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 .
Preliminary Remark
Claims 20-24 are canceled.
Election/Restrictions
Applicant’s election without traverse of Group I, and species (I)(a) and (II)(a) in the reply filed on April 27, 2026 is acknowledged. All species requirements have been withdrawn herein and examined to all embodiments.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The IDS received on August 1, 2024 is proper and is being considered by the Examiner.
Drawings
The drawings received on December 8, 2023 are acceptable.
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 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.
Claims 12, 14 and 15 are indefinite for reciting limitations followed by the phrase, “such as,” because it become unclear whether the limitations are actively required or not.
Claim 12 is indefinite for the following reasons. Claim 12 depends from claim 1. Step (iii) of claim 1 recites the step of, “labeling the 5-formylcytosine” residue. Claim 12 refers to this step as comprising “converting the 5-formylcytosine (5fC) residue to a uracil analog”. The Office notes that conversion is not synonymous with labeling because when a conversion occurs, 5fC no longer exists and therefore, 5fC cannot be labeled. Therefore, it becomes indefinite how a conversion of 5fC to 5fU which is a different structure is considered labeling of 5fC.
Claim 16 recites the phrase, “sequencing the polynucleotide following (iii) to produce a treated nucleotide sequence”. This is indefinite because the polynucleotide is “treated” with the reagents at the conclusion of step (iii). The sequencing reaction generates a complementary strand of the product of step (iii) and does not “produce” a treated nucleotide sequence.
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 1-3, 9, 12, 15, and 16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ost, Toby (WO 2014/083118 A1, published June 2014; IDS ref).
With regard to claim 1, Ost teaches a method of identifying a modified cytosine residue in a sample nucleotide sequence (“method of identifying a modified cytosine residue in a sample nucleotide sequence”, page 2, lines 28-29), the method comprising:
providing a population of polynucleotide which comprises the sample nucleotide sequence (“providing a population of polynucleotides which comprise the sample nucleotide sequence”, page 2, lines 30-31);
oxidizing the modified cytosine residue in the population to form a 5-formylcytosine (5fC) residue through a non-enzymatic, one-electron process (“treating a first portion of said population with a metal (VI) oxo complex1”, page 2, lines 33-34);
labelling the 5fC residue (“treating said first portion of said population … with bisulfite2”, page 2, lines 34-35); and
identifying the labelled residue within the population (“identifying the residue in the first and second nucleotide sequences which corresponds to a cytosine residue in the sample nucleotide sequence”, page 3, lines 1-3), wherein the modified cytosine residue is 5hmC (“present inventors have recognised metal (VI) oxo complexes … may be useful in catalysing the selective oxidation of 5hmC residues in polynucleotides to 5fC residues”, page 2, lines 22-24).
With regard to claims 2, 3, and 9 step (ii) involves metal oxo-species (see above, also “metal (VI) oxo complexes, such as ruthenate, may be useful … selective oxidation of 5hmC residues … to 5fC residues”, page 2, lines 22-24; also metal (VI) atom is coordinated with … manganate …”, page 4, lines 26-29).
With regard to claims 12 and 15, step (iii) comprises converting 5fC to a uracil analogue (see “[u]nder the bisulfite reaction conditions that are used to convert 5-formylcytosine to uracil, 5-carboxycytosine is observed to convert to uracil too”, page 7, lines 14-20).
With regard to claim 16, the artisan teaches sequencing the resulting product and identifying the modified cytosines present(“identification of uracil at position in both the first and second nucleotide sequences which corresponds to a cytosine residue in the sample nucleotide sequence is indicative that the cytosine residue in the sample nucleotide sequence is cytosine, 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC)”, claim 24; also “[p]olynucleotides may be sequenced using any convenient low or high throughput sequencing technique or platform”, page 20, lines 4-5).
Therefore, Ost anticipates the invention as claimed.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 4, 10, 11, 18, 19, and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Ost, Toby (WO 2014/083118 A1, published June 2014; IDS ref) in view of Tanabe et al. (JACS, June 2007, vol. 129, pages 8034-8040; IDS ref).
The teachings of Ost have already been discussed above.
While Ost teaches the conversion of 5hmC in DNA sequences of a sample into 5fC, wherein the 5fC is subsequently converted into 5fU via bisulfite, the artisan do not teach the conversion of 5mC (claim 17) in the DNA sequences into 5fC via means of a photocatalyst (claim 4), utilizing a photocatalyst wherein the single-electron oxidant is an organic single-electron oxidant (claim 10), such as those listed in claim 11.
Ost does not teach that the product mole ratio of 5fC to modified cytosine residues to 10:90 or more (claim 18), 2:1 or higher (claim 19).
Tanabe et al. teach a 5-methylated cytosine in a DNA strand can be converted into 5fC, for the detection of the methylated cytosine (“photosensitization of an NQ-tethered duplex showed that mC was efficiently one-electron oxidized into 5-formylcytosine, while the corresponding normal C did not undergo such an oxidation”, page 8035, 1st column, 1st paragraph).
Tanabe et al. teach that the photo oxidation reaction is performed in the presence of a photocatalyst that is an organic agent, 1,4-naphthoquinone (NQ) (see page 8034, 2nd column).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Ost with the teachings of Tanabe et al., thereby arriving at the invention as claimed for the following reasons.
As discussed above, Ost already teaches the importance of being able to identify the presence of modified cytosine residues, such as methylated and hydroxymethylated cytosine residues in a DNA sequence:
“5-methylcytosine (5mC) is a well-known epigenetic DNA mark that plays important roles in gene silencing and genome stability, and if found enriched at CpG dinucleotides … 5mCs can be oxidized to 5-hydroxymethylcytosine (5hmC)” (page 1, lines 8-11)
Since Ost already taught that a modified cytosine can be first converted into 5fC and subsequently converted into 5fU, allowing their detection from non-modified cytosines, one of ordinary skill in the art would have also had a reasonable expectation of success that means of converting methylcytosines to 5fCs (as taught by Tanabe et al.) can also be combined with the teachings of Ost, and be detected by a subsequent conversion into 5fUs (much like the 5hmCs), yielding a predictable outcome.
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
As to the conversion ratio of 5fC from 5hmC, the Office asserts that the method disclosed by Ost would have resulted in the conversion of the modified cytosines into 5fCs as the claims employ the reagents as presently employed.
According to In re Best 195 USPQ 430, 1997, the court stated that, “Patent Office can require applicant to prove that prior art products do not necessarily or inherently possess characteristics of his claimed product wherein claimed and prior art products are identical or substantially identical, or are produced by identical or substantially identical processes; burden of proof is on applicant” (pp. 430).
Lastly, with regard to the use of the single-electron oxidants recited in claim 11, based on the teachings provided by Tanabe et al., arriving at other single-electron oxidant catalyst that would have allowed conversion of the methylated cytosines into 5fCs would have been well-within the purview of the ordinarily skilled artisan in the field of organic chemistry, wherein such determination would have required routine experimentation, absent evidence to the contrary that such reagent yielded a superior product or provided unexpected outcome.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Claims 5 is rejected under 35 U.S.C. 103 as being unpatentable over Ost, Toby (WO 2014/083118 A1, published June 2014; IDS ref) in view of Tanabe et al. (JACS, June 2007, vol. 129, pages 8034-8040; IDS ref), as applied to claims 4, 10, 11, 18, 19, and 25 above, and further in view of Jin et al. (Advanced Synthesis & Catalyst, 2019, vol. 361, pages 4685-4690).
The teachings of Ost and Tanabe et al. have already been discussed above.
While Tanabe et al. teach an organic photocatalyst that converts 5-methylcytosine into 5-fC, the artisans do not teach all types of such photocatalyst which could be utilized for this purpose.
Jin et al. teach a photocatalyst that also converts 5-methylcytdine into 5-formylcytidine, wherein the photocatalysts has an absorbance maximum range between 300-600 nm:
“we present a facile opto-transformation under mild conditions to product 5-formylcytidine [5fC] and its analogous from 5-methylcytidine under the promotion of a small organic molecular photosensitizer without disturbing other vulnerable C-H bonds in other biomolecules” (page 4686, 1st column, 1st paragraph)
“Upon irradiation with near-UV light (365 nm) … major oxidative product f5C was isolated in 67% yield in an aqueous solution” (page 4686, 1st column, bottom paragraph)
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Ost and Tanabe et al. with the teachings of Jin et al., thereby arriving at the invention as claimed because one of ordinary skill in the art would have recognized that the
utilization of other photocatalyst reagents (other than that of Tanabe et al.) that have been demonstrated to be successful in converting 5-methylcytosines into 5-formylcytosines would have yielded the same predictable product that is useful in determining the methylation status of DNA sequences in a subject.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Claims 13 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Ost, Toby (WO 2014/083118 A1, published June 2014; IDS ref) in view of Tanabe et al. (JACS, June 2007, vol. 129, pages 8034-8040; IDS ref), as applied to claims 4, 10, 11, 18, 19, and 25 above, and further in view of Berney et al. (Nature, November 2018, vol. 2, pages 332-348; IDS ref).
The teachings of Ost and Tanabe et al. have already been discussed above.
While Ost teaches that the 5fC containing DNA is eventually sequenced, the artisans do not teach that the 5fC containing DNA is isolated by labeling with a tag (claim 13), such as a biotin (claim 14).
Berney et al. teach a method of isolating DNA containing 5fCs by use of biotin labeling and isolated for detection:
“5fC has been selectively labelled using … biotin group is then attached, enabling affinity isolation of DNA fragments containing 5fC using streptavidin-coated beads. The bound DNA fragments containing 5fCs are subsequently released from the beads, followed by PCR and DNA sequencing” (page 337, 2nd column, 2nd full paragraph)
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Ost and Tanabe et al. with the teachings of Berney et al., thereby arriving at the invention as claimed because by doing so one of ordinary skill in the art would have been motivated to isolate only the DNAs containing 5fCs from the sample so as to purify them and treat them for conversion into 5fUs in a method of sequencing reaction of Ost, as isolation of desired target nucleic acids before sequencing reaction had been a well-established practice in the art of nucleic acid sequencing reaction.
Conclusion
No claims are allowed.
Claims 6-8 are free of prior art. The prior art does not teach or suggest the use of polyoxometalate (claim 6), comprising tungsten (claim 7), being decatungstic acid, phosphotungstic acid, and its salt (claim 8), as photocatalyst in a method of converting modified cytosines of a DNA sequence into 5-formylcytosine residue in a non-enzymatic, one-electron process. Claims 6-8 are objected to for being dependent on a rejected base claim, however.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
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.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 June 19, 2026
/YJK/
1 Occurs via hydrogen atom transfer (HAT). The high-valent metal oxo complex abstracts a single hydrogen atom from the hydroxyl group of 5hmC, generating a radical intermediate and reducing the metal center by one oxidation state.
2 Claim 12 evidences that “labeling” also includes treatment via bisulfite where 5fC is converted to a uracil base.
Prosecution Insights