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 .
This Office Action is in reply to Applicants’ correspondence of 5/20/2026. Applicants’ remarks and amendments have been fully and carefully considered but are not found to be sufficient to put this application in condition for allowance. Any rejections or objections not reiterated herein have been withdrawn in light of the amendments to the claims or as discussed in this Office Action. This Action is FINAL.
Interview Summary
Applicant’s summary of the Interview conducted on May 12, 2026 is acknowledged.
Claim Status
Claims 1, 3, 5-6, and 8-10 are pending and being examined on the merits.
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.
Response to Remarks
Applicant notes that they do not rely “on a narrow construction requiring particular asparatic-acid position” and notes the support for the claim language in the specification. It is acknowledged that claim language of “a polymerase containing aspartic acid” has support in the specification, the Examiner notes that said example in the specification of polymerase 9N coordinating with metal ions of Mg and Cu is an embodiment of the invention (Embodiment I paragraph [0052]) and does not further limit the claim.
Applicant submits, in regards to claim 6, that “a person of ordinary skill would understand the claimed linker as the chemical linkage connecting the marker to the base of the second nucleotide analog, consistent with the Specification”. The Applicant specifically points to paragraphs [0025, 0027, and 0029] for support. The Examiner notes here that in paragraph [0027] the exact phrase is that “the linker comprises at least one of alkyl, allyl, azido-methylene, 2-nitrobenzyl and di-sulfhydryl”. The exact claim language from claim 6 is that “the linker is formed from”, implying that the linker is a specific structure that is synthesized from these groups in their pre-attached forms. If the Applicant wishes to make the claim more consistent with the language of the specification, it may be prudent to change the language of claim 6 from “the linker is formed from” to “the linker is [[formed from]]”.
Maintained Claim Rejections - 35 USC § 103
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 5/20/2026 have been fully considered but they are not persuasive for the following reasons.
The following responses will be broken into the argument sections as presented in the Remarks of 5/20/2026 (pages 7-11).
Divergent Technical Fields and Objections (pg 7-8 of Remarks)
Applicant argues that the SBB process taught by Dambacher does not involve the complex background interference that is present in Hu and which requires the solution of phosphorothioate dNTPs. Applicant additionally argues that sequencing speed “is a critical performance metric” of Dambacher which makes the incorporation of something that decreases speed counter-intuitive.
These arguments are not persuasive. First, the central problem of Hu is non-specific amplification, but not necessarily in the background of complex template mixtures. Hu also demonstrates increased specificity in the background of a single template and primer complex (Figure 1).
Second, Applicant asserts that a “critical performance metric” of the methodology of Dambacher is speed. No citation is provided from Dambacher that indicates that speed is a “critical performance metric”, and the Examiner has not found evidence that speed of the reaction is critical to the functionality of the methodology of Dambacher. Furthermore, while a purported advantage of the SBB system of Dambacher is speed, Dambacher also teaches that specificity of cognate nucleotide pairing is important (paragraph [0100]) and indicates that different polymerases have different specificities for the “next correct nucleotide” (paragraph [0189]). Therefore, the addition of a beneficial effect at the expense of speed is not counter-intuitive, but rather a conscious choice that would result in an expected beneficial outcome of increased specificity.
It is noted that Applicant themselves note the advantage which would motivate combination of references, indicating that Hu teaches “enhanced product purity”.
Teaching Away and Lack of Motivation (pg 8 of Remarks)
Applicant argues that there is no motivation to combine Hu with Dambacher given that Dambacher does not contain the complex background of Hu and relies on speed. As noted above, Hu demonstrates that slowing of polymerization, and thus increased specificity, occurs in backgrounds with a singular template and not a complex mixture (Figure 1). As also noted above, Dambacher’s methodology is not “speed-sensitive” but rather is a more rapid approach than previous approaches and speed itself is not inherent to the functionality of the methodology. The incorporation of a speed-modifier would not create a significant barrier to the proposed combination but rather teaches a different beneficial effect that could be advantageous in the method of Dambacher, which relies on the correct identification of the next cognate nucleotide. “[A] given course of action often has simultaneous advantages and disadvantages, and this does not necessarily obviate motivation to combine.” (MPEP 2141.02 (VI). Where the prior art contains ‘apparently conflicting’ teachings each reference must be considered for its “power…to suggest solutions to one of ordinary skill in the art, considering the degree to which one reference might accurately discredit another.’ In re Young, 927 F.2d 588, 591 (Fed.Cir.1991).” (MPEP 2143.01 (II)).
Mechanistic Disparity (pg 8 of Remarks)
Applicant argues that the chemical systems of Hu and Dambacher are fundamentally different, wherein the inhibition of the covalent bond-forming step as taught by Hu would not be applicable to the sequencing method that depends on the stable formation of a metal-ion-chelated, non-covalent complex. The Examiner respectfully disagrees. Hu does not teach, and Applicant does not point to a specific citation, that it is specifically the covalent bond-forming chemical step that is being inhibited by the modified dNTPs of Hu. Hu merely teaches that the polymerization rate is slowed through measurement of reaction times, but does not provide mechanistic details as to how the amplification processes are being slowed. Therefore, there is no evidence provided that the phosphorothioate dNTPs of Hu would not work with the methodology of Dambacher.
2.1 Altered Metal Coordination Chemistry (pg 9 of Remarks)
It does not appear as if the Applicant is making a specific argument here. Applicant suggests that the substitution of a Sulfur atom at the a-phosphate would “fundamentally alter the coordination mode” of the catalytic metal ions in the polymerase active site but does not provide evidence of this. Applicant is advised that MPEP 716.01(c) makes clear that “[t]he arguments of counsel cannot take the place of evidence in the record” (In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965)). Thus, Applicant should not merely rely upon counsel’s arguments in place of evidence in the record.
It is noted that the Response above should not be construed as an invitation to file an after final declaration. See MPEP 715.09.
Destruction of the Critical Chelation Structure (pg 9 of Remarks)
Regarding Applicant’s arguments concerning what skilled artisans would or would not know, Applicant is advised that MPEP 716.01(c) makes clear that “[t]he arguments of counsel cannot take the place of evidence in the record” (In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965)). Thus, Applicant should not merely rely upon counsel’s arguments in place of evidence in the record.
It is noted that the Response above should not be construed as an invitation to file an after final declaration. See MPEP 715.09.
3. The “Thio Effect” Literature Reinforces the Incompatibly and Step-Specific Nature of the Modification (pg 9-10 of Remarks)
Step-specific modulation (Werneburg): Applicant notes that the teaches of Werneburg indicate the phosphorothioate modifications effect is “intimately tied to the chemistry of the incorporation transition state and its fidelity check”. However, Werneburg, similar to Hu, is only measuring the polymerization rate of the reaction, not necessarily examining the mechanistic method by which the “thio effect” is slowing the rate of polymerization. Werneburg acknowledges that the “thio effect” differs from between different polymerase depending on the “detailed mechanisms” but does not offer insight into what said mechanism is that slows down catalytic incorporation.
Chemical step as rate-limiting (Wong): Similar to Werneburg, Wong is also only measuring the effect on the amount of final product to determine effect on polymerization rate generated when using phosphorothioate analogs (Figure 3). Wong does not state that it is the formation of the covalent bond itself that is slowing the reaction rather than some other detailed mechanistic factor that would point to why Hu would not be compatible with Dambacher.
Stereochemical specificity (Romaniuk): While it is true that SP and RP isomers of dNTPaS are different in terms of SP being a substrate and RP not being a substate, this is a fact that is mentioned by Hu, who teaches that said stereoisomers do not need to be separated (“Since DNA polymerases use only Sp diastereomers, interestingly, the separation of the Sp and Rp diastereomers of dNTPαS is not necessary, as their mixtures can still allow the DNA synthesis; DNA Polymerase Recognition of dNTPαS I”). Therefore, this stereochemical specificity would not be a significant barrier for the incorporation of the teaching of Hu into the methodology of Dambacher.
For the reasons presented above, the 103 rejections against all claims are maintained.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to 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
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