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 .
Applicant’s submission filed on March 13, 2026 has been entered and considered. Rejections and/or objections not reiterated from the previous action mailed December 16, 2025 are hereby withdrawn. The following rejections and/or objections are either newly applied or are reiterated and are the only rejections and/or objections presently applied to the instant application. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Election/Restrictions
Applicant’s election without traverse of Group 1, claims 1 and 6-8 in the reply filed on November 13, 2025 has been acknowledged.
In view of the prior art, the non-elected invention, Group 2, claims 2-5, have been rejoined.
In view of the above noted withdrawal of the restriction requirement, Applicant is advised that if any claim presented in a continuation or divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application.
Once a restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Claims 1 and 6 have been amended. Claims 3-4 and 8 have been canceled. Claims 9 and 10 are newly added.
Claims 1-2, 5-7, and 9-10 are pending and examined on the merits.
Priority
Applicant claims foreign priority to Taiwan patent application TW111150673 filed on December 29, 2022. Receipt is acknowledged of certified copies of papers received in the original language as required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on April 11, 2023 and January 16, 2024 are in compliance with the provisions of 37 CFR 1.97 and are being considered by the examiner.
Applicant is reminded that the listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Rejections - 35 USC § 112 (Written Description)
Claims 1-2 and 5-7 and 9-10 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 claims 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.
This is a new rejection necessitated by Applicant’s amendment. However, this rejection shares substantial similarity to the rejection as previously set forth in the office action dated December 16, 2025 Any aspect of Applicant’s traversal that pertains to the rejection as newly set forth will be provided following the new statement of rejection.
Claim 1 encompasses aptamers comprising SEQ ID NO:7 and SEQ ID NO:9 which are capable of binding to a genus of methylated DNA fragments derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, a promoter of BRCA2, or a combination thereof. However, the specification discloses aptamers consisting of SEQ ID NO:7 which is capable of binding to species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 (see Table 5, SEQ: actgcgactg cgcggcgtga gctcgctgag acttcctgga cgggggacag gctgtggggt ttctcagata actgggccc, primers italicized) and single-stranded methylated DNA fragments comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 (see Table 5, SEQ: gacggttg ggatgcctga caaggaattt cctttcgcca cactgagaaa tacccgcagc ggcccaccca ggcctgactt ccgggtggtg cgtgtgctgc gtgtcgcgtc acggcgtcac gtggccagcg cgggcttgtg gcgcgagctt ctgaaactag gcggcagagg cggagccgct gtggcactgc tgcgcctctg ctgcgcctcg ggtgtc ttttgcggcg gtgggtcgcc gccgggagaa gcgtgagggg, primers italicized) and SEQ ID NO:9 which is capable of binding to species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 (see Table 7, SEQ: gcagac tgggtggcca atccagagcc ccgagagacg cttggctctt tctgtccctc ccatcctctg attgtacctt gatttcgtat tctgagaggc tgctgctt, primers italicized).
Claim 2 encompasses a method for detecting a genus of methylated DNA fragments in a genus of samples comprising mixing the aptamers having SEQ ID NO:7 and SEQ ID NO:9 with the sample so that the DNA aptamer binds to methylated DNA to form a complex and detecting the complex. However, the specification only discloses a method for detecting the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 (see Table 5) which can be detected by the aptamer of SEQ ID NO:7 and single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 (see Table 7) which can be detected by the aptamer of SEQ ID NO:9.
Dependent claim 5 encompasses a genus of method of detection through DNA amplification.
Claim 6 encompasses a method of selecting a DNA aptamer capable of binding to a genus of methylated DNA fragments comprising use of the SELEX process and wherein the DNA aptamers comprise SEQ ID NO:7 and SEQ ID NO:9 and wherein the methylated DNA fragment is derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, a promoter of BRCA2, or a combination thereof. However, the specification discloses a method of selecting aptamers comprising SEQ ID NO:7 which is capable of binding to species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 (see Table 5) and SEQ ID NO:9 which is capable of binding to species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 (See Table 7).
Dependent claim 7 encompasses a genus of single-stranded candidate DNA aptamers having 20-80 nucleotides for use in the method of selecting a DNA aptamer.
Newly added Claim 9 encompasses a DNA aptamer selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragments derived from the promoter of BRCA1 comprising the nucleotide sequence of an amplification product obtained by using a primer pair of SEQ ID NO:10 and SEQ ID NO:11 or a primer pair of SEQ ID NO:14 and SEQ ID NO:15.
Newly added Claim 10 encompasses a DNA aptamer selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragments derived from the promoter of BRCA2 comprising the nucleotide sequence of an amplification product obtained by using a primer pair of SEQ ID NO:12 and SEQ ID NO:13.
Under the written description guidelines (see MPEP 2163) the Examiner is directed to determine whether one skilled in the art would recognize that the Applicant was in possession of the claimed invention as a whole at the time of filing. The following considerations are critical to this determination.
To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. An original claim may lack written description support when (1) the claim defines the invention in functional language specifying a desired result but the disclosure fails to sufficiently identify how the function is performed or the result is achieved or (2) a broad genus claim is presented but the disclosure only describes a narrow species with no evidence that the genus is contemplated. See Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1349-50 (Fed. Cir. 2010) (en banc). The written description requirement is not necessarily met when the claim language appears in ipsis verbis in the specification. "Even if a claim is supported by the specification, the language of the specification, to the extent possible, must describe the claimed invention so that one skilled in the art can recognize what is claimed. The appearance of mere indistinct words in a specification or a claim, even an original claim, does not necessarily satisfy that requirement." Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 968, 63 USPQ2d 1609, 1616 (Fed. Cir. 2002).
Accordingly, to satisfy the written description requirement, the specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1562-63, 19 USPQ2d 1111 (Fed. Cir. 1991). See also MPEP 2163.
Actual Reduction to Practice
With regard to claim 1 encompassing aptamers comprising SEQ ID NO:7 and SEQ ID NO:9 which are capable of binding to a genus of methylated DNA fragments derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, a promoter of BRCA2, or a combination thereof, the specification only provides examples of binding of single-stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments from BRCA2 comprising the sequences between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 by the aptamer having SEQ ID NO:7 (See Table 5) and examples of binding of single-stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15 by the aptamer having SEQ ID NO:9 (See Table 7). The specification provides no indication that the DNA aptamers comprising SEQ ID NO:7 and SEQ ID NO:9 are able to bind methylated DNA fragments other than those of the single-stranded BRCA1 or BRCA2 sequences as disclosed. The specification also has not shown that the aptamer of SEQ ID NO:7 is able to detect single-stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15 nor that the aptamer of SEQ ID NO:9 is able to detect single stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments from BRCA2 comprising the sequences between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which is encompassed by the amended claim language regarding combinations thereof.
With regard to claim 2 encompassing a method for detecting methylated DNA fragments in a sample comprising mixing the aptamers having SEQ ID NO:7 and SEQ ID NO:9 with the sample so that the DNA aptamer binds to methylated DNA to form a complex and detecting the complex, the specification only provides detection of methylated DNA fragments comprising the single-stranded sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and the single-stranded sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which are detectable by the aptamer having SEQ ID NO:7 (Table 5) and detection of methylated DNA fragments comprising the single-stranded sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 which are detectable by the aptamer having SEQ ID NO:9 (Table 7).
With regard to dependent claim 5 encompassing a genus detecting steps comprising DNA amplification, as stated above, the specification only describes a method wherein the methylated DNA fragment comprises the single-stranded sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and the single-stranded sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 detectable by the aptamer of SEQ ID NO:7 and wherein the methylated DNA fragment comprises the single-stranded sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 detectable by the aptamer of SEQ ID NO:9.
With regard to claims 6 encompassing a method of selecting a DNA aptamer capable of binding methylated DNA fragments comprising use of the SELEX process and wherein the DNA aptamers comprise SEQ ID NO:7 and SEQ ID NO:9, the specification only provides support for a method of selecting DNA aptamers capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which can be detected by the aptamer having SEQ ID NO: 7 and the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers SEQ ID NO:14 and SEQ ID NO:15 which can be detected by the aptamer having SEQ ID NO:9. The specification provides no indication that the method of selecting a DNA aptamer would generate a DNA aptamer capable of binding methylated DNA fragments other than those of the BRCA1 or BRCA2 sequences as disclosed. The specification also has not shown that the aptamer of SEQ ID NO:7 is able to detect single-stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15 nor that the aptamer of SEQ ID NO:9 is able to detect single stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments from BRCA2 comprising the sequences between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which is encompassed by the amended claim language regarding combinations thereof.
Accordingly, Applicant did not demonstrate a reduction to practice of aptamers comprising SEQ ID NO: 7 and SEQ ID NO: 9 which are capable of binding any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, or a combination thereof, methods of detection of any methylated DNA fragment using aptamers comprising SEQ ID NO: 7 and SEQ ID NO: 9, or methods of selecting a DNA aptamer capable of binding any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, or a combination thereof; nor did Applicant adequately set forth in terms of distinguishing identifying characteristics as evidenced by other descriptions of the invention that are sufficiently detailed to show that Applicant was in possession of the claimed genus of aptamers binding any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, or a combination thereof, methods of detecting the genus of methylated DNA fragments using aptamers, and selecting aptamers which can bind to the genus of methylated DNA fragments derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, or a combination thereof. Further, Applicant provided evidence of binding of aptamers comprising SEQ ID NO: 7 and SEQ ID NO: 9 which are each capable of binding to specific methylated BRCA1 and BRCA2 fragments.
With regard to claim 7 encompassing a genus of single-stranded candidate DNA aptamers having 20-80 nucleotides for use in the method of selecting a DNA aptamer. The specification only provides support for a method of selecting DNA aptamers capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which can be detected by the aptamer having SEQ ID NO: 7 and the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers SEQ ID NO:14 and SEQ ID NO:15 which can be detected by the aptamer having SEQ ID NO:9.
With regard to newly added claim 9, encompassing a DNA aptamer selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragments derived from the promoter of BRCA1 comprising the nucleotide sequence of an amplification product obtained by using a primer pair of SEQ ID NO:10 and SEQ ID NO:11 or a primer pair of SEQ ID NO:14 and SEQ ID NO:15. The specification only provides support for an aptamer having SEQ ID NO:7 which is capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and an aptamer having SEQ ID NO:9 which is capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 between the primers of SEQ ID NO:14 and SEQ ID NO:15.
With regard to newly added claim 10, encompassing a DNA aptamer selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragments derived from the promoter of BRCA2 comprising the nucleotide sequence of an amplification product obtained by using a primer pair of SEQ ID NO:12 and SEQ ID NO:13. The specification only provides support for an aptamer having SEQ ID NO:7 which is capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO:12 and SEQ ID NO:13.
Disclosure of structure
Applicant’s claims to aptamers comprising SEQ ID NO: 7 and SEQ ID NO: 9 only provides working examples of DNA aptamers which are capable of binding to methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and SEQ ID NO:14 and SEQ ID NO:15 and the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13; methods of detecting a methylated DNA fragment comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and SEQ ID NO:14 and SEQ ID NO:15 and the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13; and methods of selecting a DNA aptamer which is capable of binding to methylated DNA fragments having the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and SEQ ID NO:14 and SEQ ID NO:15 and the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13. Specifically, Applicant has provided working examples of an aptamer having SEQ ID NO:7 which is capable of binding to single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 (See Table 5) and an aptamer having SEQ ID NO:9 which is capable of binding to single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 (See Table 7).
While Applicant did provide examples wherein methylated fragments of BRCA1 and BRCA2 promoters having the sequences as detailed above were used to confirm the ability of the isolated aptamers to bind methylated BRCA1 and BRCA2 fragments comprising the specific sequences as compared to a negative control of unmethylated BRCA1 and BRCA2 fragments comprising the specific sequences, Applicant does not provide any indication that the aptamers would bind any other methylated DNA fragment besides those listed above nor does Applicant provide any indication that the aptamer having SEQ ID NO:7 would bind to single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 or that the aptamer having SEQ ID NO:9 would bind to single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13. Accordingly, the method of detection of a methylated DNA fragment by using the instantly claimed aptamer is also limited to detection of the methylated BRCA1 and BRCA2 fragments as detailed above and the method of selecting an aptamer comprising SEQ ID NO: 7 and SEQ ID NO: 9 would be limited to an aptamer which specifically bind to the methylated BRCA1 and BRCA2 fragments as detailed above.
Applicant’s specification discloses that single-stranded methylated and unmethylated poly-GC fragments comprising the structure as shown on Pg. 15 were used in a SELEX method in order to select an aptamer capable of binding to methylated DNA fragments from a library of DNA aptamers. Applicant does not indicate which bases of the poly GC target fragment were methylated nor does Applicant provide any structural information about the instantly claimed aptamers including 2D or 3D structure or which structural domains of the aptamer are responsible for binding to methylated DNA, both of which would be known to be important for determination of the functional ability of the aptamer by one of ordinary skill in the art. Applicant also provides no information about the specific recognition sequence of the aptamer which is capable of binding to methylated DNA. Thus, there is no way to determine what particular targets are able to be recognized by the aptamer based on sequence information. Although the SELEX process of identifying an aptamer is well-known, the prior art is silent with respect to specific aptamers which are capable of binding to any methylated DNA fragment and the instant specification does not indicate a relationship between the structure of the claimed aptamer and its functional ability to bind to or identify the genus of all methylated DNA fragments as claimed. Therefore, a skilled artisan would not know whether the aptamers as instantly claimed would bind to any methylated DNA fragments or could be used to detect any methylated DNA fragments nor would a skilled artisan be able to predict which methylated DNA fragments beyond those having the sequences of BRCA1 and BRCA2 as detailed above are likely to be bound and/or detected by the instantly claimed aptamer.
STATE OF THE ART & QUANTITY OF EXPERIMENTATION
The DNA aptamer of the claimed invention, the methods of using the DNA aptamer for detection of methylated DNA, and method of selecting an aptamer for binding to methylated DNA is not well established. Although the method of making aptamers capable of specific binding using the SELEX process is well known, one of skill in the art would neither expect or predict a successful outcome of binding the genus of any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, BRCA2, or a combination thereof; detection of the genus of any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, BRCA2, or a combination thereof; or selecting a DNA aptamer capable of binding to the genus of any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, BRCA2, or a combination thereof using the aptamers as instantly claimed. Additionally, it would not be predictable that the aptamer as instantly disclosed could be used for detection of any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, BRCA2, or a combination thereof across any type of sample.
Although the prior art is silent as to specific aptamers which are able to bind to methylated DNA, Domenyuk et al. (WO 2017/161357 A1, found in IDS dated 01/16/2024) discloses oligonucleotide probes, i.e. aptamers, which may be a nucleic acid molecule (Para. [0006]) including DNA (Para. [0012], line 1) and which can be used to assess the presence or level of biomarkers in a biological sample (e.g., a nucleic acid) via contact between the aptamer and a selected biological sample allowing for binding between the aptamer and target molecules (Para. [0121], lines 1-8). Domenyuk discloses wherein an aptamer can be used to identify “biosignatures” of the biological samples (Para [0121], line 9) and wherein the biosignature can be methylation (Para. [0121], line 14). Additionally, Domenyuk discloses use of the SELEX method for generating an aptamer (Para. [00194], lines 1-6) which can be used to isolate and identify aptamers which bind to “any envisionable target” (Para. [0206], lines 3-4, see also Para. [00215], lines 1-2). Domenyuk discloses that a variety of primary, secondary, and tertiary structures of nucleic acids are known to exist, including hairpin loops, bulges, and pseudoknots (Para. [00214], lines 1-3). Domenyuk also discloses that, in aptamer selection, aptamers can have various binding affinities to any given target which is related to their structure and that analysis of the two dimensional structure of an aptamer is important in order to identify aptamers which have high affinities to a particular target (Para. [00355], lines 1-7). Thus, Domenyuk provides support for variations in predictability of aptamer binding and that knowledge of structural information is important for predicting aptamer biding affinity for a particular target.
In the closest related art such as antibodies which bind to methylcytosine and proteins which are capable of binding to methylated DNA such as zinc finger proteins, binding to cytosine is somewhat unpredictable. Sasai et al. (2010, Sequence-specific recognition of methylated DNA by human zinc-finger proteins. Nucleic acids research, 38(15), 5015-5022) discloses that in mammalian proteins which can recognize methylate DNA, binding occurs either to methylated DNA or to unmethylated consensus sequences (Abstract) and that zinc finger proteins capable of recognizing methylated DNA can bind either to methylated sequences but also unmethylated sequences and that binding to methylated DNA by these proteins is sequence-specific, with the nucleotides surrounding the methylation site directly contributing to binding affinity (Introduction also Discussion, paras. 1-3). Thus, the disclosure of Sasai et al. indicates that the ability to bind to methylated DNA is influenced by not only the methylation site, but the sequences surrounding the methylation site and without that knowledge, binding affinity would be unpredictable.
In art comparing detection of methylation by antibodies and proteins, Suter et al. (2008, Label-free quantitative DNA detection using the liquid core optical ring resonator. Biosensors and Bioelectronics, 23(7), 1003-1009) discloses that in a comparison between methylation binding antibodies and methyl binding proteins, binding of anti-5-methylcytidine antibody has stronger affinity for single stranded DNA (ssDNA) than double stranded DNA (dsDNA) (Abstract; Pg. 1019, right col., top para.) whereas the methyl binding protein MBD-2 has stronger affinity for double stranded DNA than single stranded DNA (Abstract, Pg. 1018, right col, last line). The disclosure of Suter et al. indicates that there is some level of unpredictability of methylation binding affinity based on ssDNA targets and dsDNA targets. As the instantly claimed aptamer was selected using a ssDNA library system and binding to methylated BRAC1/BRCA2 fragments was determined using a ssDNA system, it is not necessarily predictable that the aptamer as claimed will be able to bind any methylated DNA fragment especially given the lack of detailed information about the aptamer’s recognition sequence.
Applicant has claimed aptamers comprising SEQ ID NO: 7 and SEQ ID NO: 9 which bind to a genus of methylated DNA fragments derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, BRCA2, or a combination thereof; a method of detection of a genus of methylated DNA fragments derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, BRCA2, or a combination thereof using the aptamers, and a method of selection of aptamers which are able to bind to a genus of methylated DNA fragments derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, BRCA2, or a combination thereof. However, the specification has only disclosed aptamers consisting of SEQ ID NO: 7, which binds to single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO: 10 and SEQ ID NO: 11 and single-stranded methylated DNA fragments comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 (See Table 5), and SEQ ID NO: 9 which binds to single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO: 14 and SEQ ID NO: 15 (See Table 7).
Accordingly, the specification has disclosed use of an aptamer having SEQ ID NO:7 to detect single-stranded methylated BRCA1 fragments between the primers of SEQ ID NO: 10 and SEQ ID NO: 11 and single-stranded methylated BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 and an aptamer having SEQ ID NO:9 to detect single-stranded methylated BRCA1 fragments between the primers of SEQ ID NO: 14 and SEQ ID NO: 15. Thus, the specification does not contain information which is sufficient to show that Applicant was in possession of the claimed genus of aptamers consisting of SEQ ID NO:7 and SEQ ID NO:9 which bind to any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, BRCA2, or a combination thereof. Additionally, the state of the art indicates that the specificity of compounds which bind to any methylated DNA is highly variable and would require undue experimentation thus one of ordinary skill in the art would neither expect or predict that the instantly claimed aptamers would be able to bind any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, BRCA2, or a combination thereof.
CONCLUSION
Therefore, the Examiner concludes that there is insufficient written description for the instantly claimed genus of aptamers comprising SEQ ID NO:7 and SEQ ID NO:9 binding to any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, and a combination thereof; methods for detecting any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, and a combination thereof using aptamers comprising SEQ ID NO:7 and SEQ ID NO:9; and methods for selecting a DNA aptamer which binds to any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, and a combination thereof wherein the aptamer comprises SEQ ID NO: 7 and SEQ ID NO: 9. Specifically, there is limited description of the ability of aptamers comprising SEQ ID NO: 7 to bind to any methylated DNA fragments beyond the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO: 10 and SEQ ID NO: 11 and the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 and aptamers comprising SEQ ID NO:9 to bind to any methylated DNA fragments beyond the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO: 14 and SEQ ID NO: 15.
Claim Rejections - 35 USC § 112
(Scope of Enablement)
Claims 1-2, 5-7, and 9-10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a DNA aptamer having SEQ ID NO:7 which is able to bind to single-stranded methylated BRCA1 promoter fragments comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and to single-stranded methylated BRCA2 promoter fragments comprising the sequences between primers of SEQ ID NO: 12 and SEQ ID NO: 13 and a DNA aptamer having SEQ ID NO:9 which is able to bind to single-stranded methylated BRCA1 promoter fragments comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15; a method of detection of the specific single-stranded methylated BRCA1 promoter fragments comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and the specific single-stranded methylated BRCA2 promoter fragments comprising the sequences between primers of SEQ ID NO: 12 and SEQ ID NO: 13 using the DNA aptamer having SEQ ID NO:7 and detection of the specific single-stranded methylated BRCA1 promoter fragments comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15 using the DNA aptamer having SEQ ID NO:9; and a method of selection a DNA aptamer having SEQ ID NO:7 using single-stranded methylated BRCA1 promoter fragments comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and to single-stranded methylated BRCA2 promoter fragments comprising the sequences between primers of SEQ ID NO: 12 and SEQ ID NO: 13 and selection of a DNA aptamer having SEQ ID NO:9 using single-stranded methylated BRCA1 promoter fragments comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15, does not reasonably provide enablement for a DNA aptamer consisting of SEQ ID NO: 7 or SEQ ID NO: 9 which is capable of specifically binding to any methylated DNA fragment wherein the methylated DNA fragment is derived from a promoter of a tumor suppressor gene selected from a promoter of BRCA1, a promoter of BRCA2, or a combination thereof; a method for detecting any methylated DNA fragment using an aptamer having SEQ ID NO:7 or SEQ ID NO:9; and a method for selecting a DNA aptamer which specifically binds to any methylated DNA fragment wherein the methylated DNA fragment is derived from a promoter of a tumor suppressor gene selected from a promoter of BRCA1, a promoter of BRCA2, or a combination thereof using the aptamer having SEQ ID NO:7 or SEQ ID NO:9.
The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
SCOPE OF THE INVENTION
Claim 1 encompasses aptamers comprising SEQ ID NO:7 and SEQ ID NO:9 which are capable of binding to a genus of methylated DNA fragments derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, a promoter of BRCA2, or a combination thereof. However, the specification discloses aptamers consisting of SEQ ID NO:7 which is capable of binding to species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 (see Table 5, SEQ: actgcgactg cgcggcgtga gctcgctgag acttcctgga cgggggacag gctgtggggt ttctcagata actgggccc, primers italicized) and single-stranded methylated DNA fragments comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 (see Table 5, SEQ: gacggttg ggatgcctga caaggaattt cctttcgcca cactgagaaa tacccgcagc ggcccaccca ggcctgactt ccgggtggtg cgtgtgctgc gtgtcgcgtc acggcgtcac gtggccagcg cgggcttgtg gcgcgagctt ctgaaactag gcggcagagg cggagccgct gtggcactgc tgcgcctctg ctgcgcctcg ggtgtc ttttgcggcg gtgggtcgcc gccgggagaa gcgtgagggg, primers italicized) and SEQ ID NO:9 which is capable of binding to species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 (see Table 7, SEQ: gcagac tgggtggcca atccagagcc ccgagagacg cttggctctt tctgtccctc ccatcctctg attgtacctt gatttcgtat tctgagaggc tgctgctt, primers italicized).
Claim 2 encompasses a method for detecting a genus of methylated DNA fragments in a genus of samples comprising mixing the aptamers having SEQ ID NO:7 and SEQ ID NO:9 with the sample so that the DNA aptamer binds to methylated DNA to form a complex and detecting the complex. However, the specification only discloses a method for detecting the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 (see Table 5) which can be detected by the aptamer of SEQ ID NO:7 and single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 (see Table 7) which can be detected by the aptamer of SEQ ID NO:9.
Dependent claim 5 encompasses a genus of method of detection through DNA amplification.
Claim 6 encompasses a method of selecting a DNA aptamer capable of binding to a genus of methylated DNA fragments comprising use of the SELEX process and wherein the DNA aptamers comprise SEQ ID NO:7 and SEQ ID NO:9 and wherein the methylated DNA fragment is derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, a promoter of BRCA2, or a combination thereof. However, the specification discloses a method of selecting aptamers comprising SEQ ID NO:7 which is capable of binding to species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 (see Table 5) and SEQ ID NO:9 which is capable of binding to species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 (See Table 7).
Dependent claim 7 encompasses a genus of single-stranded candidate DNA aptamers having 20-80 nucleotides for use in the method of selecting a DNA aptamer.
Newly added Claim 9 encompasses a DNA aptamer selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragments derived from the promoter of BRCA1 comprising the nucleotide sequence of an amplification product obtained by using a primer pair of SEQ ID NO:10 and SEQ ID NO:11 or a primer pair of SEQ ID NO:14 and SEQ ID NO:15.
Newly added Claim 10 encompasses a DNA aptamer selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragments derived from the promoter of BRCA2 comprising the nucleotide sequence of an amplification product obtained by using a primer pair of SEQ ID NO:12 and SEQ ID NO:13.
The factors to be considered in determining whether undue experimentation is required are summarized In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988). The Court in Wands states: “Enablement is not precluded by the necessity for some 'experimentation.'” Clearly, enablement of a claimed invention cannot be predicated on the basis of quantity of experimentation required to make or use the invention. “Whether undue experimentation is needed is not a single simple factual determination, but rather is a conclusion reached by weighing many factual considerations.” (Wands, 8 USPQ2d 1404). The factors to be considered in determining whether undue experimentation is required include: (1) the quantity of experimentation necessary, (2) the amount or direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims. While all of these factors are considered, a sufficient amount for a prima facie case is discussed below.
The office has analyzed the specification in direct accordance to the factors outlined in In re Wands. MPEP 2164.04 states: "[W]hile the analysis and conclusion of a lack of enablement are based on factors discussed in MPEP 2164.01(a) and the evidence as whole, it is not necessary to discuss each factor in written enablement rejection." These factors will be analyzed, in turn, to demonstrate that one of ordinary skill in the art would have had to perform "undue experimentation" to make and/or use the invention and therefore, Applicant's claims are not enabled commensurate with the scope of the invention.
Actual Reduction to Practice
With regard to claim 1 encompassing aptamers comprising SEQ ID NO:7 and SEQ ID NO:9 which are capable of binding to a genus of methylated DNA fragments derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, a promoter of BRCA2, or a combination thereof; the specification only provides examples of binding of single-stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments from BRCA2 comprising the sequences between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 by the aptamer having SEQ ID NO:7 (See Table 5) and examples of binding of single-stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15 by the aptamer having SEQ ID NO:9 (See Table 7). The specification provides no indication that the DNA aptamers comprising SEQ ID NO:7 and SEQ ID NO:9 are able to bind methylated DNA fragments other than those of the single-stranded BRCA1 or BRCA2 sequences as disclosed. The specification also has not shown that the aptamer of SEQ ID NO:7 is able to detect single-stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15 nor that the aptamer of SEQ ID NO:9 is able to detect single stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments from BRCA2 comprising the sequences between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which is encompassed by the amended claim language regarding combinations thereof.
With regard to claim 2 encompassing a method for detecting methylated DNA fragments in a sample comprising mixing the aptamers having SEQ ID NO:7 and SEQ ID NO:9 with the sample so that the DNA aptamer binds to methylated DNA to form a complex and detecting the complex, the specification only provides detection of methylated DNA fragments comprising the single-stranded sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and the single-stranded sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which are detectable by the aptamer having SEQ ID NO:7 (Table 5) and detection of methylated DNA fragments comprising the single-stranded sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 which are detectable by the aptamer having SEQ ID NO:9 (Table 7).
With regard to dependent claim 5 encompassing a genus detecting steps comprising DNA amplification, as stated above, the specification only describes a method wherein the methylated DNA fragment comprises the single-stranded sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and the single-stranded sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 detectable by the aptamer of SEQ ID NO:7 and wherein the methylated DNA fragment comprises the single-stranded sequence of BRCA1 fragments between the primers of SEQ ID NO:14 and SEQ ID NO:15 detectable by the aptamer of SEQ ID NO:9.
With regard to claim 6 encompassing a method of selecting a DNA aptamer capable of binding methylated DNA fragments comprising use of the SELEX process and wherein the DNA aptamers comprise SEQ ID NO:7 and SEQ ID NO:9, the specification only provides support for a method of selecting DNA aptamers capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which can be detected by the aptamer having SEQ ID NO: 7 and the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers SEQ ID NO:14 and SEQ ID NO:15 which can be detected by the aptamer having SEQ ID NO:9. The specification provides no indication that the method of selecting a DNA aptamer would generate a DNA aptamer capable of binding methylated DNA fragments other than those of the BRCA1 or BRCA2 sequences as disclosed. The specification also has not shown that the aptamer of SEQ ID NO:7 is able to detect single-stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15 nor that the aptamer of SEQ ID NO:9 is able to detect single stranded methylated DNA fragments from BRCA1 comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated DNA fragments from BRCA2 comprising the sequences between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which is encompassed by the amended claim language regarding combinations thereof.
Accordingly, Applicant did not demonstrate a reduction to practice of aptamers comprising SEQ ID NO: 7 and SEQ ID NO: 9 which are capable of binding any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, or a combination thereof, methods of detection of any methylated DNA fragment using aptamers comprising SEQ ID NO: 7 and SEQ ID NO: 9, or methods of selecting a DNA aptamer capable of binding any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, or a combination thereof; nor did Applicant adequately set forth in terms of distinguishing identifying characteristics as evidenced by other descriptions of the invention that are sufficiently detailed to show that Applicant was in possession of the claimed genus of aptamers binding any methylated DNA fragment derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, or a combination thereof, methods of detecting the genus of methylated DNA fragments using aptamers, and selecting aptamers which can bind to the genus of methylated DNA fragments derived from a promoter of a tumor suppressor gene selected from the group consisting of BRCA1, BRCA2, or a combination thereof. Further, Applicant provided evidence of binding of aptamers comprising SEQ ID NO: 7 and SEQ ID NO: 9 which are each capable of binding to specific methylated BRCA1 and BRCA2 fragments.
With regard to claim 7 encompassing a genus of single-stranded candidate DNA aptamers having 20-80 nucleotides for use in the method of selecting a DNA aptamer. The specification only provides support for a method of selecting DNA aptamers capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 which can be detected by the aptamer having SEQ ID NO: 7 and the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers SEQ ID NO:14 and SEQ ID NO:15 which can be detected by the aptamer having SEQ ID NO:9.
With regard to newly added claim 9, encompassing a DNA aptamer selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragments derived from the promoter of BRCA1 comprising the nucleotide sequence of an amplification product obtained by using a primer pair of SEQ ID NO:10 and SEQ ID NO:11 or a primer pair of SEQ ID NO:14 and SEQ ID NO:15. The specification only provides support for an aptamer having SEQ ID NO:7 which is capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 fragments between the primers of SEQ ID NO:10 and SEQ ID NO:11 and an aptamer having SEQ ID NO:9 which is capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA1 between the primers of SEQ ID NO:14 and SEQ ID NO:15.
With regard to newly added claim 10, encompassing a DNA aptamer selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragments derived from the promoter of BRCA2 comprising the nucleotide sequence of an amplification product obtained by using a primer pair of SEQ ID NO:12 and SEQ ID NO:13. The specification only provides support for an aptamer having SEQ ID NO:7 which is capable of binding to the species of single-stranded methylated DNA fragments comprising the sequence of BRCA2 fragments between the primers of SEQ ID NO:12 and SEQ ID NO:13.
STATE OF THE ART & QUANTITY OF EXPERIMENTATION
The DNA aptamer of the claimed invention, the methods of using the DNA aptamer for detection of methylated DNA, and method of selecting an aptamer for binding to methylated DNA is not well established and the state of the art teaches that specific binding of aptamers and of methylated DNA is highly variable. Consequently, there is ample reason to conclude that there would be a high degree of unpredictability in aptamer binding affinity and therefore subsequent use of that aptamer for detection of a broad genus of compounds.
Although the prior art is silent as to specific aptamers which are able to bind to methylated DNA, Domenyuk et al. (WO 2017/161357 A1, found in IDS dated 01/16/2024) discloses oligonucleotide probes, i.e. aptamers, which may be a nucleic acid molecule (Para. [0006]) including DNA (Para. [0012], line 1) and which can be used to assess the presence or level of biomarkers in a biological sample (e.g., a nucleic acid) via contact between the aptamer and a selected biological sample allowing for binding between the aptamer and target molecules (Para. [0121], lines 1-8). Domenyuk discloses wherein an aptamer can be used to identify “biosignatures” of the biological samples (Para [0121], line 9) and wherein the biosignature can be methylation (Para. [0121], line 14). Additionally, Domenyuk discloses use of the SELEX method for generating an aptamer (Para. [00194], lines 1-6) which can be used to isolate and identify aptamers which bind to “any envisionable target” (Para. [0206], lines 3-4, see also Para. [00215], lines 1-2). Domenyuk discloses that a variety of primary, secondary, and tertiary structures of nucleic acids are known to exist, including hairpin loops, bulges, and pseudoknots (Para. [00214], lines 1-3). Domenyuk also discloses that, in aptamer selection, aptamers can have various binding affinities to any given target which is related to their structure and that analysis of the two dimensional structure of an aptamer is important in order to identify aptamers which have high affinities to a particular target (Para. [00355], lines 1-7). Thus, Domenyuk provides support for variations in predictability of aptamer binding for a particular target based on structure and that there would be a lack of predictability regarding specificity of aptamer binding across a broad genus of targets.
In the closest related art such as antibodies which bind to methyl-cytosine and proteins which are capable of binding to methylated DNA such as zinc finger proteins, binding to cytosine is somewhat unpredictable. Sasai et al. (2010, Sequence-specific recognition of methylated DNA by human zinc-finger proteins. Nucleic acids research, 38(15), 5015-5022) discloses that in mammalian proteins which can recognize methylated DNA, binding occurs either to methylated DNA or to unmethylated consensus sequences (Abstract) and that zinc finger proteins capable of recognizing methylated DNA can bind either to methylated sequences but also unmethylated sequences and that binding to methylated DNA by these proteins is sequence-specific, with the nucleotides surrounding the methylation site directly contributing to binding affinity (Introduction also Discussion, paras. 1-3). Thus, the disclosure of Sasai et al. indicates that the ability to bind to methylated DNA is influenced by not only the methylation site, but the sequences surrounding the methylation site and without that knowledge, binding affinity would be unpredictable.
In art comparing detection of methylation by antibodies and proteins, Suter et al. (2008, Label-free quantitative DNA detection using the liquid core optical ring resonator. Biosensors and Bioelectronics, 23(7), 1003-1009) discloses that in a comparison between methylation binding antibodies and methyl binding proteins, binding of anti-5-methylcytidine antibody has stronger affinity for single stranded DNA (ssDNA) than double stranded DNA (dsDNA) (Abstract; Pg. 1019, right col., top para.) whereas the methyl binding protein MBD-2 has stronger affinity for double stranded DNA than single stranded DNA (Abstract, Pg. 1018, right col, last line). The disclosure of Suter et al. indicates that there is some level of unpredictability of methylation binding affinity based on ssDNA targets and dsDNA targets. As the instantly claimed aptamer was selected using a ssDNA library system and binding to methylated BRAC1/BRCA2 fragments was determined using a ssDNA system, it is not necessarily predictable that the aptamer as claimed will be able to bind any methylated DNA fragment especially given the lack of detailed information about the aptamer’s recognition sequence.
Since the prior art at the effective filing date of the present application did not provide guidance for DNA aptamers having SEQ ID NO: 7 and SEQ ID NO: 9 which are able to bind any methylated DNA fragments which are derived from a promoter of BRCA1, BRCA2, or a combination thereof; use of DNA aptamers having SEQ ID NO: 7 and SEQ ID NO: 9 to detect any methylated DNA fragment; and a method of selecting DNA aptamers having SEQ ID NO: 7 and SEQ ID NO: 9 which are capable of binding any methylated DNA fragment which are derived from a promoter of BRCA1, BRCA2, or a combination thereof; it is incumbent upon the instant specification to do so. The physiological art is recognized as unpredictable (MPEP 2164.03). As set forth in In re Fisher, 166 USPQ 18 (CCPA 1970), compliance with 35 USC 112, first paragraph requires: “That scope of claims must bear a reasonable correlation to scope of enablement provided by specification to persons of ordinary skill in the art; in cases involving predictable factors, such as mechanical or electrical elements, a single embodiment provides broad enablement in the sense that, once imagined, other embodiments can be made without difficulty and their performance characteristics predicted by resort to known scientific laws; in cases involving unpredictable factors, such as most chemical reactions and physiological activity, scope of enablement varies inversely with degree of unpredictability of factors involved.” Moreover, the courts have also stated that reasonable correlation must exist between scope of exclusive right to patent application and scope of enablement set forth in the patent application (27 USPQ2d 1662 Ex parte Maize!.). In view of the foregoing, due to the lack of sufficient guidance provided by the specification regarding the issues set forth above, the state of the relevant art, and the breadth of the claims, it would have required undue experimentation for one skilled in the art to make and use the instant broadly claimed invention.
CONCLUSION
In conclusion, since the art teaches methylation binding specificity is dependent on adjacent recognition sequences in methyl binding proteins, that methyl binding antibodies and proteins have differing affinities for ssDNA and dsDNA, and that target-specific aptamer specificity is influenced by things like conformational structure; and the specification does not provide ample guidance with respect to the specific structural elements which are necessary for specific binding to methylated DNA by SEQ ID NOs:7 and 9, one would be burdened with undue experimentation in order to use the claimed invention for binding of any methylated DNA fragment derived from a promoter of BRCA1, BRCA2, or a combination thereof; detecting any methylated DNA fragment in a sample using aptamers having SEQ ID NO:7 or SEQ ID NO:9; and selecting an aptamer having SEQ ID NO:7 or SEQ ID NO:9 which is capable of binding to any methylated DNA fragment derived from a promoter of BRCA1, BRCA2, or a combination thereof. Given the breadth of the claims and the limited scope of the specification, an undue quantity of experimentation is required to make and use the invention beyond the scope of a DNA aptamer having SEQ ID NO:7 which is able to bind to single-stranded methylated BRCA1 fragments comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated BRCA2 fragments comprising the sequences between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 and a DNA aptamer having SEQ ID NO:9 which is able to bind to single-stranded methylated BRCA1 fragments comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15; methods of use of DNA aptamers having SEQ ID NO:7 in order to detect single-stranded methylated BRCA1 fragments comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated BRCA2 fragments comprising the sequences between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 and DNA aptamers having SEQ ID NO:9 in order to detect single-stranded methylated BRCA1 fragments comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15; and a method of selecting a DNA aptamer having SEQ ID NO:7 using single-stranded methylated BRCA1 fragments comprising the sequences between primers of SEQ ID NO:10 and SEQ ID NO:11 and single-stranded methylated BRCA2 fragments comprising the sequences between the primers of SEQ ID NO: 12 and SEQ ID NO: 13 and selecting a DNA aptamer having SEQ ID NO:9 using single-stranded methylated BRCA1 fragments comprising the sequences between primers of SEQ ID NO:14 and SEQ ID NO:15.
Response to Arguments
Applicant's arguments filed March 13, 2026 have been fully considered but they are not persuasive.
With regard to the rejection of claims 1-6 and 8 under 35 U.S.C. 112(a) for not complying with the written description requirement, Applicant has canceled claims 2-3 and 8 rendering rejections form those claims moot. Applicant asserts that claims 1 and 6 are currently amended to recite a methylated DNA fragment comprising a nucleotide sequence selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragment is derived from the promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, a promoter of BRCA2, and a combination thereof and that Applicant was in possession of the instantly claimed aptamers at the time of filing.
With regard to the rejection of claim 1-6 and 8 under U.S.C. 112(a) for not complying with the enablement requirement, Applicant has canceled claims 2-3 and 8 rendering rejections form those claims moot. Applicant asserts that claims 1 and 6 are currently amended to recite a methylated DNA fragment comprising a nucleotide sequence selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:9 wherein the methylated DNA fragment is derived from the promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, a promoter of BRCA2, and a combination thereof are enabled and that a person having ordinary skill in the art would be able to make and use the claimed invention without undue experimentation.
Applicant’s arguments have been fully considered but are not persuasive.
In light of Applicant’s amendments to further limit the instantly claimed aptamers, the rejections under 35 U.S.C. 112(a) have been updated. While the instantly claimed aptamers consisting of SEQ ID NO:7 and SEQ ID NO:9 are free of the art, Applicant’s instant claims recite that “the methylated DNA fragment is derived from a promoter of a tumor suppressor gene selected from the group consisting of a promoter of BRCA1, a promoter of BRCA2, and a combination thereof”. Regarding the promoters of BRCA1 and BRCA2, Applicant’s instant specification only provides support for the specific single-stranded methylated DNA fragments derived from a promoter of BRCA1 which comprises a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 10 and SEQ ID NO: 11 or SEQ ID NO: 14 and SEQ ID NO: 15 and specific single-stranded methylated DNA fragments derived from a promoter of BRCA2 which comprises a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 12 and SEQ ID NO: 13 as instantly claimed in newly added claims 9 and 10. Further, Applicant’s instant specification only provides support for an aptamer consisting of SEQ ID NO:7 which specifically binds to the specific single-stranded methylated DNA fragments derived from a promoter of BRCA1 which comprises a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 10 and SEQ ID NO: 11 and specific single-stranded methylated DNA fragments derived from a promoter of BRCA2 which comprises a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 12 and SEQ ID NO: 13 and an aptamer consisting of SEQ ID NO:9 which specifically binds to the specific single-stranded methylated DNA fragments derived from a promoter of BRCA1 which comprises a nucleotide sequence corresponding an amplification product obtained by using primer pairs consisting of SEQ ID NO: 14 and SEQ ID NO: 15.
Similarly, Applicant’s instantly claimed method of for detecting a methylated DNA fragment in a sample comprising mixing the instantly claimed aptamers having SEQ ID NO:7 and SEQ ID NO:9 with a sample, is limited to the ability to detect a single-stranded methylated DNA fragment derived from a promoter of BRCA1 comprising a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 10 and SEQ ID NO: 11 and specific single-stranded methylated DNA fragments derived from a promoter of BRCA2 comprising a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 12 and SEQ ID NO: 13 using the aptamer having SEQ ID NO:7 and the ability to detect a single-stranded methylated DNA fragment derived from a promoter of BRCA1 which comprises a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 14 and SEQ ID NO: 15 using the aptamer having SEQ ID NO:9.
Further, Applicant’s instantly claimed method for selecting a DNA aptamer specifically binding to a methylated DNA fragment is similarly limited to use of a single-stranded methylated DNA fragment derived from a promoter of BRCA1 comprising a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 10 and SEQ ID NO: 11 and a single-stranded methylated DNA fragment derived from a promoter of BRCA2 comprising a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 12 and SEQ ID NO: 13 (which result in the selection of the instantly claimed aptamer having SEQ ID NO:7) and use of a single-stranded methylated DNA fragment derived from a promoter of BRCA1 which comprises a nucleotide sequence corresponding to an amplification product obtained by using primer pairs consisting of SEQ ID NO: 14 and SEQ ID NO: 15 (which results in the selection of the instantly claimed aptamer having SEQ ID NO:9). Thus, the support found in Applicant’s instant specification is not commensurate in scope with the claims as broadly as instantly claimed.
Conclusion
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.
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/ERIN V PAULUS/Examiner, Art Unit 1631
/ARTHUR S LEONARD/Examiner, Art Unit 1631
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