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 .
DETAILED ACTION
2. This Office Action is responsive to Applicant’s Amendment and Remarks, filed May 29, 2026. The amendment, filed May 29, 2026, is entered, wherein claims 31 and 51 – 52 are amended, claims 1 – 30 and 35 – 37 are canceled, and claims 38 – 42 and 47 are withdrawn.
Claims 31 – 34 and 38 – 52 are pending in this application and claims 31 – 34, 43 – 46, and 48 – 52 are currently examined.
Priority
3. This application is a continuation application of 17/016,992, filed September 10, 2020, which claims benefit of domestic application 62/898,152, filed September 10, 2019.
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 62/898,152, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. The domestic application 62/898,152 does not provide support for the recitations of “no more than 5% of the nucleotide protected by the 3’-O-NH2 is degraded” recited in claim 43, “no more than 3% of the nucleotide protected by the 3’-O-NH2 is degraded” recited in claim 44, “no more than 2% or no more than 1% of the nucleotide protected by the 3’-O-NH2 is degraded” recited in claim 45, “no more than 3% of the nucleotide protected by the 3’-O-NH2 is degraded when the nucleotide comprises a cytosine nucleobase” recited in claim 46, “at least 95% of the nucleotide” recited in claim 48, “at least 97% or at least 98% of the nucleotide” recited in claim 49, and “the method adds the 3’-O- NH2 moiety in place of the 3’-O-oxime moiety to at least 98% of a population of nucleotides having the 3’-O-oxime moiety in no more than 3 hours” recited in claim 50; and the chemical structures except:
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recited in claim 51. Thus, the priority date of claims 43 – 46 and 48 – 51 is September 10, 2020.
Withdrawn Rejections
4. The rejection of claims 31 – 34, 43 – 46, and 48 – 52 in the previous Office Action, mailed March 6, 2026, under 35 U.S.C. 103 as being unpatentable over Benner in view of Polyakov et al. has been considered and is withdrawn in view of the amended claim 31.
The following are maintained / modified / new grounds of rejection necessitated by Applicant’s Amendment and Remarks, filed May 29, 2026, wherein claims 31 and 51 – 52 are amended, claims 1 – 30 and 35 – 37 are canceled, and claims 38 – 42 and 47 are withdrawn. Previously cited references have been used to establish the maintained / modified / new grounds of rejection.
New Claim Rejections - 35 USC § 112
5. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 31 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. The claim recites that “one of R3 and R4 is not H”. However, the originally filed specification does not provide adequate written description support for this amended limitation. The specification discloses that R3 and R4 can be independently selected from H, CH3, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl, or (heteroalicyclyl)alkyl, and further states that the moiety at the 3’position of the nucleotide can be an aldoxime (such that one of R3 or R4 is hydrogen) or a ketoxime (neither of R3 or R4 is hydrogen) (para. [0012]). However, the specification does not describe the broader amended limitation now claimed. The disclosure of aldoxime and ketoxime embodiments does not reasonably convey possession of a general limitation requiring that “one of R3 and R4 is not H, or neither R3 nor R4 is H”, independent of those disclosed oxime embodiments. As claimed, the limitation broadly encompasses substituent combinations based on the absence of hydrogen at one or both of R3 and R4, without being limited to the aldoxime and ketoxime structures described in the specification. Accordingly, the originally filed disclosure does not reasonably convey to one of ordinary skill in the art that Applicant was in possession of the full scope of the amended limitation at the time of filing.
Maintained / Modified / New Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
i. Determining the scope and contents of the prior art.
ii. Ascertaining the differences between the prior art and the claims at issue.
iii. Resolving the level of ordinary skill in the pertinent art.
iv. Considering objective evidence present in the application indicating obviousness or
nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 31 – 34, 43 – 46, and 48 – 52 are rejected under 35 U.S.C. 103 as being unpatentable over Benner (US20180265537A1, cited in the PTO-892 on November 1, 2024) in view of Collins et al. (Polymer Chemistry, 2016, Vol. 7, Issue 23, page 3812 – 3826, cited in the PTO-892 on November 1, 2024).
a. Benner teaches a composition comprising an aqueous solution containing a molecule having the structure:
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wherein B is
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wherein R is CH3 (claim 1). Benner also discloses the synthesis of the above molecule as follow (fig 2):
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Thus, Benner teaches a process of modifying a nucleotide by reacting a nucleotide comprising a 3’-O-oxime with MeONH2, which reads on the limitations “reacting a nucleotide comprising a 3’-O-oxime moiety with a reagent to produce a nucleotide comprising a 3’-O-NH2 moiety”, the structure of “the nucleotide that comprises the 3’-O-oxime moiety”, and “the structure of “the nucleotide that comprises the 3’-O-NH2 moiety” of claims 31 – 34. The product triphosphate is released from the support by elution with an aqueous solution of an alkoxylamine. After preferably 90 minutes, the eluate contained the desired triphosphate as the main component of the total nucleotide material. No side products that have a 3’-OH moiety are present (para. [0035]).
However, Benner does not teach the reagent R2-ONH2, wherein the R2 is alkyl with a molecular weight greater than 36 g/mol.
Collins et al. disclose a dynamic chain termination through the addition of a monofunctional hydroxylamine in oxime-based mimics of naturally occurring mycobacterial arabins as shown below (page 17, Fig. 8):
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The scheme above shows the exchanges of O-methyl and O-N=C with O-tert-butyl and O-NH2, respectively.
It would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the claimed invention to substitute the alkoxylamine in the reaction of modifying nucleotide with O-oxime moiety as taught by Benner with the O-tert-butylhydroxylamine used in the above reaction shown in figure 8 in view of Collins et al. because Collins et al. teach the reaction between O-tert-butylhydroxylamine with arabins, wherein arabins contains O-N=C bonds that reacts with O-tert-butylhydroxylamine to yield -ONH2. One would have been obvious to substitute the alkoxylamine with O-tert-butylhydroxylamine because both Benner and Collins et al. disclose the O-N=C moiety on a sugar. One of the ordinary skill in the art would have a reasonable expectation of success by substituting the alkoxylamine in the reaction of modifying nucleotide with O-oxime moiety as taught by Benner with the O-tert-butylhydroxylamine used in view of Collins et al. as Benner teaches the production of triphosphate nucleotide and Collins et al. disclose the possible reagent that would react with O-N=C to yield O-NH2 for a predictable result.
With respect to claims 43 – 46, Benner teaches reacting a nucleotide comprising a 3’-O-oxime moiety with an alkoxyamine to produce a corresponding nucleotide comprising a 3’-O-NH2 moiety. Benner teaches methoxyamine for this conversion and Collins et al. teach O-tert-butylhydroxylamine as an alternative R-ONH2 reagent suitable for reacting with oxime moieties. Substitution of O-tert-butylhydroxylamine form methoxyamine would have been a simple substitution of one known reagent for another known reagent within the same functional class to perform the same oxime-to-ONH2 conversion with predictable results. Benner further teaches that the desired triphosphate is obtained as the main component of the total nucleotide material and does not disclose detectable degradation of the 3’-O-NH2 protected nucleotide product. Accordingly, the method of Benner as modified by Collins et al. would have been reasonably expected to produce the claimed 3’-O-NH2 protected nucleotide produce with degradation no greater than the recited upper limits.
For claims 48 – 50, the claims recite the consumption of nucleotide comprising 3’-O-oxime moiety and the specific time for achieving the specified consumption of nucleotide comprising 3’-O-oxime moiety. Benner teaches reacting 3’-O-oxime modified nucleotide with an alkoxyamine to produce the corresponding 3’-ONH2 modified nucleotide, and further teaches that the desired nucleotide is obtained as the main component of the nucleotide material after 90 minutes, which is within the claimed time period of no more than 3 hours. Although Benner does not explicitly disclose the consumption of the 3’-O-oxime modified nucleotide, the consumption of 3’-O-oxime modified nucleotide is a result-effective variable for the claimed method. It would have been obvious for one of ordinary skill in the art to adjust the known reaction parameters, including reaction time, concentration of reagents, temperature, and etc, to increase consumption to the desired levels.
Claims 31 – 34, 43 – 46, and 48 – 50 are rejected under 35 U.S.C. 103 as being unpatentable over Benner (US20180265537A1, cited in the PTO-892 on November 1, 2024) in view of Polyakov et al. (Journal of Physical Organic Chemistry, 1999, Vol. 12, Issue 5, page 357 – 363, cited in the PTO-892 on March 6, 2026).
b. Benner teaches a composition comprising an aqueous solution containing a molecule having the structure:
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wherein B is
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wherein R is CH3 (claim 1). Benner also discloses the synthesis of the above molecule as follow (fig 2):
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The product triphosphate is released from the support by elution with an aqueous solution of an alkoxylamine. After preferably 90 minutes, the eluate contained the desired triphosphate as the main component of the total nucleotide material. No side products that have a 3’-OH moiety are present (para. [0035]).
However, Benner does not teach the reagent R2-ONH2, wherein the R2 is alkyl with a molecular weight greater than 36 g/mol .
Polyakov et al. teach the reaction of an O-alkyl oximes with O-alkyloxylamines:
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wherein the O-alkyloxylamine is ethyoxyamine (page 358, Right Col., Scheme 2), which yields MeONH2 (page 359, Right Col., Scheme 4).
It would have been prima facie obvious to substitute MeONH2 as taught by Benner with other O-alkyloxylamine with longer carbon chain as the alkoxylamine reagent for the reaction of a nucleotide comprising a 3’-O-oxime moiety with an alkoxyamine to produce a corresponding nucleotide comprising a 3’-O-NH2 moiety in view of Polyakov et al. because Polyakov et al. teach that alkoxyamine homologs react with oxime compounds through the same oxime exchange reaction. In particular, Polyakov et al. teach reaction a methoxy-substituted oxime with ethoxyamine to produce the corresponding ethoxy-substituted oxime and methoxyamine. Thus, Polyakov et al. demonstrate that replacing methoxyamine with an alkyl homolog, such as ethoxyamine would have been expected to participate in the same reaction with an oxime moiety. Moreover, it has long been established that this type of difference, which is varying the size of a chain, constitutes a form of homology, and is a fact of very close structural similarity, rending the homolog obvious. As was stated in In re Grose, 201 USPZ 57, 63, “The known structural relationship between adjacent homologues, for example, supplies a chemical theory upon which a prima facie case of obviousness of a compound may rest.” See specifically In re Shetty, 195 USPQ 753; In re Wilder, 195 USPQ 426 and Ex Parte Greshem, 121 USPQ 422, all of which feature a compound with a C2 link rejected over a compound with a C1 link. Similarly, In re Chupp, 2 USPQ2d 1437 and In re Coes, 81 USPQ 369 have a compound with a C1 link unpatentable over prior art showing C2 link. Note Ex parte Agouridas, 65 USPQ2d 1142, where a C4 chain was held obvious over a C3 chain. Note also In re Schaub, 190 USPQ 324, 326, where compounds with C5 and C6 chains were called “adjacent homologs in the classic sense”. Ex parte Ruddy, 121 USPQ 427 has a C3 link unpatentable over a C1 link. Ex parte Nathan, 121 USPQ 349 found the insertion of a C2H4 link obvious. In all of these cases, the variation was found to be obvious on the basis of close structural similarity; no secondary teaching was employed. As was stated directly in THE GENERAL TIRE & RUBBER COMPANY v. JEFFERSON CHEMICAL COMPANY, INC., 182 USPQ 70 (1974): “If any structural change is obvious to one skilled in the art, a substitution of the next higher homolog would seem to be.” Note also In re Jones, 21 USPQ2d 1942, which states at 1943 “Particular types or categories of structural similarity without more, have, in past cases, given rise to prima facie obviousness”; one of those listed is “adjacent homologues and structural isomers”. Similar is In re Schechter and LaForge, 98 USPQ 144, 150, which states “a novel useful chemical compound which is homologous or isomeric with compounds of the prior art is unpatentable unless it possesses some unobvious or unexpected beneficial property not possessed by the prior art compounds.” Note also In re Deuel, 34 USPQ2d 1210, 1214 which states, “Structural relationships may provide the requisite motivation or suggestion to modify known compounds to obtain new compounds. For example, a prior art compound may suggest its homologs because homologs often have similar properties and therefore chemists of ordinary skill would ordinarily contemplate making them to try to obtain compounds with improved properties.” Therefore, one of the ordinary skill in the art would have had a reasonable expectation of success to substitute MeONH2 as taught by Benner with other O-alkyloxylamine with longer carbon chain as the alkoxylamine reagent for the reaction of a nucleotide comprising a 3’-O-oxime moiety with an alkoxyamine to produce a corresponding nucleotide comprising a 3’-O-NH2 moiety in view of Polyakov et al. because it is known in the art that homologs often have similar properties and the result is predictable.
With respect to claims 43 – 46, Benner teaches reacting a nucleotide comprising a 3’-O-oxime moiety with an alkoxyamine to produce a corresponding nucleotide comprising a 3’-O-NH2 moiety. Benner teaches methoxyamine for this conversion and Polyakov et al. teach that homologous alkoxyamine reagents react with oxime compounds through the same oxime exchange reaction. Thus, Polyakov et al. demonstrate that an alkyl homolog of methoxyamine, such as ethoxyamine, would have been expected to participate in the same type of oxime reaction. Substitution of methoxyamine of Benner with ethoxyamine or other homologous R2-ONH2 alkoxyamine reagent, wherein R2 is alkyl and has a molecular weight greater than 36 g/mol, would have been a simple substitution of one known reagent for another known reagent within the same functional class to perform the same oxime-to-ONH2 conversion with predictable results. Benner further teaches that the desired triphosphate is obtained as the main component of the total nucleotide material and does not disclose detectable degradation of the 3’-O-NH2 protected nucleotide product. Accordingly, the method of Benner as modified by Polyakov et al. would have been reasonably expected to produce the claimed 3’-O-NH2 protected nucleotide produce with degradation no greater than the recited upper limits.
For claims 48 – 50, the claims recite the consumption of nucleotide comprising 3’-O-oxime moiety and the specific time for achieving the specified consumption of nucleotide comprising 3’-O-oxime moiety. Benner teaches reacting 3’-O-oxime modified nucleotide with an alkoxyamine to produce the corresponding 3’-ONH2 modified nucleotide, and further teaches that the desired nucleotide is obtained as the main component of the nucleotide material after 90 minutes, which is within the claimed time period of no more than 3 hours. Although Benner does not explicitly disclose the consumption of the 3’-O-oxime modified nucleotide, the consumption of 3’-O-oxime modified nucleotide is a result-effective variable for the claimed method. It would have been obvious for one of ordinary skill in the art to adjust the known reaction parameters, including reaction time, concentration of reagents, temperature, and etc, to increase consumption to the desired levels.
Responses to Applicant’s Remarks:
Applicant’s Remarks, filed May 29, 2026, have been fully considered and are found to be not persuasive.
Applicant argues that Benner does not teach or suggest replacing the methyl of methoxyamine with any other group, and in particular provides no motivation for replacing the methyl with a non-aromatic, sterically bulkier R2 group and Collins et al. do not cure the deficiency because Collins et al. do not teach replacing methoxyamine with tert-butylhydroxylamine and Collins et al. only show that tert-butylhydroxylamine can participate in a different oxime exchange context. However, the argument is not persuasive. The rejection does not require Benner to explicitly teach replacing methoxyamine with tert-butylhydroxylamine. Benner teaches reacting a nucleotide comprising a 3’-O-oxime moiety with an alkoxyamine to produce a nucleotide comprising a 3’-O-NH2 moiety. Collins et al. teach that tert-butylhydroxylamine is an R-ONH2 reagent suitable for reacting with oxime moieties. Therefore, substituting tert-butylhydroxylamine for methoxyamine would have been a simple substitution of one known R-ONH2 reagent for another within the same functional class to perform the same oxime-to-ONH2 conversion with predictable results.
Applicant believes that the alkoxyamine reagent with R2 moieties having more steric bulk than smaller moieties would produce fewer unwanted modifications. Applicant points to the experimental data in Figure 1A, which confirm that R2 identity is not a mere matter of routine substitution. The data show that the R2 moieties having molecular weight greater than 36 g/mol result in better yield. The data also show that the -C(CH3)3 reagent demonstrates the lowest level of unwanted nucleotide degradation. The argument is not persuasive. Applicant appears to rely on alleged unexpected results, which demonstrate that larger or more sterically bulky R2 groups provide improved yield, increased conversion, and reduced degradation. However, the evidence cited by Applicant is not commensurate in scope with the claims. The claims broadly encompass numerous R2 groups having a molecular weight greater than 36 g/mol, while Applicant’s data appear limited to only selected tested species. A showing of improved results for one or a limited number of species is insufficient to represent the full scope of the claimed genus. Therefore, data of improved results for a limited number of species does not establish unexpected results across the full scope of the claimed genus.
Applicant argues that the Office has not shown that selecting an R2 group with molecular weight greater than 36 g/mol would have been a routine or predictable modification because Applicant’s data allegedly demonstrate that R2 size significantly affects degradation, conversion, and yield. However, the argument is not persuasive because the claimed R2 limitation is met by tert-butylhydroxylamine, which Collins et al. teach as a known R-ONH2 reagent capable of reacting with oxime moieties. Thus, the rejection does not depend on selecting the claimed R2 through routine optimization alone. Instead, the prior art provides a specific known reagent within the claimed scope, and its use in Benner would have been a simple substitution for methoxyamine to perform the same reaction.
Applicant argues that Collins et al. teach oxime exchange under acidic conditions, whereas Benner requires pH above 6 to avoid degradation of the nucleotide substrate, and therefore a person of ordinary skill in the art would not have reasonably expected the reagent of Collins et al. to successfully perform Benner’s reaction under Benner’s conditions. The argument is not persuasive because the rejection does not require importing the reaction conditions of Collins et al. into Benner. Benner provides the nucleotide substrate and suitable reaction conditions for performing the oxime-to-ONH2 conversion. Collins et al. is relied upon for teaching tert-butylhydroxylamine as a known R-ONH2 reagent reactive with oxime moieties. One of ordinary skill in the art would have maintained Benner’s suitable pH conditions while substituting the known R-ONH2 reagent.
Regarding Polyakov et al., Applicant argues that Polyakov et al. is technically unrelated to Benner’s nucleotide chemistry and only teaches oxime exchange in different small-molecule systems, so it does not support substituting methoxyamine analogs in Benner’s method. The argument is not persuasive. Polyakov et al. is not relied upon to teach Benner’s nucleotide substrate or all details of Benner’s method. Instead, Polyakov et al. is relied upon to show that homologous alkoxyamine reagents participate in oxime exchange chemistry. This supports the predictability of substituting methoxyamine with a homologous alkoxyamine reagent in Benner’s oxime-to-ONH2 conversion.
Conclusion
No claim is found to be allowable.
Applicant's amendment necessitated the maintained / modified / 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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/H.Y.L./Examiner, Art Unit 1693
/SCARLETT Y GOON/Supervisory Patent Examiner, Art Unit 1693
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