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 .
Application Status
This action is written in response to applicant’s correspondence received 06/11/2024. Claims 1-20 are currently pending and examined herein.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Objections
Claims 1, 7, 8, 11 and 20 are objected to because of the following informalities:
MPEP 608.01(m) states, “Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations.” In the instant case, the claims have subcomponents labeled with “a.”, “b.”, etc., which all end in periods. Amending the claims to have a close parentheses instead of a period after those labels, e.g., “a)”, “b)”, etc., would obviate this objection. Appropriate correction is required.
Claim 4 is objected to because it contains a minor typographical error: the term “strepatavidin” appears to be a typographical error and is assumed to mean “streptavidin”. Appropriate correction is required.
Claim 20 is further objected to because of the following informalities: the claim recites, “PCR components or transcription components optionally RNA product”. This sentence is grammatically incorrect and lacks clarity. It appears to be missing punctuation (such as, “…transcription components, and optionally an RNA product”). Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 7 and 13 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, 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 7 recites wherein the NCS comprises: a. between 500 and 1000 nucleotides; b. a G/C content of between 45% and 55%. This language is considered to be indefinite because, absent a coordinating conjunction such as “and”, “or”, “and/or”, etc., it is not clear whether the NCS requires both a. and b., or whether a. and b. are alternatives.
Amending claim 7 to add the appropriate conjunction (and, or, and/or, etc.), and thus clarify whether the components are alternatives or are both required, would obviate this rejection.
Claim 13 recites the term “the variant T7 RNA polymerase”. There is insufficient antecedent basis for this term. Neither claim 13 nor the claims upon which it depends recite a variant T7 RNA polymerase.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
Determining the scope and contents of the prior art.
Ascertaining the differences between the prior art and the claims at issue.
Resolving the level of ordinary skill in the pertinent art.
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 1, 4-6, 8-9, 11-12, and 14-19 are rejected under 35 U.S.C. 103 as being unpatentable over WIPO Publication 2021/058145 A1 to Conrad (hereinafter ‘Conrad’).
Regarding claims 1, 5 and 11, Conrad teaches a DNA polynucleotide, a kit comprising said DNA polynucleotide (and reagents for performing an in vitro transcription reaction), and method for producing an RNA composition using said DNA polynucleotide, comprising synthesizing, amplifying, and transcribing a DNA template comprising, in order from 5’ to 3’: a 5’ NCS, a phage promoter sequence, a 5’ UTR, a polypeptide coding sequence, a 3’ UTR, and a 3’ poly(dT) sequence that includes more than 100 nucleotides:
The invention relates to a DNA polynucleotide, a kit comprising said DNA polynucleotide, and a method for in vitro transcribing (IVT) RNA using said DNA polynucleotide, wherein said DNA polynucleotide comprises…a T7 promoter sequence…a nucleotide sequence encoding the RNA to be transcribed; and wherein the method comprises…providing said DNA polynucleotide as an IVT template, and…in vitro transcribing said IVT template in the presence of a T7 polymerase and ribonucleotide triphosphates. (Abstract)
The encoded RNA can be an in-vitro transcribed RNA according to the invention, in particular an mRNA or a non-coding RNA…an mRNA comprises preferably a 5’ UTR, a coding sequence and a 3’ UTR…The 3’ UTR starts after the stop codon of the coding sequence and can be followed by a poly A tail. (p. 20 ln 10-25)
a polyA tail refers to a sequence comprising, preferably 5 to 300, covalently linked adenines…the polyA tail is transcribed from an IVT template comprising a polyT- stretch at the 3 ’ end of the IVT template. (p. 33 ln 25-26, p. 34 ln 1-2)
“GAATT” is advantageous…as upstream sequence directly adjacent to the T7 promoter as it had a positive effect on the strength of the T7 promoter. (p. 91 ln. 10-15)
the IVT template is generated by few or one cycle(s) of PCR (p. 37 ln 30-31)
Regarding claims 1 and 5, while Conrad does not explicitly teach that methods of using the DNA polynucleotide comprising the non-coding sequence upstream of the T7 promoter result in lower dsRNA contamination compared to a DNA polynucleotide without the upstream NCS, it is noted that the method requires the structure of the DNA template, and the active steps are merely synthesis, amplification, and use of the template to generate RNA. Thus, insofar as Conrad teaches a substantially identical structure to the claimed DNA template on which the method is based, Conrad teaches a structure which necessarily inherently possesses the same properties and would result in the same outcomes (MPEP 2112.01).
Regarding claim 11, it is noted that the preamble states an intended use for the kit, which is “producing an RNA composition with reduced levels of dsRNA”. The claim also recites an intended, “use in an in vitro transcription reaction” for the DNA template. These statements of intended use are not considered limiting because they do not result in a structural difference between the claimed invention and prior art (MPEP 2111.02).
It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have modified the basic DNA template comprising a 5’ and 3’ UTR, coding sequence, and polyA tail, as taught by Conrad, to include the upstream NCS “GAATT”, as also taught by Conrad. The ordinary artisan would have been motivated to do so, with a reasonable expectation of success, based on Conrad’s statement that the upstream NCS was advantageous for in vitro transcription.
Regarding claims 4, 12, 18 and 19, Conrad teaches wherein the polymerase is T7 phage polymerase, as described above.
Regarding claim 6, Conrad teaches capping the RNA (p. 33 ln 9-11).
Regarding claim 8, Conrad teaches wherein the NCS does not comprise any of the listed sequences, but is instead simply an AT-rich upstream NCS.
Regarding claim 9, Conrad teaches wherein said DNA-template is synthesized in vitro, as described above.
Regarding claims 14-15, Conrad teaches wherein the DNA template comprises a 3’ polydT sequence (for transcription into a polyA sequence) of more than 100 nucleotides located 3’ to the 3’ UTR, as described above.
Regarding claims 16-17, Conrad teaches wherein the kit comprises buffers, reagents and enzymes for amplifying and transcribing the template (p. 47 ln 19-25). Further, it would have been obvious to include in any kit all elements required to synthesize and use the template.
Claims 3 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Conrad (cited above), as applied to claims 1, 4-6, 8-9, 11-12, and 14-19, in view of Cavac (Cavac et al. High-salt transcription of DNA cotethered with T7 RNA polymerase to beads generates increased yields of highly pure RNA. Journal of Biological Chemistry, 2021; 297.)
Conrad renders obvious the method of claim 1 and the DNA template comprising the 5’ NCS, phage promoter, 5’ UTR, ORF, 3’UTR, and poly(dT), as well as wherein the polymerase is a T7 polymerase, as described above.
Conrad does not teach wherein the template has a biotin at the 5’ end, or wherein the T7 polymerase is fused to streptavidin.
Cavac teaches an in vitro transcription system in which the DNA template has a biotin attached to the 5’ end and the T7 polymerase has streptavidin:
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Cavac further teaches that while dsRNA contamination from in vitro synthesized RNA can invoke the innate immune response (p. 1), this approach addresses that issue because it results in a dramatically higher yield of RNA with a dramatically reduced amount of double-stranded impurities (p. 2):
In this research, we present a novel method of in vitro transcription that allows promoter-directed transcription while preventing primer extension activity, thereby dramatically reducing double-stranded impurities. In brief, by increasing salt concentrations in solution, we reduce all protein–nucleic acid interactions. To selectively restore promoter binding, we tether both T7 RNA polymerase and promoter DNA to a solid support (beads). This drives their association even at high salt concentrations. Near elimination
of RNA rebinding and extension not only results in a dramatic reduction in longer, primer-extended products, but also nets a dramatic increase in the yield of encoded RNA.
It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have modified the DNA template as recited in claim 1 to include Cavac’s tethered system, which brings the polymerase and template into close proximity via biotin-streptavidin tagging. The ordinary artisan would have been motivated to do so, and had a reasonable expectation of success, based on Cavac’s teachings that this approach yielded dramatically increased amounts of purified RNA, with dramatically reduced dsRNA contamination, for use in therapies where invocation of the innate immune response is not desirable.
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Conrad (cited above), as applied to claims 1, 4-6, 8-9, 11-12, and 14-19, in view of Zageno (In Vitro Transcription Troubleshooting. 17 December 2020. Accessed via web on 08/28/2026 at go.zageno.com/blog/in-vitro-transcription-troubleshooting).
Conrad renders obvious the method of claim 1 and the recited DNA template comprising the 5’ NCS, phage promoter, 5’ UTR, ORF, 3’UTR, and poly(dT), as well as wherein the polymerase is a T7 polymerase, as described above. Conrad also teaches wherein the DNA template is linear, as described above.
Conrad further teaches where the template is linear and double-stranded (p. 28 ln 16-17).
Conrad does not clearly teach wherein the template is blunt-ended.
Zageno teaches wherein one known cause of longer than expected transcripts from in vitro transcription is a template with a 3’ overhang. Zageno further suggests using a restriction enzyme that produces 5’ overhangs or blunt-ended fragments to prevent this outcome. Lastly, Zageno teaches that templates must be linearized to allow complete transcription.
It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have tried modifying the DNA template as taught by Conrad to be linear and to have either a 5’ overhang or blunt ends. The ordinary artisan would have been motivated by Zageno’s teachings that these modifications can address possible pitfalls of in vitro transcription, such as incomplete transcription or excessively long transcripts.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Conrad (cited above), as applied to claims 1, 4-6, 8-9, 11-12, and 14-19, in view WIPO Publication 2022/084748 A1 to Spindle Biotech, Inc. (hereinafter ‘Spindle’).
Conrad renders obvious the method of claim 1 and the recited DNA template comprising the 5’ NCS, phage promoter, 5’ UTR, ORF, 3’UTR, and poly(dT), as well as wherein the polymerase is a T7 polymerase, as described above.
Conrad does not teach wherein the T7 polymerase comprises at least four variations selected from the group consisting of Kl72L, P266L, H772R, N748X, R756M, Q758X, and E775V.
Spindle teaches “a modified polypeptide, wherein the modified polypeptide comprises a variant T7 RNA polymerase or a functional fragment thereof, wherein the variant T7 RNA polymerase comprises at least four variations selected from the group consisting of K172L, P266L, H772R, N748X, R756M, Q758X, and E775V”.
Spindle further teaches that, “RNA polymerases described herein can include a wild type RNA polymerase or a variant RNA polymerase comprising one or more amino acid substitutions that may affect DNA recognition, DNA binding affinity, polymerase activity, or stability of the polymerases”.
It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have modified the wild type T7 polymerase, as taught by Conrad, to comprise the at least four of the variations suggested by Spindle. The ordinary artisan would have been motivated, and would have had a reasonable expectation of success, based on Spindle’s teachings that said variants may affect DNA recognition, DNA binding affinity, polymerase activity, or stability of the polymerase.
Conclusion
No claim is allowed at this time.
Claim 2 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMANDA M ZAHORIK whose telephone number is (703)756-1433. The examiner can normally be reached M-F 8:00-16:00 EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached on (571) 270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AMANDA M ZAHORIK/Examiner, Art Unit 1636
/BRIAN WHITEMAN/ Primary Examiner, Art Unit 1636
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