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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 1/13/2026 has been entered.
Response to Amendment
The amendment to the claims filed on 1/13/2026 does not comply with the requirements of 37 CFR 1.121(c) because amended claim 1 does not contain all of the required markings to indicate new claim text (“or X is sulfur (S) and”). Amendments to the claims filed on or after July 30, 2003 must comply with 37 CFR 1.121(c) which states:
(c) Claims. Amendments to a claim must be made by rewriting the entire claim with all changes (e.g., additions and deletions) as indicated in this subsection, except when the claim is being canceled. Each amendment document that includes a change to an existing claim, cancellation of an existing claim or addition of a new claim, must include a complete listing of all claims ever presented, including the text of all pending and withdrawn claims, in the application. The claim listing, including the text of the claims, in the amendment document will serve to replace all prior versions of the claims, in the application. In the claim listing, the status of every claim must be indicated after its claim number by using one of the following identifiers in a parenthetical expression: (Original), (Currently amended), (Canceled), (Withdrawn), (Previously presented), (New), and (Not entered).
(1) Claim listing. All of the claims presented in a claim listing shall be presented in ascending numerical order. Consecutive claims having the same status of “canceled” or “not entered” may be aggregated into one statement (e.g., Claims 1–5 (canceled)). The claim listing shall commence on a separate sheet of the amendment document and the sheet(s) that contain the text of any part of the claims shall not contain any other part of the amendment.
(2) When claim text with markings is required. All claims being currently amended in an amendment paper shall be presented in the claim listing, indicate a status of “currently amended,” and be submitted with markings to indicate the changes that have been made relative to the immediate prior version of the claims. The text of any added subject matter must be shown by underlining the added text. The text of any deleted matter must be shown by strike-through except that double brackets placed before and after the deleted characters may be used to show deletion of five or fewer consecutive characters. The text of any deleted subject matter must be shown by being placed within double brackets if strike-through cannot be easily perceived. Only claims having the status of “currently amended,” or “withdrawn” if also being amended, shall include markings. If a withdrawn claim is currently amended, its status in the claim listing may be identified as “withdrawn—currently amended.”
(3) When claim text in clean version is required. The text of all pending claims not being currently amended shall be presented in the claim listing in clean version, i.e., without any markings in the presentation of text. The presentation of a clean version of any claim having the status of “original,” “withdrawn” or “previously presented” will constitute an assertion that it has not been changed relative to the immediate prior version, except to omit markings that may have been present in the immediate prior version of the claims of the status of “withdrawn” or “previously presented.” Any claim added by amendment must be indicated with the status of “new” and presented in clean version, i.e., without any underlining.
(4) When claim text shall not be presented; canceling a claim.
(i) No claim text shall be presented for any claim in the claim listing with the status of “canceled” or “not entered.”
(ii) Cancellation of a claim shall be effected by an instruction to cancel a particular claim number. Identifying the status of a claim in the claim listing as “canceled” will constitute an instruction to cancel the claim.
(5) Reinstatement of previously canceled claim. A claim which was previously canceled may be reinstated only by adding the claim as a “new” claim with a new claim number.
As noted above, the amendment under consideration herein fails to comply with 37 CFR 1.121 because the claim listing does not contain the required markings indicating new claim text added to claim 1. Thus, the amendment could be considered non-responsive. However, in the interest of compact prosecution the amendment at issue will not be considered non-responsive. However, any future responses failing to comply with 37 CFR 1.121 will be held non-responsive, and will not be considered.
Claim Status
Claims 1, 3, 5-6, and 8-10 are pending and being examined on the merits.
Drawings
The objection to the drawings (Figure 2) is withdrawn in light of Applicant’s amendment to the figure.
Claim Objections
The objection to claim 1 has been withdrawn in light of Applicant’s amendment to the claim.
Claim Rejections - 35 USC § 112b - Indefiniteness
The rejection of claims 1, 3, 5-6, and 8-10 under 35 U.S.C. 112(b) as presented in the Office Action of 10/17/2025 is withdrawn in light of Applicant’s amendments to the claims.
Claim Interpretation
In claim 1, applicant has added the limitation that the polymerase used for the reaction is “a polymerase containing aspartic acid”. However, no further structural limitations are defined in the claim regarding the position of this aspartic acid residue in the polymerase protein in the claim itself or in the specification. The only mention of aspartic acid in the specification occurs at paragraph [0072], and does not indicate the position of this residue here either. Therefore, given the broadest reasonable interpretation, the aspartic acid residue can be at any location within the polymerase employed in this methodology.
In claim 6, it is noted that the groups which the linker comprises at least one of (alkyl, allyl, azido-methylene, 2-nitrobenzyl and di-sulfhydryl) appear to be in their pre-attached forms. These groups would have to be external groups, and not used as part of the chain linking R3 to R4. Therefore, the examiner is interpreting these groups as being in their “pre-attached” or unincorporated forms.
Applicant is cautioned against the introduction of new matter in response to this interpretation.
Claim Rejections - 35 USC § 103
Withdrawn
The rejection of claims 1, 5-6, and 8-9 under 35 U.S.C. 103 as being unpatentable over Dambacher et al. (hereinafter “Dambacher”; US 2018/0208983 A1, cited on IDS submitted on 10/25/2024) in view of Vosberg and Eckstein (Journal of Biological Chemistry, 1982), and the rejection of claims 3 and 10 over Dambacher et al. (hereinafter “Dambacher”; US 2018/0208983 A1, cited on IDS submitted on 10/25/2024) in view of Vosberg and Eckstein (Journal of Biological Chemistry, 1982) as applied to claims 1, 5-6, and 8-9 above, and further in view of Bentley et al. (hereinafter “Bentley”; Nature, 2008) are withdrawn in light of Applicant’s amendments to the claims.
New (Necessitated by Amendments)
Claims 1, 5-6, and 8-9 are rejected under 35 U.S.C. 103 as being unpatentable over Dambacher et al. (hereinafter “Dambacher”; US 2018/0208983 A1, cited on IDS submitted on 10/25/2024) in view of Hu et al. (hereinafter “Hu”; Analytical Chemistry 2020).
Regarding claim 1: Dambacher teaches a gene sequencing method in which a sequencing primer is hybridized onto a nucleic acid molecule to be detected to form a hybrid template strand and a primer strand (S1; paragraphs [0009, 0043, 0099, and 0106]).
Dambacher teaches next performing base pairing on a first nucleotide analog (“reversible terminator nucleotide”) and the nucleic acid molecule to be detected, and linking the first nucleotide analog to the primer strand (S2; paragraph [0009]). Dambacher teaches that the first nucleotide analog has a blocking group attached to the 3’-OH of the sugar of the nucleotide analog and that the base is any one of A, G, C and T (S2; paragraphs [0008 and 0050]).
Dambacher teaches performing base pairing on a second nucleotide analog and the nucleic acid molecule to be detected, the second nucleotide analog forming a complex with the nucleic acid molecule to be detected and the first nucleotide analog under the action of metal ions and a polymerase, wherein the second nucleotide analog has a marker (S3; paragraph [0009]). Dambacher teaches a polymerase that contains aspartic acid (TherminatorTM, paragraphs [0192, 0349]). Dambacher does not exclusively teach that the TherminatorTM polymerase contains aspartic acid, however those of skill in the art know that the protein sequence of this polymerase includes aspartic acids. Moreover, neither the claim nor the specification indicates where the aspartic acid is located within the protein (see Claim Interpretation above). Dambacher teaches that the catalytic metal ions stabilize the ternary complex via chelation upon the contacting step between the first and second nucleotide analog (paragraph [0115]). Dambacher teaches that the labeled nucleotide analog (second nucleotide analog with a marker) has a structure wherein X=O, R=hydroxy (-OH), R3=A, G, C or T, Linker=linker, and R4 is the marker (S3; Figure 2 and paragraph [0050]). Dambacher teaches that the metal ions are divalent metal ions Mg2+, Cu2+, Zn2+, Mn2+, or Ca2+ (S3; paragraphs [0011 and 0125]).
Dambacher teaches subsequently detecting the marker, and identifying a base in the nucleic acid molecule to be detected (S4; paragraph [0009]).
Dambacher teaches removing the blocking group and the second nucleotide analog, and repeating S2-S4 to perform a next cycle of sequencing (S5; paragraph [0009]).
Dambacher does not teach that the alpha phosphate group is S (Y group on the alpha phosphate of the chemical formula presented in S3). However, incorporation of a modification on the alpha phosphate of a nucleotide analog was known in the art, as taught by Hu.
Hu teaches a nucleotide analog termed dNTPαS, which reads on Y is sulfur (Results and Discussion – Synthesis of all dNTPαS and Figure 1).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Dambacher to incorporate a modified nucleotide analog at the alpha phosphate position, as taught by Hu. One would be motivated to use this modified nucleotide analog given the assertion by Hu that this modified nucleotide significantly enhances the specificity of a polymerization reaction (Figure 6D and Conclusions paragraph 4). One would have a reasonable expectation of success given that Hu teaches that this type of modified base is readily incorporated into growing DNA strands in a manner similar to natural nucleotides, albeit slightly slower (Conclusions paragraph 2). Additionally, Hu teaches the enhancement of specificity using Bst, Taq, and Klenow fragment, all of which Dambacher lists as polymerases that can be used for their methodology (paragraph [0191]).
Regarding claim 5: Dambacher teaches that the marker comprises a cyanine (paragraph [0201]).
Regarding claim 6: Dambacher teaches that the linker comprises at least one of alkyl and allyl (Formulas 3a-3d on pg 32 if o = 10 and paragraph [0183], respectively).
Regarding claim 8: Dambacher teaches detecting the marker within a reaction mixture using a fluorescence detector (paragraph [0100]).
Regarding claim 9: Dambacher teaches a step in which a buffer containing a metal chelator is added to be bonded with and remove the metal ions so as to release the second nucleotide analog from the primer strand and the metal chelator is ethylenediaminetetraacetic acid (“EDTA”; paragraphs [0108, 0115, and 0145]).
Claims 3 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Dambacher et al. (hereinafter “Dambacher”; US 2018/0208983 A1, cited on IDS submitted on 10/25/2024) in view of Hu et al. (hereinafter “Hu”; Analytical Chemistry 2020) as applied to claims 1, 5-6, and 8-9 above, and further in view of Bentley et al. (hereinafter “Bentley”; Nature, 2008; cited on PTO-892 of 6/26/2025).
The teachings of Dambacher in view of Hu are detailed in the rejection of claims 1, 5-6, and 8-9 above. Relevant to the instantly rejected claims, Dambacher in view of Hu teaches a nucleotide analog that contains a blocking group attached to the 3’OH group of the sugar. However, they do not teach that this blocking group comprises at least one of azido-methylene, allyl, 2-nitrobenzene methyl and azoic compounds (claim 3). They also do not teach removal of this blocking group by photocleavage or by adding an organic reagent, and the organic reagent comprises at least one of a sulfhydryl group reagent, an organic phosphine reagent and sodium hydrosulfite (claim 10). However, inclusion of a removable blocking group on the 3’OH of a nucleotide sugar in the form of azido-methylene and removal via an organic phosphine reagent was known in the art, as taught by Bentley.
Regarding claim 3: Bentley teaches a nucleotide analog comprising a 3’-O-azidomethyl group (DNA sequencing using reversible terminators, paragraph 2 and Supplementary Figure 1A).
Regarding claim 10: Bentley teaches addition of tris(2-carboxyethyl)phosphine (TCEP) (which reads on organic phosphine reagent) to remove an azidomethyl blocking group (DNA sequencing using reversible terminators, paragraph 2).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Dambacher in view of Hu with the method of Bentley given the assertion by Bentley that “[t]he use of 3′-modified nucleotides allowed the incorporation to be driven essentially to completion without risk of over-incorporation” and usage of TCEP to remove the blocking moiety “regenerate[s] a 3′ hydroxyl group ready for the next cycle of nucleotide addition” (DNA sequencing using reversible terminators, paragraph 2). One would have a reasonable expectation of success given that Bentley successfully employs the blocking moiety to control sequential additions of nucleotides in a sequencing reaction.
Response to Remarks
Applicant's arguments filed on 1/13/2026 have been fully considered but they are not persuasive for the following reasons.
Applicant has traversed the rejections of claims 1, 5-6, and 8-9 over Dambacher in view of Vosberg and Eckstein and claims 3 and 10 further in view of Bentley (given that Bentley does not rectify the deficiencies of Dambacher in view of Vosberg and Eckstein). Arguments regarding Dambacher in view of Vosberg and Eckstein are deemed moot in light of Applicant’s amendments to the claims and the new grounds of rejection presented above in light of said amendments.
Applicant argues on page 7 of Remarks that it is “well-known in the prior art that in single-molecule DNA polymerization by DNA Polymerase I (Klenow Fragment), all a-thio-dNTPs were incorporated more slowly, at 40% to 65% of the rate for the corresponding native dNTPs” (Pugiliese et al., cited on IDS of 1/13/2026). However, this does not teach away from modifying Dambacher in view of Hu, given that Hu specifically acknowledges that “Attenuating DNA polymerase kinetics, namely, reducing the enzymatic rate of dNTPαS incorporation, can give a mismatched dNTP substrate sufficient time to dissociate from the extension site, thereby enhancing the specificity on DNA polymerization” (Conclusions, paragraph 2).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAILEY E CASH whose telephone number is (571)272-0971. The examiner can normally be reached Monday-Friday 8:30am-6pm ET.
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/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683