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 .
The Response of 6 Feb. 2026 has been entered.
Claims 1-31 are currently pending. Claims 4, 8, 9, 16, 18 and 26-31 are withdrawn as being drawn to a nonelected species (claims 4, 8, 9, 16, 18) or invention (claims 26-31).
Claims 1-3, 5-7, 10-15, 17 and 19-25 are considered here with respect to the elected species of: imidazolide nucleoside-5'-monophosphate as the species of activated nucleoside; RNA as the species of polynucleotide; enzymatic addition as the species of method for producing the polynucleotide having a 5’-monophosphate; a structure of formula I, wherein X is guanine, R1 and R2 are -OH and n is 2 as the species of cap structure; and identity of nucleotide at 1st or 2nd position as the species of bias.
Any rejection not reiterated herein has been withdrawn.
Response to Arguments
Applicant's arguments filed 6 Feb. 2026 have been fully considered but they are not persuasive.
Applicant argues that the fact that Sawai and Shimazu share common authors and there is large time gap between publication dates indicates that the cited combination would not have been predictable. This is not persuasive because Applicant has not provided any specific rationale as to why one of ordinary skill would regard the cited combination as unpredictable. Sawai teaches a method substantially similar to the claimed method wherein an activated nucleoside 5' di- or tri-phosphate (an imidazolide 5’-di-phosphate or 5’-triphosphate, which can comprise a guanosine base and a ribose sugar) is reacted with the population of oligoribonucleotides to produce capped oligoribonucleotides. The method of Sawai falls within the scope of the instant claims (the cap is within the scope of formula (I) of claim 14) and differs only from the elected species in that the activated nucleoside is an imidazolide guanosine-5'-monophosphate (rather than diphosphate) and the cap comprises GppN (rather than 7mGpppN). Shimazu teaches that substantially the same method can be carried out using an activated nucleoside monophosphate and an unmodified base, rendering the claimed method obvious.
Applicant further argues that Shimazu's teaching regarding use of guanosine merely states that application of the method to guanosine is in progress, and that Sawai (published many years later) fails to report success of any such experiments. This is not persuasive because Sawai does indeed teach use of activated guanosine in the capping method (e.g., p. 5839, Scheme 2). Sawai differs from the elected species only in that the guanosine is not 7-methylated and the activated nucleoside has one rather than two phosphates. However, Shimazu teaches that the same capping method can be carried out using an activated nucleoside monophosphate with an unmodified base and further suggests use of unmethylated guanosine. In view of the highly similar structures and methodologies of the methods of Shimazu and Sawai (using the same activated imidazolide nucleoside and the same mechanism), one of ordinary skill would have had a reasonable expectation of success in carrying out the method of Sawai with an activated guanosine-monophosphate. Moreover, as set forth below, one of ordinary skill would have been motivated to use an unmethylated guanosine, e.g. to study the effects of 7-methylation on gene expression.
Applicant further cites Sun, Fuchs and Warminski as teaching that chemical synthesis of capped RNA is difficult for RNAs longer than a few nucleotides. This is not persuasive because Sun, Fuchs and Warminski deal with chemical synthesis methods rather than the coupling method of Sawai/Shimazu. Sawai exemplifies capping of longer RNAs (including a 72-residue tRNA) (Sawai, p. 5340), and further distinguishes the method from chemical synthesis approaches as referred to by Sun, Fuchs and Warminski (Sawai, p. 5386, 1st ¶).
Claim Rejections - 35 USC § 112(a) (new matter)
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.
Claim 25 is rejected under 35 U.S.C. 112(a) 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.
Claim 25 recites "the efficiency of template switching is enhanced by at least 2-fold compared with reverse transcribing 5' capped polynucleotides that do not comprise in the cap an unmethylated guanosine". Claim 25 has been amended to depend from claim 24 (which in turn depends from claims 21, 20, 14, 3 and 2) rather than from claim 19. Claim 19 recites that the nucleoside cap comprises guanosine. The original specification states that the increased template switching efficiency recited in claim 25 is limited to cases in which the cap comprises unmethylated guanosine (e.g., Published Spec. US20220195424, [0018]; [0058]; [0176]; [0185]). Claim 25 as amended thus comprises new matter.
Claim Rejections - 35 USC § 112(b) (indefiniteness)
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.
Claims 24-25 are rejected under 35 U.S.C. 112(b) 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.
Claim 24 recites "The method according to guanosine and one, two, three or four phosphates between the guanosine cap and the first nucleotide at the 5′ endclaim 21…" It is unclear how the above recitation limits the claim (the above appears to be a typographical error).
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 1-3, 5-7, 10-15, 17 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over the combination of Sawai et al., The Journal of Organic Chemistry 64.16 (1999): 5836-5840 (cited in IDS of 10 Nov. 2021) in view of Shimazu et al., Tetrahedron letters 31.2 (1990): 235-238, as evidenced by Cowling, Biochemical Journal 425.2 (2010): 295-302 (each previously cited).
Regarding claims 1-3, 10 and 19, Sawai teaches a method for chemically capping a population of oligoribonucleotides having a 5' monophosphate in an aqueous media, comprising:(a) combining an activated nucleoside 5' di- or tri-phosphate (an imidazolide 5’-di-phosphate or 5’-triphosphate) with the population of oligoribonucleotides, to produce a reaction mix; and(b) incubating the reaction mix such that a nucleophilic substitution reaction displaces the imidazole group on the activated nucleoside and produces reaction products that each comprise an oligoribonucleotide linked to a 5' nucleoside cap by a 5' to 5' polyphosphate linkage (p. 5838-5840, under Results and Discussion; Scheme 2). The activated nucleoside can comprise a methylated guanosine base and a ribose sugar (7-methylguanosine 5’-diphosphate imidazolide, or Impp7mG) (under Preparation of the Capped Oligoribonucleotides by the Capping Reaction of 5‘-Monophosphorylated Oligoribonucleotides with Impp7mG in Aqueous Solution by Mn2+ or Mg2+ Catalyst; Scheme 2).
Regarding the recitation in claim 1 that "members of the population of polynucleotides each comprise at least 18 nucleotides", Sawai teaches that the method can be carried out with oligoribonucleotides of varying lengths from 6 to 72 nucleotides (p. 5839, right col., 1st full ¶ to p. 5840, last ¶), and it would have thus been obvious to carry out the method with RNAs of 18 or longer nucleotides.
Regarding claim 5, the recitation that the oligoribonucleotides are “of a cell”, “of a virus”, etc. is a product-by-process limitation that is limiting only with respect to any structure necessarily implied by the process (see MPEP 2113). The recitation that the oligoribonucleotides are “of a cell”, “of a virus”, etc. do not necessarily imply any particular structure to the claimed oligoribonucleotides that would distinguish those of Sawai. Moreover, Sawai teaches performing the capping reaction with yeast tRNAphe (i.e. an oligoribonucleotide of a yeast cell) as the oligoribonucleotide (p. 5840, right col.) and it would have been obvious to carry out the reaction with any similar RNA species derived from a cell, virus, etc.
Regarding claims 6-7, Sawai teaches that “the 5‘-monophosphorylated oligoribonucleotides can be obtained easily by … kination of natural or synthetic 5‘-hydroxyl oligoribonucleotides with polynucleotide kinase” (p. 5839, right col., 1st full ¶). Thus, it would have been obvious to obtain the oligoribonucleotides used in the method of Sawai via addition of a phosphate using polynucleotide kinase, as recited in claims 6-7.
Claims 1-3, 5-7, 10-15, 17 and 19 differ from Sawai in that: the activated nucleoside is an imidazolide guanosine-5'-monophosphate (elected species and claims 1, 13); the 5’ cap comprises guanosine-diphosphate (GppN) (elected species and claims 14, 15, 19); the reaction mix has a pH of 5-6.5 (claim 11); the incubation is for less than 10 hours at a temperature of less than 60 °C (claim 12); and the incubation is either at 50°C for 5 hours, 37°C for 4 hours, or room temperature for 4 hours (claim 13).
Shimazu teaches a substantially similar method as in Sawai for chemically synthesizing RNA cap structures in aqueous medium, and teaches that the activated nucleoside imidazolide can be a nucleoside monophosphate (p. 235, last ¶ to p. 236, last ¶) and can have a guanosine base (p. 238, last ¶).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to use the method of Sawai for chemically capping oligoribonucleotides in an aqueous medium via reaction of an activated imidazolide nucleoside is an imidazolide guanosine-5'-monophosphate (creating a GppN cap structure) because it would have been obvious to combine prior art elements according to known methods to yield predictable results. Carrying out the method of Sawai using an imidazolide guanosine-5'-monophosphate as the activated nucleoside would have led to predictable results with a reasonable expectation of success because Shimazu teaches a substantially similar method via the same mechanism (using an activated imidazolide to produce a 5’-5’ phosphate coupling via nucleophilic substitution) and under the same aqueous conditions and shows that the activated nucleoside can be a nucleoside monophosphate and have a guanosine base (compared to use of a nucleoside-diphosphate and a 7-methylguanosine base in Sawai). One of ordinary skill would have been motivated to carry out the method of Sawai using an imidazolide guanosine-5'-monophosphate as the activated nucleoside in order to produce a range of cap structures, e.g. for testing, experimentation and the like. For example, Cowling evidences that the methyl group on 7-methylguanosine caps plays a functional role in several steps of gene expression, and that such roles have been studied by experiments comparing methylated and unmethylated cap structures (Cowling, under PROCESSES DEPENDENT ON CAP METHYLATION).
Regarding the pH range in claim 11, Shimazu teaches that the “pH of the reaction medium had a considerable effect on the pyrophosphate formation. Hydrolysis of the phosphorimidazo1id.e bond of ImpA was predominant below pH 6.0. The high pH above 7.5 stabilized the phosphorimidazolide bond and decreased the yield of the AppA.” (p. 236, last ¶). It would have thus been obvious that the reaction of the cited combination could be carried out within a pH range of 6-7.5, which overlaps and renders obvious the claimed range. Moreover, Shimazu teaches that pH is a result-effective variable that significantly influences product formation, and it would have thus been obvious for one of ordinary skill to vary the pH using routine experimentation to vary the yield of the reaction (see MPEP 2144.05).
Regarding the temperature and reaction time values recited in claims 12 and 13, Shimazu teaches that “the reaction completed in 10 days, 2 days and 4 h at 4°C, 25°C and 50°C, respectively” and that “the reaction rate was markedly accelerated by a high temperature” (p. 236, last ¶). It would have thus been obvious to carry out the reaction at, e.g., 50°C for 4 hours, which falls within the range of claim 12 and is substantially similar to the 50°C for 5 hours time/temp recited in claim 13 (it would have been obvious that a reaction according to the cited combination at 50°C could have an incubation period extending from 4 hours to 5 or more hours, e.g. to ensure completion). Moreover, Shimazu teaches that temperature is a result-effective variable that significantly influences the reaction time, and it would have thus been obvious for one of ordinary skill to vary the temperature using routine experimentation to vary the time of the reaction (see MPEP 2144.05).
Claims 20-25 are rejected under 35 U.S.C. 103 as being unpatentable over the combination of Sawai in view of Shimazu, as applied to claims 1-3, 5-7, 10-15, 17 and 19, further in view of Zhu et al., Biotechniques 30.4 (2001): 892-897, as evidenced by (in the case of claim 25) Wulf et al., Nucleic acids research 50.1 (2022): e2-e2 (previously cited).
The teachings of Sawai in view of Shimazu are set forth above. Regarding claims 20-25, Sawai further teaches that capped oligoribonucleotides made by the capping method can be ligated with target RNA to give full length mRNA which can be applied to molecular biology applications (p. 5840, last ¶).
Claims 20-25 differ from the combination of Sawai in view of Shimazu, as applied to claims 1-3, 5-7, 10-15, 17 and 19, in that: the capped polynucleotide comprises a 3' polyA tail or ligated adapter for priming reverse transcriptase and the method further comprises reverse transcribing the capped polynucleotides to form a cDNA population (claim 20); the cDNA population comprises a sequence at the 3'-end complementary to a template switching oligonucleotide (TSO) (claim 21); the method further comprises amplifying (claim 22) and sequencing (claim 23) the cDNAs; the reverse transcribing comprises template switching between the capped polynucleotides and the TSO (claim 24); and the efficiency of template switching is enhanced by at least 2-fold compared with reverse transcribing 5' capped polynucleotides that do not comprise in the cap an unmethylated guanosine (claim 25).
Zhu teaches a method for generating a cDNA library from poly(A)-tailed RNA, comprising reverse transcribing the RNA using an oligod(T) primer (which binds poly(A) in the RNA) and a TSO (which is complementary to the 3' end of the cDNA) to form a cDNA population; and amplifying and sequencing the cDNA population (p. 893, 2nd full ¶; p. 893-894, under MATERIALS AND METHODS). The method allows for efficient generation of long cDNAs that are difficult to produce using standard reverse transcription methods due to premature termination (leading to sequence bias) (p. 893, 2nd full ¶).
Regarding claim 24, the reverse transcription comprises template switching between the polynucleotides and the TSO (p. 894-895, under Principle of SMART Library Construction).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to use the method of Sawai in view of Shimazu for chemically capping oligoribonucleotides in an aqueous medium wherein the capped polynucleotides are reverse transcribed to cDNA (e.g., after ligating capped oligonucleotides to target RNA, as suggested by Sawai) using a TSO as taught by Zhu because it would have been obvious to combine prior art elements according to known methods to yield predictable results. One of ordinary skill would have been motivated to carry out a TSO RT/amplification method as taught by Zhu with capped polynucleotides generated by the method of Sawai in view of Shimazu because Zhu teaches the TSO method allows for generation of less biased cDNA libraries than conventional methods due to less premature termination of RT. Carrying out a TSO RT/amplification method as taught by Zhu with capped polynucleotides generated by the method of Sawai in view of Shimazu would have led to predictable results with a reasonable expectation of success because Sawai teaches that capped oligonucleotides can be ligated with target RNA, and the capped RNA can be then be used in various molecular biology applications (i.e. it would have been prima facie obvious to use capped RNA generated by the method of Sawai in view of Shimazu for any purpose/applications for which such RNA is used in the art).
Regarding claim 25, Wulf evidences that a GppN cap structure as taught by the cited combination has a more than two-fold greater template switching efficiency relative to other cap structures, such as ApppN (Wulf, Fig. 2C). Claim 25 is construed herein such that “5' capped polynucleotides that do not comprise in the cap an unmethylated guanosine” can mean any cap structure not comprising unmethylated guanosine, such as those compared in Fig. 2C of Wulf. The increased template switching efficiency disclosed in the specification could potentially serve as the basis for unexpected results sufficient to overcome the prima facie case of obviousness, but Applicant bears the burden of producing objective evidence establishing that the differences in results are in fact unexpected and unobvious and of both statistical and practical significance (MPEP 716.02(b)) and any unexpected results must be commensurate in scope with the claims the evidence is offered to support (MPEP 716.02(d)).
Conclusion
Applicant's amendment necessitated the 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ROBERT J YAMASAKI whose telephone number is (571)270-5467. The examiner can normally be reached M-F 930-6 PST.
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/ROBERT J YAMASAKI/Primary Examiner, Art Unit 1657
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