Assay section in section 2.2 of page 423).
With regard to claim 18, quantification is performed (see Fig. 4A, also “the proposed strategy was evaluated by quantitative analysis [of] the target DNA”, page 425).
Therefore, Liu et al. anticipate the invention as claimed.
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.
Claims 3 and 27 are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al. (Talanta, 2018, vol. 176, pages 422-427) in view of Li et al. (Talanta, 2018, vol. 178, pages 974-979).
The teachings of Liu et al. have already been discussed above.
While Liu et al. teach a quadruplex forming region of the oligonucleotide that also contains a stem forming region when unbound to target nucleic acid that falls within Applicants’ general formula G3+N2G3+N2G3+X2G3, the artisans do not specifically disclose all possible such sequences, and therefore, do not explicitly teach the sequence of SEQ ID NO: 1 (claim 3), nor 2-aminopurine as part of the sequence for the detectable signal.
While Liu et al. explicitly suggest that their method is applicable for clinical diagnosis, the artisans do not explicitly teach the conventionally knowns steps involved in applying the disclosed method in an actual application of obtaining a clinical diagnosis:
“The proposed method has potential applications in DNA-based molecular diagnostics” (Abstract)
“This detection platform might provide a versatile sensing platform for DNA-based molecular diagnostics” (page 423, 1st column 1st paragraph).
Li et al. teach a sensor comprising a G-quadruplex forming nucleic acid structure comprising an embedded detectable moiety, 2AP, which allows the detection of a quadruplex formation (see Scheme 1):
“quencher-free fluorescent probe is labeled by 2-AP incorporated into a G-rich sequence … H1 is unfolded and forms a G-quadruplex structure upon the addition of a target miRNA, which can result in evident fluorescence enhancement” (page 975, 1st column, 1st paragraph)
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Liu et al. with Li et al., thereby arriving at the invention as claimed for the following reasons.
With regard to the application of the method taught by Liu et al. and following their explicit suggestion to apply it in a clinical diagnostic method (i.e., claim 27), one of ordinary skill in the art would have been naturally led and motivated to employ the conventional steps of obtaining a bodily fluid, extracting target nucleic acids correlated with a condition therefrom, and contacting the extracted sample containing the target nucleic acids utilizing the oligonucleotide probe taught by Liu et al. engineered to contains a target specific region for the target nucleic acids, thereby arriving at a diagnostic method for the condition.
With regard to the specific sequence of claim 3, (i.e., SEQ ID NO: 1), while Liu et al. did not explicitly teach all types of quadruplex forming sequences that can be used in their method, one of ordinary skill in the art would have been fully capable of arriving at the presently claimed sequence because the guidance in the art already suggest the use of GC rich sequences that form self-complementarity to arrive at such a quadruplex structure. Additionally, the fact that the actual probe sequence of Liu et al. comprises a quadruplex forming region which is encompassed by Applicants’ own generic sequence as claimed in claim 2 evidence that any such sequence based on the present understanding of the art would be capable of arriving at such a sequence.
With regard to incorporating a label, 2AP, into the quadruplex forming sequence, one of ordinary skill in the art would have had the motivation to arrive at combining the teachings of Li et al., thereby arriving at the invention as claimed for the following reasons.
In Liu et al.’s method, the detection means relies on the intercalation of a dye (NMM) into a quadruplex structure of a probe which is formed when a hairpin probe binds to a target nucleic acid (see above).
This same principal is applied by Li et al. The difference is in that the label is incorporated into the quadruplex forming sequence itself in the form of 2AP.
In both artisans’ methods, a detectable signal relies on the formation of a quadruplex conformation and a label that is intercalated inside the quadruplex conformation. Whether that label was present in a region of the probe (as taught by Li et al.) or outside the probe (as taught by Liu et al.) would have resulted in the same predictable outcome of an observable signal based on the same quadruplex conformation.
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
Therefore, one of ordinary skill in the art would have been motivated to combine the teachings of Liu et al. and Li et al., thereby arriving at the invention as claimed, as doing so would have relied on the same detectable structure that yielded a
same predicted observable signal.
Conclusion
No claims are allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 October 8, 2025
/YJK/