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 .
Specification
The disclosure is objected to because of the following informalities:
Paragraphs [0137], [0139] and [0141] recite polynucleotide sequence without reciting their sequence identifiers, SEQ ID NO: 6-8, respectively. Appropriate correction is required.
Claims Summary
Claim 1 is directed to a DNA-stabilized metal cluster-based nucleic acid-sensor, comprising:
At least one template nucleotide sequence for silver quantum cluster (AgQC) formation;
At least one target-recognition nucleotide sequence, having a length of 15-50 nt (claim 4); and
At least one nucleotide sequence for intra-molecular hybridization, comprising:
At least one nucleotide sequence which is partially complementary to the target-recognition sequence, and
At least one nucleotide sequence which is partially complementary to the template sequence for AgQC formation (claim 6)
The sensor comprises a stem-loop structure in the absence of a target nucleotide sequence, comprising SEQ ID NO: 1, 2 or 3 (claim 13). The nucleotide sequences of a), b) and c) are part of a single nucleotide strand (claim 2), having a length of 35-89 nt (claim 3). The sensor comprises at least one AgQC (claim 5).
The target-recognition nucleotide sequence of b) comprises at least two partial target-recognition nucleotide sequences (claim 7), and is located in the 5’-region of the single nucleotide strand (presumably a single strand of a), b) and c)) and at least one partial target-recognition nucleotide sequence is located in the 3’-region of a single nucleotide strand (claim 8). The template nucleotide sequence for AgQC formation comprises a stem-loop structure (claim 9).
The sensor comprises at least two excitation maxima and at least two emission maxima in the visible and/or near infrared (NIR) spectrum which are at least 40 nm apart from one another (claim 10). The sensor has a fluorescence spectrum with a first excitation wavelength in the range of 350-550 nm, and a second excitation wavelength in the range of 450-750 nm (claim 11). The sensor has a detection limit of at least 10 nM (claim 12).
Claim 14 is directed to a method for detecting a target polynucleotide, comprising:
Providing a DNA-stabilized metal cluster-based nucleic acid-sensor according to claim 1, in a concentration of 0.1 to 10 µM (claim 15);
Providing a sample comprising the target polynucleotide;
Mixing the sensor with the target polynucleotide;
Measuring the intensities of two fluorescence maxima of the sensor; and
Further comprising (in claim 16) calculating the concentration of the target polynucleotide from the ratio of intensities of two fluorescence maxima of the sensor measured in step iv.
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 3, 4, 8, 10-12 and 14-16 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.
Regarding claims 3, 4, 10-12, and 15 the phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d). The metes and bounds of the claims cannot be determined.
Claim 7 is directed to an embodiment wherein the sensor is composed of at least two partial target-recognition nucleotide sequences. Claim 8 (dependent on claim 7) is directed to an embodiment wherein the partial target-recognition nucleotide sequences are located in the 5’ or 3’ region of a single nucleotide strand. Claim 9 (dependent on claim 7) is directed to an embodiment wherein the template sequence for the AgQC formation comprises a stem-loop structure. The structures outlined in claims 7-9 match the description of Figure 2, reproduced below (wherein (3)a and (3)b represent the partial target-recognition sequences):
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When the target sequence binds (represented in part B) the stem-loop structure of the template sequence for the AgQC is still present. However, claims 7-9 depend from claim 1 which states that the sensor comprises a stem-loop structure in the absence of a target nucleotide sequence, thus implying that the stem-loop structure is not present when the target nucleotide sequence is present. It appears that the language in claim 1 about the stem-loop structure is particular to the construct as set forth in Figure 1, reproduced below:
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In Figure 1, the stem-loop is absent when the target polynucleotide sequence is bound. However, in that construct, there are no partial target-recognition nucleotide sequences. The metes and bounds of the claims cannot be determined.
Claim 8, lines 2-3 recite the limitation "the single nucleotide strand" in claim 7. There is insufficient antecedent basis for this limitation in the claim. The metes and bounds of the claim cannot be determined.
Claim 8, line 4 recites the limitation “a single nucleotide strand” without identifying the strand. The metes and bounds of the claim cannot be determined.
Claims 14 and 15 are directed to methods of detecting a target polynucleotide comprising steps of providing a sensor, providing a sample comprising the target polynucleotide, mixing the sensor with the sample, and measuring intensities of two fluorescence maxima of the sensor. However, there is no step indicating how a target polynucleotide is detected. While all of the technical details of a method need not be recited, the claims should include enough information to clearly and accurately describe the invention and how it is to be practiced. The minimum requirements for method steps minimally include a contacting step in which the reaction of the sample with the reagents necessary for the assay is recited, a detection step in which the reaction steps are quantified or visualized, and a correlation step describing how the results of the assay allow for the determination. The metes and bounds of the claims cannot be determined.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 4-7, 9-12 and 14-16 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims encompass a large genus of nucleic-acid sensors. According to claim 1, the sensor comprises three nucleotide sequences (a sequence for AgQC formation, a target-recognition sequence, and a sequence for intra-molecular hybridization) which comprises a stem-loop structure in the absence of a target nucleotide sequence. Claim 1 does not require that the three sequences be part of a single strand (as in claim 2). Thus the structure of the nucleic-acid sensor, as written, encompasses three separate sequences that are not connected, as long as one of them forms a stem-loop structure in the absence of a target nucleotide sequence.
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, methods of making the claimed product, or any combination thereof.
The specification has provided one species of a nucleic-acid sensor that meets the structural and functional requirements of claim 1. That structure comprises the three nucleotide sequences as a single sequence, see Figure 1 (reproduced above). There are no examples of sensors having three disconnected sequences that form a stem-loop in the absence of a target nucleotide sequence. See paragraph [0128] which describes a single sequence or partially overlapping sequences. Accordingly, in the absence of sufficient recitation of distinguishing identifying characteristics, the specification does not provide adequate written description of the claimed genus. Amendment of claim 1 to incorporate the limitation of claim 2 would overcome this rejection.
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 1-5 and 12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yang et al. (WO 2015/007293 A1, cited in the IDS filed 7/26/2023, “Yang”). The claims are summarized above and correlated with the teachings of the prior art in bold font below.
Yang discloses stem-loop silver nanocluster probes that detect miRNA in biological samples (see abstract). The probe comprises a polycytosine loop sequence consisting of from 6-12 cytosine nucleotides that function as a scaffold for silver nanoclustering, a target complementary sequence comprising at least 21 nucleotides in length, and an anchoring sequence consisting of from 2-12 nucleotides, wherein part of the anchoring sequence is complementary to the target complementary sequence (see page 2, lines 5-19) (claims 1-4). An example of Yang’s probe is in Figure 1, reproduced below:
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Yang’s probe comprises a template nucleotide sequence for AgQC formation (“loop for AgNC”), a target-recognition nucleotide sequence (“sensor for miRNA-21”), and nucleotide sequence for intra-molecular hybridization (“forms loop in the absence of miRNA”) which has a stem-loop structure in the absence of a target nucleotide sequence and whose structure is disturbed when the target nucleotide sequence binds the sensor for miRNA-21 (claim 1, aspect of stem-loop structure). Figure 3 shows a full stem-loop structure and two partial stem-loop structures in the absence of a target nucleotide sequence. Silver clusters are disclosed (see page 10, lines 9-11) (claim 5). Target nucleotide concentration detected is, for example, 0.1 µM (100 nM) (see page 5, lines 9-13) (claim 12). Therefore, the claims are anticipated by the prior art.
Conclusion
No claim is allowed.
Claim 13 is objected to for being dependent on a rejected claim, but would otherwise be allowable if rewritten in independent format. SEQ ID NO: 1, 2 and 3 are free of the prior art of record.
Regarding the subject matter of a sensor comprising at least two excitation maxima and at least two emission maxima (for a single target nucleotide sequence), as in claims 10, 11 and 14-16, Yang et al. (WO 2015/007293 A1, applied in the anticipation rejection above)) does not teach or fairly suggest the use of two different fluorescent probes for a single target nucleotide sequence. Yang et al. suggests multiplex target detection (see page 6, lines 27-29, page 14, lines 29-31, and page 20, lines 15-18) with different maximal excitation/emission wavelengths of probes. However, the instantly claimed sensors and methods of using the sensors differ from Yang et al. because the instantly claimed sensors and methods of using the sensors employ two probes having different maximal excitation/emission wavelengths for the same target.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to Stacy B. Chen whose telephone number is 571-272-0896. The examiner can normally be reached on M-F (7:00-4:30). If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Thomas Visone, can be reached on 571-270-0684. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/STACY B CHEN/Primary Examiner, Art Unit 1672
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