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 .
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.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 June 9, 2026 has been entered.
The amendment filed June 9, 2026 has been entered. Claims 4, 7-11, 15, 18, 21, 23, 26, and 32-33 are cancelled.
Applicant’s arguments filed December 15, 2025 were fully considered but they were not persuasive. Rejections and response to arguments are addressed below.
Claims 1-3, 5-6, 12-14, 16-17, 19-20, 22, 24-25, 27-31, and 34 are pending in this application.
Priority
This application is a continuation of U.S. Patent Application No.: 17/199,921, filed March 12, 2021, which is a continuation of U.S. Patent Application No.: 16/309,622, filed December 13, 2018, which is a 371 U.S. National Phase of International Application PCT/US2017/037126, filed June 13, 2017, which claims the benefit of the filing date under 35 U.S.C. §119(e), of U.S. Provisional Application No. 62/349,970, filed on June 14, 2016, and U.S. Provisional Application No. 62/492,402, filed on May 1, 2017.
Claim Interpretation
The Examiner notes that the target oligonucleotide with sequence SEQ ID NO: 2 contains a 2'-O-methoxyethylribose modified sugar moiety (optionally substituted) as described on page 10 of instant specifications (paras. 1-2). Thus a method for separating SEQ ID NO: 2 meets the limitations of instant claims 19-20 and 25.
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 1-2, 5-6, 12, 14, 16-17, 22, 24, 27-31, and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Puma (WO 96/01268, IDS filed on November 26, 2024) in view of Templeton (US 2009/0275122, IDS filed on November 26, 2024) and Bonilla (CRC Press, 2011, cited on PTO-892).
Regarding claims 1-2, 14, 24, 31, and 34: Puma teaches a method for separating oligonucleotide phosphorothioates (thiolated oligonucleotide) from a mixture containing the target oligonucleotide and a product-related impurity (abstract, pg. 7, lines 218-29, separation of oligos not having DMT protecting groups). The method comprising the steps of: a) adding salt to the mixture (pg. 9, lines 5-7, salts such as sodium chloride must be added to the load and to the equilibration and wash buffers); b) loading column with optimum column loads ranging up to about 200 OD units/mL resin (pg. 9, lines 25-27) c) washing the hydrophobic adsorbent with an aqueous salt solution (pg. 9, lines 5-7, salts such as sodium chloride must be added to the load and to the equilibration and wash buffers, pg. 11, lines 8-10, column was washed with appropriate equilibration buffer after application of sample); d) eluting the target oligonucleotide with a eluting solution (pg. 8, lines 25-27, elution is most effectively accomplished with water); and e) collecting the eluent comprising the target oligonucleotide; wherein the product-related impurity includes at least one n-1 impurity, thereby separating the target oligonucleotide from the product-related impurity (pg. 11, lines 14-17, pg. 12, Table 1). Puma teaches a method wherein the salt is ammonium acetate in a phenyl Sepharose matrix (pg. 15, lines 8-15, the column was equilibrated and washed with ammonium acetate). Puma teaches column loads can go as high as 650 OD units/mL packing (i.e. capacity, pg. 8, line 31). Puma teaches an example wherein the column load is 385 OD units/mL (pg. 16, Table 5). Given a loading amount of 385 OD units/mL and a maximum load of 650 OD units/mL equates to approximately 59% of loading capacity. Puma explicitly states that the phenyl-sepharose columns results in effective separation of oligonucleotide phosphorothioates from phosphodiesters in high yields (pgs. 7-8, bridging para.). Puma also states that oligonucleotides can also be separated by length (i.e. encompassing n-1 impurities, pg. 8, lines 7-11). Puma teaches that the samples to be purified via hydrophobic chromatography possess PO and n-1 impurities (pg. 13, table 3). Puma teaches that following purification with ammonium acetate, the final product purity of the isolated product is improved (pg. 14, table 4).
Puma does not teach wherein the salt is ammonium sulfate. Puma does not teach wherein the separation removes N+1 impurities.
However, Templeton teaches it is known in the art to equilibrate the column in hydrophobic interaction chromatography with buffers containing ammonium sulfate salt, including with a phenyl sepharose hydrophobic interaction matrices for the purification of nucleic acids (pg. 14, paras. 0137-0138). Whereas Puma teaches ammonium acetate salt in the equilibration buffer and Templeton teaches ammonium sulfate salt in the equilibration buffer both for phenyl Sepharose hydrophobic interaction chromatography in the context of oligonucleotide purification, it is prima facie obvious to substitute equivalents known for the same purpose (See MPEP 2144.06). Therefore, it would have been prima facie obvious to one of ordinary skill in the art to modify the purification method taught by Puma by replacing the ammonium acetate salt with ammonium sulfate as taught by Templeton.
Additionally, Bonilla teaches separation of PO impurities and N-1 impurities can be achieved by optimizing conditions (pg. 8, paras. 2-3). Bonilla teaches N+1 and N-1 impurities can be separated through routine optimization of stationary phase hydrophobicity and mobile phase conditions (pg. 20 para. 1, pg. 22, paras. 2-3).
Taken together it would have been prima facie obvious to substitute salts and optimize conditions for separation of the impurities as it is a routine practice in the art of chromatographic purification as established by Bonilla. A person of ordinary skill in the art would have had the motivation to do so with a reasonable expectation of success in order to improve overall purity for therapeutic purposes, and the art recognizes that resolution of these impurities can be achieved by optimizing stationary phases and mobile phase conditions.
Regarding claim 5: As discussed above, Puma teaches elution is most effectively accomplished with water (pg. 8, lines 25-27).
Regarding claim 6: Puma teaches the following calculation:
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106
703
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(pg. 14, lines 25-27). Puma teaches a method wherein product in the elution collection does not include 1-25% of total product in all fractions (pg. 16, table 5, entry 1, Elution: 75.4%, Total: 78.1%). This implies elution of the product is delayed such that percentages of the product peaks can be separated.
Regarding claim 12: Puma teaches a method wherein the hydrophobic adsorbent comprises phenyl (phenyl sepharose, pg. 19, lines 6). Puma teaches a method wherein the hydrophobic adsorbent is packed at a bed height of approximately 12 cm (pg. 19, lines 1-7, 2.2 cm diameter column wherein phenyl sepharose was packed at height:diameter ratio of 5.4:1). Puma does not explicitly teach a method wherein the hydrophobic adsorbent is packed at a bed height of at least 15 cm. However, Puma teaches column geometry has a significant effect on the requirements for equilibration buffer salt conditions -- taller columns (larger height:diameter ratio) require higher salt as compared to shorter columns (lower height:diameter ratio) (pg. 9, lines 29-31). While taller columns can be used, shorter columns work very well and are preferred for large-scale work (pg. 8, lines 29-30). Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation (See MPEP 2144.05 (II)).
Regarding claim 16: Puma teaches the method can separate oligonucleotides with a length from about 10 to about 35 nucleotides (pg. 8, lines 7-11).
Regarding claims 17, 19, 22, and 24: Puma teaches a method wherein the target oligonucleotide comprises nucleobases selected from adenine, guanine, cytosine, and thymine (GEM 91, pg. 10, lines 20-26). GEM 91 comprises sugars that are optionally (not) substituted, meeting the limitations of claim 19. GEM 91 (DNA). comprises deoxyribonucleosides (DNA) and phosphonothioate linkages, meeting the limitations of claims 22 and 24 (GEM 91, pg. 10, lines 20-26, pg. 23, lines 4-10).
Regarding claims 27-28: Puma teaches a method wherein DMT-on oligonucleotides can be purified from solutions containing DMT-off oligonucleotides (pg. 16, Table 5, lines 1-13).
Regarding claims 29-30: Puma further teaches the purification of an oligonucleotide comprising N-1 and phosphodiester oligos (P=O, pg. 11, lines 14-17). Puma demonstrated an increase in purity resulting from a decrease in the n-1 and P=O impurities:
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494
722
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(pg. 11, lines 14-17, pg. 12, table 1, run no. 5).
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Puma (WO 96/01268, IDS filed on November 26, 2024), Templeton (US 2009/0275122, IDS filed on November 26, 2024), and Bonilla (CRC Press, 2011, cited on PTO-892), as applied to claims 1-2, 5-6, 12, 14, 16-17, 19, 22, 24, 27-31, and 34 in view of Gjerde (US 2005/0019951, IDS filed on November 26, 2024).
Regarding claim 3: As discussed above, Puma teaches the method of claim 1. Puma teaches wherein salt is added to the mixture as an aqueous salt solution or the salt is dissolved directly into the mixture (pg. 9, lines 5-7, salts such as sodium chloride must be added to the load and to the equilibration and wash buffers, pg. 15, lines 13-15, the column was equilibrated and washed with ammonium acetate). Puma teaches Phenyl sepharose columns are preferably loaded at high flow rates. Rates exceeding about 250 cm/hr are found to work exceedingly well. Elution at a rate of about 150-200 cm/hr is desirable (pg. 9, lines 9-10).
Puma does not explicitly teach a method wherein the flow rate of the wash step is slower than the loading flow rate.
However, Gjerde teaches general protocols for purification of biomolecules, including using hydrophobic interaction chromatography (abstract, pg. 4, para. 0078). Gjerde teaches it is known in the art that in some cases, it is desirable to perform one or steps of a purification process at a relatively slow flow rate (e.g., the loading or wash steps) to maximize binding of an analyte of interest to an extraction medium (pg. 14, para. 0175). Although Puma and Gjerde do not teach a flow rate wherein the wash step is slower than the loading step wherein change flow rates at various steps for specific purposes is known in the art, optimization of a result-effective variable is obvious absent a showing of unexpected results (See MPEP 2144.05(II)). Therefore, it would have been prima facie obvious to one of ordinary skill in the art to modify the method of Puma whereby the wash step is slower than the loading flow rate. A person of ordinary skill in the art would have had the motivation to do so with a reasonable expectation of success in order to maximize binding of an analyte to an extraction medium.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Puma (WO 96/01268, IDS filed on November 26, 2024), Templeton (US 2009/0275122, IDS filed on November 26, 2024), and Bonilla (CRC Press, 2011, cited on PTO-892), as applied to claims 1-2, 5-6, 12, 14, 16-17, 19, 22, 24, 27-31, and 34 in view of Bonturi (Journal of Chromatography B, 2013, cited in previous action).
Regarding claim 13: As discussed above, the prior art renders obvious the method of claim 1. Puma teaches washing the hydrophobic adsorbent with an aqueous salt solution (pg. 9, lines 5-7, salts such as sodium chloride must be added to the load and to the equilibration and wash buffers, pg. 15, lines 13-15, the column was equilibrated and washed with ammonium acetate). Templeton teaches it is known in the art to equilibrate the column in hydrophobic interaction chromatography with buffers containing ammonium sulfate salt, including with a phenyl sepharose hydrophobic interaction matrices for the purification of nucleic acids (pg. 14, paras. 0137-0138).
They do not teach wherein the salt is potassium phosphate.
However, Bonturi suggests potassium phosphate as an alternative adsorption buffer for ammonium sulfate in phenyl-agarose hydrophobic interaction chromatography of nucleic acids (abstract).
Taken together, whereas the prior art teaches ammonium acetate salt, ammonium sulfate, and potassium phosphate are known salts in the equilibration buffer both for hydrophobic interaction chromatography in the context of oligonucleotide purification, it is prima facie obvious to substitute equivalents known for the same purpose, absent a showing of unexpected results (See MPEP 2144.06).
Claims 19-20 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Puma (WO 96/01268, IDS filed on November 26, 2024), Templeton (US 2009/0275122, IDS filed on November 26, 2024), and Bonilla (CRC Press, 2011, cited on PTO-892) as applied to claims 1-2, 5-6, 12, 14, 16-17, 19, 22, 24, 27-31, and 34 above in view of Swayze (WO 2015/153800, IDS filed on November 26, 2024).
Regarding claims 19-20 and 25: As discussed above, the prior art renders obvious claim 1. Puma teaches the method is applicable to chemically synthesized oligonucleotides (pg. 6, lines 29-31).
They do not teach a method wherein the target nucleotide is SEQ ID NO: 2. They do not teach wherein the target oligonucleotide comprises sugar that is optionally-substituted; two non-geminal ring atoms are bridged to form a bicyclic nucleic acid (BNA); or a ring oxygen atom of the sugar is replaced with S[[,]] or or C(R₄)(R)₂, wherein R is H or C1-C12 alkyl and combinations of these as recited by instant claim 19.
However, Swayze teaches modified oligonucleotide SEQ ID NO: 2 (pg. 24, lines 5-15). SEQ ID NO: 2 is useful for treating SOD-1 associated diseases such as amyotrophic sclerosis (abstract). Swayze also teaches “Antisense compounds of the invention can optionally contain one or more nucleosides wherein the sugar group has been modified. Such sugar modified nucleosides may impart enhanced nuclease stability, increased binding affinity, or some other beneficial biological property to the antisense compounds. In certain embodiments, nucleosides comprise chemically modified ribofuranose ring moieties. Examples of chemically modified ribofuranose rings include without limitation, addition of substituent groups (including 5' and 2' substituent groups, bridging of nongeminal ring atoms to form bicyclic nucleic acids (BNA), replacement of the ribosyl ring oxygen atom with S, N(R), or C(Ri)(R 2) (R, Ri and R2 are each independently H, C 1-C 12 alkyl or a protecting group) and combinations thereof. ”(pg. 43, lines 10-25).
Taken together, a person of ordinary skill in the art would recognize that the oligonucleotides taught by Swayze are synthesized in the same manner as taught by Puma (i.e. solid-phase oligonucleotide synthesis). Whereas the general method was made obvious over Puma and SEQ ID NO: 2 is known in the art, one of ordinary skill in the art would have expected this method to function predictably in purifying SEQ ID NO: 2 or oligonucleotides with the claimed modifications recited by instant claim 19 from product related impurities.
Response to Arguments
Applicant’s arguments filed June 9, 2026 with respect to the claims have been fully considered but they are not persuasive.
On page 7 of Applicant’s response, Applicant argues the use of ammonium sulfate or potassium sulfate results in unexpected results of improved binding of the oligonucleotide to the HIC resins, which is demonstrated by longer retention on the column compared to sodium acetate or ammonium chloride. Applicant points to the declarations of Gronk filed June 9, 2026, as well as the declaration of Gronk filed in patented grand parent case 10,974,262. In the grand parent declaration of Gronk, Gronk demonstrates unexpected binding using ammonium sulfate in phenyl resins or hexyl resins. In the declaration of Gronk filed June 9, 2026, Gronk establishes that ammonium sulfate and potassium phosphate have comparable dynamic binding capacity in phenyl, and butyl resins.
However, the instant claims are not limited to any specific resin type, but rather hydrophobic adsorbents, which are not commensurate with the data provided in the declarations, which are limited to specific resins. Furthermore, it is unclear how the dynamic binding capacity in the June 9, 2026 declaration of Gronk compares to the salts of the prior art, such as ammonium acetate of Puma. The declaration of Gronk fails to demonstrate unexpected separation for potassium sulfate across the full scope of hydrophobic adsorbents.
On page 8 of Applicant’s response, Applicant argues that Puma does not teach separating a target oligonucleotide from a mixture containing the target oligonucleotide from a product-related impurity comprising a n-1 impurity or a P=O impurity via hydrophobic chromatography. On page 9 of Applicant’s response, Applicant argues Puma teaches both ion exchange columns, phenyl 5PW and phenyl Sepharose columns are required to separate phosphorothioate from phosphodiesters (para. 2). Applicant argues the hydrophobic column disclosed in Puma is for the removal of ammonium hydroxide and oligos with no DMT protecting group, not for removing product related impurities as claimed. On pages 9-10 of Applicant’s response, Applicant argues that Puma does not consider n-1 oligonucleotides as impurity, but rather states the length of oligonucleotides that are suitable for purification by the Puma method (bridging paras.). On page 10 of Applicant’s response, Applicant points to table 3 of Puma and teaches the samples to be purified possess PO and n-1 impurities, but does not teach the percentage of n-1 oligonucleotide was reduced related to the target nucleotide. On page 11 of Applicant’s response, Applicant points to table 4 which provides purity profiles but nothing suggests the improved impurity is related to the n-1 impurity and/or P=O impurity.
However, Puma explicitly states that the phenyl-sepharose columns results in effective separation of oligonucleotide phosphorothioates from phosphodiesters in high yields (pgs. 7-8, bridging para.). Puma also states that oligonucleotides can also be separated by length (i.e. encompassing n-1 impurities, pg. 8, lines 7-11). Puma teaches that the samples to be purified via hydrophobic chromatography possess PO and n-1 impurities (pg. 13, table 3). Puma teaches that following purification with ammonium acetate, the final product purity of the isolated product is improved (pg. 14, table 4). According to the instant specification, the claimed method does not result in the outright removal of N-1, P=O impurities, Abasic, CNET, and N+1 but an improvement in overall purity (pg. 15, tables 1-2, pgs. 18-19, tables 4-6). The instant specification demonstrates reduction in impurities with a phenyl sepharose stationary phase with ammonium sulfate in the loading buffer (pg. 14, para. 1). As discussed above, Puma attributes separation capability to the stationary phase of phenyl sepharose, which is the stationary phase used in the instant application. Thus, wherein Puma utilizes the phenyl sepharose stationary phase, the resulting improvement in purity necessarily flows as a result of the method in substituting known equilibration salts for one another, absent a showing of unexpected results that are commensurate with the scope of the claims. Puma teaches that the purity analysis was performed with ion exchange chromatography, while the purification method comprised hydrophobic interaction chromatography (pg. 10, lines 20-26, pg. 11, lines 9-11, 14-17). The table cited by Applicant demonstrates % purity of a target oligonucleotide following purification, while it may possess n-1 impurity within it, this method is comparable to that performed in the instant specification which demonstrates improved purity (removal of impurities) as a result of practicing the method (see instant specification, pg. 15, tables 1-2, pgs. 18-19, tables 4-6). Puma teaches samples to be purified possess both PO and n-1 impurities prior to purification (pg. 13, table 2). Puma teaches the purity and yield of the eluted product is equivalent to that achieved using reverse phase liquid chromatography and that by proper adjustment of load and elution conditions, high purity product can be obtained (pg. 17, lines 6-11). Furthermore see newly cited Bonilla, which establishes N+1, N-1, P=O impurities are all known impurities which are known in the art to be separated through routine optimization.
On pages 12-13 of Applicant’s response, Applicant argues Gjerde, Bonturi and Swayze do not cure deficiencies described above.
See response to arguments above.
The argument presented on page 14 is moot because Capaldi is no longer used as a reference.
Applicant’s reply is considered to be a bona fide attempt at a response and is being accepted as a complete response. The 35 USC § 103 rejections are maintained for reason of record and foregoing discussion.
Conclusion
No claims are allowed in this action.
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/SAMUEL L GALSTER/Examiner, Art Unit 1693
