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 .
The claims dated 9/15/2025 are under consideration.
The amendments and arguments presented in the papers filed 9/15/2025 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 6/17/2025 listed below have been reconsidered as indicated.
a) The amendments to the specification addressing nucleotide sequence disclosure requirements is acknowledged.
The Examiner’s responses to the Remarks regarding issues not listed above are detailed below in this Office action.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Priority
The present application is a 317 national stage entry of PCT/US2021/019553 (filed 2/25/2021), which claims benefit of US provisional application 62/981,338 (filed 2/25/2020).
Priority to the ‘338 provisional application is not recognized because it does not support the broad scope of the present claims.
The ‘338 provisional application has a specification that is 5 pages in length, as compared to the present case, which has a 23 page specification.
The ‘338 provisional application provides support for the following:
A structure made of 5 nucleic acid strands, a quartz substrate, Cy3 and Cy5 as donor/acceptor and a target specific binding site is 22 nucleotides.
The present claims broadly encompass more and less than 5 strands, any type of substrate, any donor/acceptor pair and a single strand binding site of any length.
The present claims are given an earliest effective filing date of 2/25/2021, the filing date of the ‘553 PCT application.
Claim Interpretation
The claimed “incomplete 4-way DNA junction” is interpreted of the instant specification, which states (p. 3, lines 8-10):
the incomplete 4-way DNA junction is converted to a complete 4-way DNA junction when the targeted nucleic acid sequence is bound to the sensor.
The term is further interpreted in view of Fig. 8 as described in the instant specification (p. 5, line 32 to p. 6, line 6).
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 and 3-8 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.
The following are new rejections necessitated by the amendments to the claims.
Regarding claim 1, the amended claim recites:
the FRET donor and the FRET acceptor exhibit a detectable static mid-FRET state when the targeted nucleic acid sequence is not bound to the sensor;
the FRET donor and the FRET acceptor undergo detectable continuous dynamic switching between a low- FRET state and high-FRET state when the targeted nucleic acid sequence is bound to the sensor; and
the sensor is configured for detecting the continuous dynamic switching.
The recitation describes a functional property of the claimed sensor and/or a intended use. It is unclear what additional structural elements are required, if any, in order to confer the functional property or to be able to carry out the recited intended use. For example, does the claim require particular FRET donor and FRET acceptors, a particular type of substrate, a particular location or relative location of the FRET donor and FRET acceptors, or a particular length of the first, second, third or fourth arms?
Claims 3-8 depend from claim 1 or require the elements of claim 1 and are rejected for the same reason.
Regarding claim 3, the claim recites “the incomplete 4-way DNA junction is convertible to a complete 4-way DNA junction when the targeted nucleic acid sequence is bound to the sensor”. The recitation is a recitation of a functional property of the claimed sensor and/or a intended use. It is unclear what additional structural elements are required, if any, in order to confer the functional property or the ability to perform the intended use. For example, does it require a particular length or location of the single strand binding site complementary to the targeted nucleic acid sequence?
Response to the traversal of the 112(a) rejections
The Remarks argue claim 2 has been canceled and its features have been substantively incorporated into claim 1 (p. 7).
The arguments have been fully considered but are not persuasive. Claim 1, and the claims that depend from it or incorporate its structures, are rejected as described above. It is unclear if the functional and intended use language of claim 1 imparts further structural limitations on the sensor of claim 1. For example, does the language limit the sensor to having a structural depicted in Figures 1, 6, 8, 9 or 10, which the instant specification characterizes as having the claimed properties and capable of carrying out the recited intended use?
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1 and 3-8 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Ghazal (WO 2007/054682 A1).
Claim 1 as amended recites “A single-molecule sensor for detection of a nucleic acid sequence” in the preamble. The preamble sets forth the intended use of the “single-molecule sensor”, i.e., for detection of a nucleic acid sequence. Here, the body of a claim fully and intrinsically sets forth all of the structural limitations of the claimed invention, and the preamble merely states the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations. For example, the preamble does not reference any of the structural limitations or does it impose a further relationship between any of the structural limitations. Therefore, the preamble is not considered a limitation and is of no significance to claim construction.
Regarding claims 1 and 4, Ghazal teaches a sensor in Figure 27c depicted below:
PNG
media_image1.png
650
680
media_image1.png
Greyscale
The structures of the claimed “incomplete 4-way DNA junction” are identified by the quoted terms in boxes and the arrows added by the Examiner. The “incomplete 4-way DNA junction” of Ghazal further includes a “Donor” as a FRET donor and an “Acceptor” as a FRET acceptor. The “Donor” and “Acceptor” are attached to the first and second double-stranded DNA arms indicated by the Examiner. See also, Figures 1, 2 14(B), 15(B) and 30.
Ghazal further teaches the sensor is “immobilized” or anchored to a surface of a substrate via biotin/streptavidin interactions (p. 12, lines 30-33; and p. 13, lines 25-27; and p. 53, lines 10-17).
The sensor of Ghazal is a “single-molecule sensor” as it is able to capture only a single target DNA sequence at any given time.
Amended claim 1 includes three elements within a “wherein” clause, in particular:
the FRET donor and the FRET acceptor exhibit a detectable static mid-FRET state when the targeted nucleic acid sequence is not bound to the sensor;
the FRET donor and the FRET acceptor undergo detectable continuous dynamic switching between a low- FRET state and high-FRET state when the targeted nucleic acid sequence is bound to the sensor; and
the sensor is configured for detecting the continuous dynamic switching.
The “wherein” clause does not explicitly limit any of the claimed structural limitations addressed above by the teachings of Ghazal. The elements are interpreted as setting forth a property of the structural limitations as claimed and/or an intended use of the claimed structural limitations.
Regarding any intended use language, product claims must be structurally distinguishable from the prior art in terms of their structure, not their functionality. The manner of using a product does not differentiate a product claim from the prior art, if the prior art teaches all of the structural limitations of the claim. See MPEP § 2114 & § 2173.05(g). Here, Ghazal teaches all the structural limitations as presently claimed.
Regarding any claim limitations addressing a property of the claimed sensor, Ghazal teaches all the structure required by the sensor of claim 1 as described above, and thus Ghazal anticipates claim 1. Furthermore, Ghazal teaches all the structural elements required by claim 1, and as a consequence of this Ghazal’s structure has the same properties as the sensor described in claim 1.
It is further noted that the structure of the sensor of Ghazal is substantially similar to that of Figures 1, 6, 8, 9 or 10. The difference lies in the number of nucleic acid molecules that make up the sensors depicted in Figures 1, 6, 8, 9 or 10; however, the claim does not limit the number of nucleic acids that are required in the structure of the claimed sensor or that the strands are made through the hybridization of separate and individual nucleic acids.
Regarding claim 3, Ghazal teaches all the structure required by the sensor of claim 1 as described above. Claim 3 does not require any additional structural elements beyond those of claim 1. As a consequence of having all the structural features required by claim 3, Ghazal anticipates claim 3.
It is further noted that Ghazel demonstrates that upon binding of a target nucleic acid to the sensor, a “complete 4-way DNA junction” is formed (Figure 27c, Figure 30).
It is further noted that the structure of the sensor of Ghazal is substantially similar to that of Figures 1, 6, 8, 9 or 10. The difference lies in the number of nucleic acid molecules that make up the sensors depicted in Figures 1, 6, 8, 9 or 10; however, the claim does not limit the number of nucleic acids that are required in the structure of the claimed sensor or that the strands are made through the hybridization of separate and individual nucleic acids.
Regarding claim 5, Ghazal teaches contacting a biological sample with a target nucleic acid with a “sensor” as depicted in Figure 30. It is noted that the structure of the sensor in Figure 30 is encompassed by the “incomplete 4-way DNA junction” element of claim 1. As noted previously, Ghazal teaches the sensor is “immobilized” or anchored to a surface of a substrate via biotin/streptavidin interactions (p. 12, lines 30-33; and p. 13, lines 25-27; and p. 53, lines 10-17).
Ghazal further teaches detecting continuous dynamic switching of the FRET donor and the FRET acceptor between low-FRET (Tamra signal) and high-FRET (Cy5-signal) levels (Figure 30). The nature of the signal indicates whether the mismatched target or the matched target is bound by the sensor (Figure 30).
See also, p. 57, lines 14-31.
Alternatively, Ghazal teaches detecting dynamic switching of the FRET donor and the FRET acceptor by detecting the FRET ratio (Fig. 13, 29 and 32), including via a decay measurement, which “continuously” detects signals over time.
Regarding claims 6 and 7, Ghazal teaches the targeted nucleic acid includes a mutation or a “mismatch” (Figure 30). See also, p. 57, lines 14-31.
Regarding claims 7 and 8, Ghazal teaches the targeted nucleic acid includes a SNP (p. 35, lines 14-25; and p. 56, lines 12-15), a point mutation.
Response to the traversal of the 102 rejections
The Remarks argue Ghazal is directed bulk FRET while the claimed invention is directed to single-molecule FRET and claims 1, 3 and 4 have been amended to highlight this difference (p. 4).
The arguments have been fully considered but are not persuasive. The arguments are directed to the intended use of the claimed sensor, and does not identify any structural differences between the claimed sensor and that taught by Ghazal.
The Remarks argue the claimed sensor design has, in a preferred embodiment, biotin (see claim 4) and it makes it possible to immobilize sensors on a microscope slide via biotin-streptavidin interaction, ultimately enabling single-molecule FRET. This
is best illustrated in Figure 1 of the application. See p. 4.
The arguments have been fully considered but are not persuasive. It is noted that the features upon which applicant relies (i.e., biotin, microscope slide, biotin-streptavidin interaction, etc.) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). It is reiterated Ghazal further teaches the sensor is “immobilized” or anchored to a surface of a substrate via biotin/streptavidin interactions (p. 12, lines 30-33; and p. 13, lines 25-27; and p. 53, lines 10-17). There is no argument that structurally distinguishes the immobilization encompassed from claim 4 from the structure taught by Ghazal.
The Remarks argue the way the detection is achieved with the claimed sensors and claimed method is very different from Ghazal. Unlike the change in the fluorescence level (or FRET Ratio) in Ghazal, because of the inventor's single-molecule approach, the invention makes it possible to visualize conformational dynamics of each 4-way junction individually (no averaging) as a detection signal as shown in Fig. 3 of the application. See p. 4-5.
The arguments have been fully considered but are not persuasive. The arguments do not point out the particular structural elements or detection elements that are distinguished from that of Ghazal. It is noted that the features upon which applicant relies (i.e., visualizing each 4-way junction individually without averaging) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims.
The Remarks argue the invention offers several additional advantages over the Ghazal approach including: 1) Visualization of the conformational dynamics of individual 4-way DNA junctions provides a very clear detection signal; 2) The claimed sensor is not limited to DNA targets and can be used to detect miRNAs; and 3) The approach taken has the ability to create multiple sensors using the same Cy3-Cy5 FRET pair to use simultaneously in one experiment. See p. 5.
The arguments have been fully considered but are not persuasive. The arguments do not point out the particular structural elements or detection elements that are distinguished from that of Ghazal. It is noted that the features upon which applicant relies (i.e., visualizing 4-way DNA junctions, detecting miRNA targets, multiplex detection, etc.) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims.
The Remarks argue the method of claims 5-8 requires detecting continuous dynamic switching of the FRET donor and the FRET acceptor between low-FRET and high-FRET levels, wherein detection of continuous dynamic switching indicates that the targeted nucleic acid sequence is bound to the sensor. The Remarks contrast Figure 3 of the present application, and Figure 30 of Ghazal (cited in the office action), it can be seen that Ghazal simply does not detect continuous dynamic switching. The Remarks argue Figure 30 of Ghazal shows looking at the counts per second at various wavelengths (i.e., not dynamic switching) in order to make the bulk FRET detection they envision. The Remarks argue claim 5-8 are simply not anticipated by nor are they obvious in Ghazal and to highlight the difference between the sensors described and claimed in the present application and those in Ghazal, claims 1-4 have been amended to highlight that the claimed invention is directed to a single molecule sensor, and claim 1 requires that the sensor is configured to detect continuous dynamic switching. As noted above, this completely differentiates the technology of Ghazal.
The arguments have been fully considered but are not persuasive. The arguments do not identify any structural limitation required by claim 1 that is not taught by Ghazal.
Regarding claims 5-8, the Remarks do not identify any element that is required for detecting “continuous dynamic switching” that distinguishes the claimed method from that of Ghazal.
Ghazal further teaches detecting continuous dynamic switching of the FRET donor and the FRET acceptor between low-FRET (Tamra signal) and high-FRET (Cy5-signal) levels (Figure 30). The nature of the signal indicates whether the mismatched target or the matched target is bound by the sensor (Figure 30). The counts per second measurement is a continuous measurement of the Tamra and Cy5 signals over time.
See also, p. 57, lines 14-31.
Alternatively, Ghazal teaches detecting dynamic switching of the FRET donor and the FRET acceptor by detecting the FRET ratio (Fig. 13, 29 and 32), including via a decay measurement, which “continuously” detects signals over time.
Conclusion
No claims 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 JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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, Wu-Cheng Winston Shen can be reached at 5712723157. 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.
/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682