DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s Response to Election/Restriction Filed, Amendment, and Arguments/Remarks, filed 22 August 2025, have been entered. Claims 1-4, 6-9, 11, 13, 15, 17, 19, 21, 23, 25-27, and 52-53 are currently pending. Claims 1, 27, 52, and 53 are independent claims. Applicant’s election without traverse of the following species:
Chaotropic agents: a. urea;
Methods of determining presence or absence of dsRNA: c. anti-dsRNA antibody;
in a reply filed 22 August 2025 is acknowledged.
Claims 9, 11, 13, 15, 17, 19, 21, and 23 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Claims 1-4, 6-8, 25-27, and 52-53 are currently pending in the application and under examination to which the following grounds of rejection are applicable. An action on the merits follows.
Priority
The present application is a 35 U.S.C. 371 national stage filing of International Application No. PCT/US2021/016613, filed 04 February 2021, which claims priority to 62/971,777, filed 07 February 2020.
Thus, the earliest possible priority for the instant application is 07 February 2020.
Information Disclosure Statement
The information disclosure statements filed 10 November 2022, 21 May 2024, and 11 June 2024 have been considered by the Examiner.
Specification
The use of the term “Triton X-100” in [0097], “CleanCap AG” in [0097, 00101, 00104], “RiboRuler RNA” in [0099], “GelRed” in [0099], “Amersham Imager 680” in [0099], which are trade names or marks used in commerce, have been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Note that the specification has not been inspected sufficient to identify all uses of trade names and/or marks used in commerce. It is Applicant’s responsibility to ensure complete compliance.
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 1-4, 6-8, 25-27, and 52-53 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. Claims 2-4, 6-8, and 26 are included in this rejection due to their dependent on and/or encompassing of independent claim 1.
Independent claim 1 recites, “an in vitro transcription reaction mixture” in line 3, which is indefinite because it is unclear what is encompassed by “an in vitro transcription reaction mixture”. For example, it is unclear whether Applicant intends to encompass transcription reactions occurring within cells cultured in vitro or merely transcription reaction occurring extracellularly. Additionally, it is unclear what constitutes an in vitro reaction mixture, in that it is unclear whether addition of urea to the media cells would constitute addition to the reaction mixture, or whether it necessitates addition of the urea specifically into the nucleus of the cells themselves. Additionally, for acellular in vitro transcription reactions, it is unclear which components are meant to be encompassed by the term “reaction mixture”. As such, the metes and bounds of the claim cannot be determined.
Independent claims 52 and 53 each recite, “a starting reaction mixture” in lines 3 and 4-5, respectively, which is indefinite because it is unclear what is encompassed by “starting reaction mixture”. For example, it is unclear what is encompassed by the reaction mixture, what reactions are encompassed, and how the reaction mixture relates to RNA preparation. Additionally, it is unclear what is meant to be considered the start of the reaction mixture. For example, it is unclear whether adding the agent to the starting reaction mixture is meant to claim that the agent is the first thing added to the mixture, that the mixture has not yet started reacting, or that the mixture has recently started reacting. As such, the metes and bounds of the claim cannot be determined.
Claim 25 recites, “wherein the reaction mixture volume is on the order of microliters to the order of liters”, which is indefinite because it is unclear what is encompassed by the term “the order of”. As such, the metes and bounds of the claim cannot be determined.
The term “substantially free” in claim 27 is a relative term which renders the claim indefinite. The term “substantially free” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The specification recites, “The term "substantially free", as used herein, refers to a state in which relatively little or no amount of a substance to be removed (e.g., contaminants/impurities) are present. For example, "substantially free of dsRNA" means that dsRNA is present at a level less than about 2%, about 1.5%, about 1.0%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, or less (w/w) of the contaminant/impurity.” [0071]. The specification provides exemplary ranges for concentrations encompassed by “substantially free” but they present non-limiting example percentages as written. As such, the metes and bounds of the claim cannot be determined.
Claim Rejections - 35 USC § 112(a)- Scope of Enablement
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.
Claims 1-4, 6-8, 25-27, and 52-53 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for:
A method of reducing, minimizing, or inhibiting formation of double-stranded ribonucleic acid (dsRNA) during in vitro transcription or during the preparation of ribonucleic acid (RNA), comprising adding at least one chaotropic agent to an in vitro transcription reaction for the preparation of RNA, wherein the in vitro transcription reaction comprises a template nucleic acid, ribonucleotides, and an RNA polymerase; or
A method of reducing, minimizing, or inhibiting intramolecular base-pairing within a ribonucleic acid (RNA) transcript and/or intermolecular base-pairing between an RNA transcript and deoxyribonucleic acid (DNA) or another RNA during the preparation of ribonucleic acid (RNA), comprising adding at least one chaotropic agent to an in vitro transcription reaction for the preparation of RNA, wherein the in vitro transcription reaction comprises a template nucleic acid, ribonucleotides, and an RNA polymerase;
does not reasonably provide enablement for:
A method of reducing, minimizing, or inhibiting the formation of double-stranded ribonucleic acid (dsRNA) during in vitro transcription or during the preparation of ribonucleic acid (RNA), comprising adding at least one chaotropic agent to any in vitro transcription reaction comprising any components or to any starting reaction mixture comprising any components; nor
A method of reducing, minimizing, or inhibiting intramolecular base-pairing within a ribonucleic acid (RNA) transcript and/or intermolecular base-pairing between an RNA transcript and deoxyribonucleic acid (DNA) or another RNA during the preparation of ribonucleic acid (RNA), comprising adding at least one chaotropic agent to any starting reaction mixture comprising any components.
The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
The rejection addresses the issue of the absence of an enabling disclosure for reducing, minimizing, or inhibiting the formation of dsRNA/RNA base pairing during in vitro transcription or during the preparation of RNA by adding a chaotropic agent to any starting reaction mixture or to any in vitro transcription reaction mixture which does not comprise at least a template nucleic acid, ribonucleotides, and an RNA polymerase for the preparation of RNA using Applicant’s claimed methods.
The broadest independent claims, claims 52 and 53, recite methods of reducing, minimizing, or inhibiting formation of dsRNA/ RNA base pairing during the preparation of RNA comprising adding at least one chaotropic agent to a starting reaction mixture. Independent claim 1 recites a method of reducing, minimizing, or inhibiting formation of dsRNA during in vitro transcription comprising adding at least one chaotropic agent to an in vitro transcription reaction mixture. Claims 2-4, 6-8, and 25-26 dependent on claim 1, and claim 27 encompasses clam 1. Dependent claims 3-4 further limit the method to yield RNA (claim 3) or mRNA (claim 4) without requiring any of the components to produce the RNA/mRNA. Additionally, none of the dependent claims add any limitations which explicitly specify any components of the reaction mixture other than the chaotropic agents themselves.
The specification discloses RNA preparation methods which include only in vitro transcription reactions [Examples 1-20]. Example 1 teaches the general IVT conditions used for the subsequent examples in which the chaotropic agent identity and concentrations were varied [0100-0101]. The IVT conditions taught in Example 1 include a reaction mixture comprising a linearized DNA plasmid template encoding glycogen debranching enzyme, a capping agent, rNTPs, urea (or other chaotropic agent), reaction buffer (comprising buffers, salts, and other components to support transcription), T7 RNA polymerase, RNase inhibitor, IPP, and RNase-free water [01001]. None of the examples taught by the instant specification include an in vitro transcription reaction mixture lacking a template, rNTPs, or an RNA polymerase.
The art at the time of filing teaches that an IVT reaction mixtures for the preparation of RNA comprise DNA templates, RNA polymerase, a minimum of four rNTPs as substrates for RNA polymerase, buffers, divalent cations, and salts as necessary for the reaction [Xu et al. US20230076421A1, published 9 March 2023, with priority to US Provisional application No. 62/852,613, filed 24 May 2019, 0022].
Neither the specification nor the art at the time of filing teaches a reaction mixture for the preparation of RNA or an in vitro transcription reaction which does not comprise a template nucleic acid, rNTPs, and an RNA polymerase. Thus, in view of the criticality of a template nucleic acid, rNTPs, and an RNA polymerase to the preparation of RNA in an in vitro transcription reaction, and the breadth of the claims, an ordinarily skilled artisan at the time of filing the instant application would have considered the reducing, minimizing, or inhibiting formation of dsRNA/base pairing and producing RNA/mRNA from any reaction mixture or any in vitro transcription reaction mixture other than reaction mixtures comprising a template nucleic acid, rNTPs, and an RNA polymerase as highly unpredictable. As such it would have required undue experimentation to practice the scope of applicant’s invention as claimed.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-4, 6-7, 25-27, and 52-53 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Xu [US20230076421A1, published 9 March 2023, with priority to US Provisional application No. 62/852,613, filed 24 May 2019].
Regarding claims 1 and 52, Xu discloses the addition of a chaotropic agent (e.g., urea as elected) to in vitro transcription reaction to serve as a destabilizer of base pairing [0109]. Therefore, by teaching that the urea is a destabilizer of base pairing, Xu teaches that the urea reduces, minimizes, or inhibits base pairing, e.g., formation of dsRNA. Additionally, by teaching to add urea to an in vitro transcription reaction, Xu is teaching to add at least one chaotropic agent (e.g., urea as elected) to a starting reaction mixture (claim 52).
Regarding claims 2 and 53, Xu teaches that the formation of dsRNA comprises base pairing, which includes at least intermolecular base pairing between an RNA transcript and another RNA during in vitro transcription, such that an RNA-RNA duplex is used as a control when testing for the dsRNA formed during the transcription reaction [0109, 0128].
Regarding claims 3-4, Xu teaches that the in vitro transcription reaction yields RNA, including mRNA [0009, 0127, 0129, Table 2].
Regarding claims 6-7, as discussed above Xu teaches adding urea (the elected species) to an in vitro transcription reaction to serve as a destabilizer of base pairing [0109].
Regarding claim 25, Xu teaches reaction volumes of 20 µl [0012-0013, 0127].
Regarding claim 26, Xu teaches determining the presence or absence of dsRNA using an anti-dsRNA antibody (as elected) [0128].
Regarding claim 27, Xu teaches a composition comprising RNA prepared according to the method, wherein the composition is substantially free of dsRNA [0128, Table 2]. Note that the instant specification indicates an example range for “substantially free of dsRNA” to include that dsRNA is present at a level less than about 2% (w/w) of the contaminant/impurity [0071]. Xu teaches that dsRNA amounts in Table 2 are denoted “low” signal when the dsRNA is about 2 ng [0128]. Accordingly, several of their in vitro transcribed compositions are substantially free of dsRNA, having much less than 2% dsRNA by weight [Table 2]. For example, the first entry in Table 2A is for Yersinia phage phiR8-01, wherein at 24oC, 11.9 µg of RNA was produced with “low” dsRNA, indicating about 2 ng dsRNA / 11.9 µg total RNA = 0.017% dsRNA by weight [Table 2].
Accordingly, by teaching all of the limitations of instant claims 1-4, 6-7, 25-27, and 52-53, Xu anticipates the instant invention as claimed.
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:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. 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, 25-27, and 52-53 are rejected under 35 U.S.C. 103 as being unpatentable over Xu [US20230076421A1, published 9 March 2023, with priority to US Provisional application No. 62/852,613, filed 24 May 2019]; in view of Pan et al. [1997, Journal of Molecular Biology, 273, 7-13]; and Griko et al. [2001, Protein Science, 10, 845-853].
Regarding claims 1 and 52, Xu discloses the addition of a chaotropic agent (e.g., urea as elected) to in vitro transcription reaction to serve as a destabilizer of base pairing [0109]. Therefore, by teaching that the urea is a destabilizer of base pairing, Xu teaches that the urea reduces, minimizes, or inhibits base pairing, e.g., formation of dsRNA. Additionally, by teaching to add urea to an in vitro transcription reaction, Xu is teaching to add at least one chaotropic agent (e.g., urea as elected) to a starting reaction mixture (claim 52).
Regarding claims 2 and 53, Xu teaches that the formation of dsRNA comprises base pairing, which includes at least intermolecular base pairing between an RNA transcript and another RNA during in vitro transcription, such that an RNA-RNA duplex is used as a control when testing for the dsRNA formed during the transcription reaction [0109, 0128].
Regarding claims 3-4, Xu teaches that the in vitro transcription reaction yields RNA, including mRNA [0009, 0127, 0129, Table 2].
Regarding claims 6-7, as discussed above Xu teaches adding urea (the elected species) to an in vitro transcription reaction to serve as a destabilizer of base pairing [0109].
Regarding claim 25, Xu teaches reaction volumes of 20 µl [0127].
Regarding claim 26, Xu teaches determining the presence or absence of dsRNA using an anti-dsRNA antibody (as elected) [0128].
Regarding claim 27, Xu teaches a composition comprising RNA prepared according to the method, wherein the composition is substantially free of dsRNA [0128, Table 2]. Note that the instant specification defines “substantially free of dsRNA” to mean that dsRNA is present at a level less than about 2% (w/w) of the contaminant/impurity [0071]. Xu teaches that dsRNA amounts in Table 2 are denoted “low” signal when the dsRNA is about 2 ng [0128]. Accordingly, several of their in vitro transcribed compositions are substantially free of dsRNA, having less than 2% dsRNA by weight, e.g., the first entry in Table 2A is for Yersinia phage phiR8-01, wherein at 18oC, 13.7 µg of RNA was produced with “low” dsRNA, indicating about 2 ng dsRNA / 11.9 µg total RNA = 0.017% dsRNA [Table 2].
Regarding claim 8, Xu does not teach that the urea is at a concentration of from about 0.1 M to about 1.6 M.
However, Pan and Griko cure this deficiency.
Pan teaches the folding kinetics of large RNAs in the presence of urea, wherein an RNA denatured from an intramolecularly dsRNA (e.g., native) state to an unfolded state by increasing concentrations of urea [Figure 2], and wherein the RNA is renatured following denaturation in the presence of various concentrations of urea [Figure 3]. Figure 2 shows that the fraction of native/folded RNA is about 50% at a urea concentration of 1M and about 10% at a urea concentration of 3.5M. Figure 3b shows the fraction of natively folded RNA (e.g., intramolecular dsRNA) overtime following addition of urea to previously denatured RNA, wherein 0.8 M urea allowed native refolding with a maximal fraction of native RNAs of about 80%, whereas 2.0 M urea allowed native refolding with a maximal fraction of native RNAs of only about 20%. Pan also teaches that 0 to 1 M urea does not significantly denature the RNA [column 7 ¶ 2], but that misfolded structures are destabilized at 0.8 M urea [column 8 ¶ 2]. Pan further teaches that as the urea concentration increases beyond 1 M, both the native state and the misfolded structures become destabilized [column 8 ¶ 2]. Therefore, an ordinarily skilled artisan would have been motivated to use a urea concentration of about 0.8 M to destabilize misfolded RNA structures (e.g., unwanted intramolecular dsRNA interactions) and to use a urea concentration of about 1 M – 2 M to destabilize both native RNA structures and misfolded RNA structures.
Additionally, Griko teaches that T7 RNA polymerase will denature in the urea concentration range of 2.0-5.0 M, wherein tertiary structure of the polymerase is lost [column 9 ¶ 1]. Therefore, an ordinarily skilled artisan would be motivated to keep the urea concentration below 2.0 M to prevent denaturation of the T7 RNA polymerase in an in vitro transcription reaction.
Also note that, generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. “[W]here 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.” In reAller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (Claimed process which was performed at a temperature between 40°C and 80°C and an acid concentration between 25% and 70% was held to be prima facie obvious over a reference process which differed from the claims only in that the reference process was performed at a temperature of 100°C and an acid concentration of 10%.); see also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 (“The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages.”); In re Hoeschele, 406 F.2d 1403, 160 USPQ 809 (CCPA 1969). See MPEP 2144.05.
Given the teaching of Pan that RNA base pairing structures can be disrupted at urea concentrations of 0.8-2M; the corresponding motivation taught by Pan to use a urea concentration of about 0.8 M to destabilize misfolded RNA structures (e.g., unwanted intramolecular dsRNA interactions) and to use a urea concentration of about 1 M – 2 M to destabilize both native RNA structures and misfolded RNA structures; and the motivation taught by Griko to keep the urea concentration below 2.0 M to prevent denaturation of the T7 RNA polymerase in an in vitro transcription reaction; it would have been prima facie obvious to an ordinarily skilled artisan at the time of filing the instant application to modify the methods and composition of Xu to include the urea at a concentration of from about 0.1 M to about 1.6 M (e.g., about 0.8 M or about 1.0 to <2.0 M) with a reasonable expectation of success of reducing dsRNA formation.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Dr. KATIE L PENNINGTON whose telephone number is (703)756-4622. The examiner can normally be reached M-Th 8:30 am - 5:30 pm, Friday 8:30 am - 12:30 pm CT.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maria G. Leavitt can be reached on (571) 272-1085. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
DR. KATIE L. PENNINGTON
Examiner
Art Unit 1634
/KATIE L PENNINGTON/Examiner, Art Unit 1634
Dr. A.M.S. Wehbé
/ANNE MARIE S WEHBE/Primary Examiner, Art Unit 1634