CHAOTROPIC AGENTS FOR REDUCING FORMATION OF DOUBLE-STRANDED RNA
20230080988 · 2023-03-16
Assignee
Inventors
- Xijun PIAO (South San Francisco, CA, US)
- Wayne CHANG (Milpitas, CA, US)
- Benjamin E. LINDENMUTH (San Rafael, CA, US)
- Xiaowei WANG (Hillsborough, CA, US)
Cpc classification
C12Q2521/107
CHEMISTRY; METALLURGY
C07H1/00
CHEMISTRY; METALLURGY
C12Q2527/125
CHEMISTRY; METALLURGY
C12Q1/6806
CHEMISTRY; METALLURGY
C12Q1/6806
CHEMISTRY; METALLURGY
C12Q2521/107
CHEMISTRY; METALLURGY
C12Q2527/125
CHEMISTRY; METALLURGY
A61P35/00
HUMAN NECESSITIES
International classification
Abstract
The present disclosure provides methods of reducing, minimizing, or inhibiting the formation of double-stranded ribonucleic acid (dsRNA) during the preparation of ribonucleic acid (RNA), such as messenger ribonucleic acid (mRNA), by adding at least one chaotropic agent to a starting reaction mixture. The present disclosure provides methods 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), by adding at least one chaotropic agent to a starting reaction mixture.
Claims
1. A method of reducing, minimizing, or inhibiting the formation of double-stranded ribonucleic acid (dsRNA) during in vitro transcription, comprising adding at least one chaotropic agent to an in vitro transcription reaction mixture.
2. 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 in vitro transcription, comprising adding at least one chaotropic agent to an in vitro transcription reaction mixture.
3. The method of claim 1 or 2, wherein the transcription yields ribonucleic acid (RNA).
4. The method of claim 2 or 3, wherein the RNA is messenger RNA (mRNA).
5. The method of any one of claims 2 to 4, wherein the amount or yield of RNA is not significantly reduced by the addition of the at least one chaotropic agent.
6. The method of any one of claims 1 to 5, wherein the at least one chaotropic agent is selected from the group consisting of urea, formamide, sodium salicylate, ethanol, sodium perchlorate, arginine, n-butanol, thiourea, and 2-propanol.
7. The method of claim 6, wherein the at least one chaotropic agent is urea.
8. The method of claim 7, wherein the urea is at a concentration of from about 0.1M to about 1.6M.
9. The method of claim 6, wherein the at least one chaotropic agent is formamide.
10. The method of claim 9, wherein the formamide is at a concentration of from about 0.1M to about 2.8M.
11. The method of claim 6, wherein the at least one chaotropic agent is sodium perchlorate.
12. The method of claim 11, wherein the sodium perchlorate is at a concentration of from about 0.01M to less than about 0.15M.
13. The method of claim 6, wherein the at least one chaotropic agent is sodium salicylate.
14. The method of claim 13, wherein the sodium salicylate is at a concentration of from about 0.005M to less than about 0.1M.
15. The method of claim 6, wherein the at least one chaotropic agent is arginine.
16. The method of claim 15, wherein the arginine is at a concentration of from about 0.01M to less than about 0.2M.
17. The method of claim 6, wherein the at least one chaotropic agent is ethanol.
18. The method of claim 17, wherein the ethanol is at a concentration of from about 0.4M to less than about 1.6M.
19. The method of claim 6, wherein the at least one chaotropic agent is thiourea.
20. The method of claim 19, wherein the thiourea is at a concentration of from about 0.1M to about 0.2M.
21. The method of claim 6, wherein the at least one chaotropic agent is 2-propanol.
22. The method of claim 21, wherein the 2-propanol is at a concentration of about 0.4M.
23. The method of claim 6, wherein the at least one chaotropic agent is n-butanol.
24. The method of claim 23, wherein the n-butanol is at a concentration of from about 0.16M to about 0.24M.
25. The method of any one of the preceding claims, wherein the reaction mixture is on the order of microliters to the order of liters.
26. The method of any one of the preceding claims, wherein the presence or absence of dsRNA is determined using denaturing gel electrophoresis, native gel electrophoresis, anti-dsRNA antibody, intact mass spectrometry, and/or controls for dsRNA.
27. A composition comprising RNA prepared according to the method of any one of the preceding claims, wherein the composition is substantially free of dsRNA.
28. An in vitro transcription reaction mixture comprising at least one chaotropic agent for use in the preparation of ribonucleic acid (RNA).
29. The reaction mixture of claim 28, wherein the RNA is substantially free of double-stranded ribonucleic acids (dsRNA).
30. The reaction mixture of claim 28 or 29, wherein the RNA is messenger RNA (mRNA).
31. The reaction mixture of any one of claims 28-30, wherein the at least one chaotropic agent is selected from the group consisting of urea, formamide, sodium salicylate, ethanol, sodium perchlorate, arginine, n-butanol, thiourea, and 2-propanol.
32. The reaction mixture of claim 31, wherein the at least one chaotropic agent is urea.
33. The reaction mixture of claim 32, wherein the urea is at a concentration of from about 0.1M to about 1.6M.
34. The reaction mixture of claim 31, wherein the at least one chaotropic agent is formamide.
35. The reaction mixture of claim 34, wherein the formamide is at a concentration of from about 0.1M to about 2.8M.
36. The reaction mixture of claim 31, wherein the at least one chaotropic agent is sodium perchlorate.
37. The reaction mixture of claim 36, wherein the sodium perchlorate is at a concentration of from about 0.01M to less than about 0.15M.
38. The reaction mixture of claim 31, wherein the at least one chaotropic agent is sodium salicylate.
39. The reaction mixture of claim 38, wherein the sodium salicylate is at a concentration of from about 0.005M to less than about 0.1M.
40. The reaction mixture of claim 31, wherein the at least one chaotropic agent is arginine.
41. The reaction mixture of claim 40, wherein the arginine is at a concentration of from about 0.01M to less than about 0.2M.
42. The reaction mixture of claim 31, wherein the at least one chaotropic agent is ethanol.
43. The reaction mixture of claim 42, wherein the ethanol is at a concentration of from about 0.4M to less than about 1.6M.
44. The reaction mixture of claim 31, wherein the at least one chaotropic agent is thiourea.
45. The reaction mixture of claim 44, wherein the thiourea is at a concentration of from about 0.1M to about 0.2M.
46. The reaction mixture of claim 31, wherein the at least one chaotropic agent is 2-propanol.
47. The reaction mixture of claim 46, wherein the 2-propanol is at a concentration of about 0.4M.
48. The reaction mixture of claim 31, wherein the at least one chaotropic agent is n-butanol.
49. The reaction mixture of claim 48, wherein the n-butanol is at a concentration of from about 0.16M to about 0.24M.
50. The composition of claim 27, wherein the presence or absence of dsRNA is determined using denaturing gel electrophoresis, native gel electrophoresis, anti-dsRNA antibody, intact mass spectrometry, and/or controls for dsRNA.
51. The reaction mixture of any one of claims 28 to 49, wherein the presence or absence of dsRNA is determined using denaturing gel electrophoresis, native gel electrophoresis, anti-dsRNA antibody, intact mass spectrometry, and/or controls for dsRNA.
52. A method of reducing, minimizing, or inhibiting the formation of double-stranded ribonucleic acid (dsRNA) during the preparation of ribonucleic acid (RNA), comprising adding at least one chaotropic agent to a starting reaction mixture.
53. 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 a starting reaction mixture.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DETAILED DESCRIPTION
[0061] It is to be understood that this disclosure is not limited to particular methods and experimental conditions described, as such methods and conditions may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the disclosure will be limited only by the appended claims.
[0062] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. As used herein, the term “about,” when used in reference to a particular recited numerical value, means that the value may vary from the recited value by no more than 1%. For example, as used herein, the expression “about 100” includes 99 and 101 and all values in between (e.g., 99.1, 99.2, 99.3, 99.4, etc.). The terms “Figure” and “Fig.” are used interchangeably throughout the specification.
[0063] Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the compositions and methods and uses, the preferred methods and materials are now described. All patents, applications and non-patent publications mentioned in this specification are incorporated herein by reference in their entireties.
Definitions
[0064] The terms “reduce”, “minimize”, and “inhibit”, as used herein, or grammatical equivalents of the same, indicate values that are relative to a baseline measurement. For example, in the context of reducing, minimizing, or inhibiting dsRNA formation during the preparation of mRNA, an in vitro transcription reaction is carried out in the absence and in the presence of the tested chaotropic agent, and dsRNA quantities are subsequently compared for the same amount of mRNA produced from the two in vitro transcription reactions.
[0065] The terms “impurities” and “contaminants”, used interchangeably herein, refer to substances inside a confined amount of liquid, gas, or solid product, which differ from the chemical composition of the target material or compound, e.g., mRNA. Possible contaminants and impurities resulting during the synthesis of mRNA/in vitro transcription include, without limitation, polymerases, dsRNA, DNA, unincorporated NTPs, prematurely aborted RNA sequences, salts, and DTT.
[0066] As used herein, the term “in vitro” refers to events that occur in an artificial environment, e.g., in a test tube or reaction vessel, in cell culture, etc., instead of within a multi-cellular organism. In vitro synthesis, as used herein, refers to the cell-free synthesis of biological macromolecules, e.g., mRNA, in a reaction mix comprising biological extracts and/or defined reagents.
[0067] The phrase “starting reaction mixture”, as used herein, refers to the mixture in which the transcription reaction/preparation of RNA (for example, mRNA) takes place. The phrases “starting reaction mixture” and “in vitro transcription reaction mixture” and “transcription mixture” are used interchangeably herein. In certain embodiments, the chaotropic agent is added to the “starting reaction mixture” at the initiation of the reaction. In certain embodiments, the chaotropic agent is added to the “starting reaction mixture” after the transcription reaction has been initiated/carried out for a period of time.
[0068] The term “chaotropic agent”, as used herein, refers to a molecule that disrupts non-covalent bonds (for example, without limitation, hydrogen bonds, van der Waals forces, and hydrophobic interactions). Chaotropic agents can disrupt the structure of/denature macromolecules such as proteins and nucleic acids.
[0069] As used herein, the term “isolated” refers to a substance that has been (1) separated from at least some of the components with which it is associated when initially produced, whether in nature or in an experiment. The term “isolated” also refers to a substance that has been (2) produced, prepared, and/or manufactured by the hand of man. In certain embodiments, the RNA synthesized using the methods disclosed herein is isolated. In one embodiment, additional steps carried out to purify the RNA product remove enzymes, plasmids, and/or other small molecules to get the final pure “isolated” RNA (for example, isolated mRNA).
[0070] As used herein, the term “pure”, when used to describe a substance, indicates that the substance is substantially free of other components. The percent purity of isolated substances can be calculated and does not include excipients (e.g., buffer, solvent, water, etc.).
[0071] 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.
[0072] As used herein, the term “nucleic acid” refers to any biomolecule/macromolecule that is or can be incorporated into a polynucleotide chain. In some embodiments, a nucleic acid is a compound and/or substance that is or can be incorporated into a polynucleotide chain via a phosphodiester linkage. In some embodiments, “nucleic acid” refers to individual nucleic acid residues (e.g., nucleotides and/or nucleosides). In some embodiments, “nucleic acid” refers to a polynucleotide chain comprising individual nucleic acid residues. As used herein, the term “nucleic acid” may encompass RNA (for example, mRNA, tRNA, rRNA, miRNA) or DNA. As used herein, the term “nucleic acid” includes nucleic acid analogs, for example, analogs having other than a phosphodiester backbone. For chemically synthesized molecules, nucleic acids can comprise nucleoside analogs such as analogs having chemically modified bases or sugars, backbone modifications, etc.
[0073] As used herein, the term “poly A tail” refers to a chain of adenine nucleotides. In certain embodiments, the poly A tail is to be added to an RNA transcript. In certain embodiments, the poly A tail exists at the 3′ end of an RNA transcript. A poly A tail is typically about 5 to about 300 nucleotides in length.
[0074] The term “DNA template”, as used herein, refers to a polynucleotide template for RNA polymerase (for example, for in vitro transcription). The DNA template comprises a sequence for a gene of interest.
[0075] As used herein, the term “subject” refers to a human or any non-human animal (e.g., mouse, rat, rabbit, dog, cat, cattle, swine, sheep, horse, or primate). The terms “subject”, “individual”, and “patient” are used interchangeably herein.
[0076] Additional definitions for the following terms and other terms are set forth throughout the specification.
Messenger Ribonucleic Acid (mRNA)
[0077] The term “messenger RNA (mRNA)”, as used herein, refers to a polynucleotide that encodes at least one polypeptide. The terms “mRNA” and “RNA transcript” are used interchangeably herein. An “RNA transcript” refers to a ribonucleic acid produced by an in vitro transcription reaction using a DNA template and an RNA polymerase. An RNA transcript typically includes the coding sequence for a gene of interest (i.e., a polynucleotide encoding a polypeptide or protein of interest) and, in certain embodiments, a poly A tail. Polypeptides and/or proteins of interest may be selected from, without limitation, biologics, antibodies, vaccines, therapeutic proteins or peptides, cell penetrating peptides, secreted proteins, plasma membrane proteins, cytoplasmic or cytoskeletal proteins, intracellular membrane bound proteins, nuclear proteins, proteins associated with human disease, targeting moieties, and any proteins having diagnostic or therapeutic utility. mRNA as described herein encompasses modified and unmodified RNA. mRNA as described herein may contain one or more coding and non-coding regions.
[0078] mRNA integrity is assessed to determine whether or not the mRNA is intact (vs. degraded). mRNA integrity can be determined using methods well known in the art, for example, RNA agarose gel electrophoresis (Ausubel, et al. 1997 Current Protocols in Molecular Biology), capillary electrophoresis, HPLC, and size exclusion chromatography. RNA integrity (for example, mRNA integrity) is distinct from RNA purity.
[0079] mRNAs may be synthesized according to any of a variety of known methods. For example, mRNAs may be synthesized via in vitro transcription (IVT). In vitro transcription allows for template-directed synthesis of RNA molecules of any sequence from short oligonucleotides to oligonucleotides of several kilobases in μg to kg quantities. Briefly, IVT is typically carried out employing a linear or circular DNA template containing a promoter, a pool of ribonucleotide triphosphates, a buffer system that may include DTT and magnesium ions, and an appropriate RNA polymerase (e.g., T3, T7 or SP6 RNA polymerase), pyrophosphatase, and/or RNAse inhibitor.
[0080] According to certain embodiments, the methods described herein are used to prepare RNA (for example, mRNA) of various lengths. In some embodiments, the synthesized mRNA is of or greater than about 200 base pairs (bp) to about 20 kb, i.e., about 200 bp, 300 bp, 400 bp, 500 bp, 600 bp, 700 bp, 800 bp, 900 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 3 kb, 3.5 kb, 4 kb, 4.5 kb, 5 kb 6 kb, 7 kb, 8 kb, 9 kb, 10 kb, 11 kb, 12 kb, 13 kb, 14 kb, 15 kb, or 20 kb in length. In certain embodiments, the synthesized mRNAs are about 1 kb to about 5 kb in length.
[0081] In certain embodiments, the synthesized mRNA includes 5′ and/or 3′ untranslated region(s).
[0082] In certain embodiments, a 5′ cap and/or a 3′ poly A tail can be added independently to the RNA product (for example, transcript product of in vitro transcription (IVT)). In other embodiments, a 5′ cap can be added during IVT. In still other embodiments, a 3′ poly A tail is encoded into the DNA template (reagent of the transcription reaction). Thus, the methods described herein can, in specific embodiments, include adding a 5′ cap and/or a 3′ poly A tail during IVT.
[0083] The methods described herein are scalable and allow cost-effective, large-scale production of pharmaceutical-grade mRNA. The mRNA yield (e.g., from in vitro transcription) can be quantified, for example, via UV absorbance, RNA blotting or Northern blotting, ribonuclease protection assays, Q-PCR (e.g., QRT-PCR). In terms of the scalability of the RNA (for example, mRNA) prepared according to the methods disclosed herein, it can be prepared on the μg, mg, g, and even kg scale. In certain embodiments of the methods disclosed herein, about 1 to about 7 mg/mL, about 1 to about 6 mg/mL, about 1 to about 5 mg/mL, about 1 to about 4 mg/mL, about 1.5 to about 3.5 mg/mL mRNA is synthesized.
[0084] In certain embodiments, mRNA prepared using a method described herein maintain a high degree of integrity. As used herein, the term “mRNA integrity” generally refers to the quality of the mRNA after transcription. mRNA integrity can be determined using methods well known in the art, for example, by RNA agarose gel electrophoresis (e.g., Ausubel, et al. 1997 Current Protocols in Molecular Biology), capillary electrophoresis, HPLC, size exclusion chromatography. In further embodiments, mRNA synthesized according to the methods of the instant disclosure has a comparable integrity to mRNA synthesized without the use of at least one chaotropic agent. In still further embodiments, mRNA synthesized according to the methods of the instant disclosure has an integrity no more than about 15% less than the integrity of mRNA synthesized without the use of at least one chaotropic agent. In yet further embodiments, mRNA synthesized according to the methods of the instant disclosure has an integrity no more than about 10% less, about 9% less, about 8% less, about 7% less, about 6% less, about 5% less, about 4% less, about 3% less, about 2% less, or about 1% less than the integrity of mRNA synthesized without the use of at least one chaotropic agent.
[0085] Generally speaking, the integrity of mRNA depends on transcription conditions, DNA template length and quality, and even different evaluation methods.
[0086] In certain embodiments, the purity of the mRNA is determined by evaluating the presence or absence of contaminants. For example, the presence or absence of dsRNA can be determined using denaturing gel electrophoresis, native gel electrophoresis, anti-dsRNA antibody, intact mass spectrometry, and/or controls for dsRNA.
Transcription Reaction Mixture
[0087] The in vitro transcription mixture (starting reaction mixture) generally comprises a DNA template, a transcription buffer, nucleotide triphosphates (NTPs) (natural or modified), magnesium ion, and RNA polymerase(s). RNase inhibitor(s) and/or pyrophosphatase can be added to an in vitro transcription mixture in certain embodiments.
[0088] RNA polymerases are generally known in the art. Exemplary RNA polymerases include, without limitation, phage RNA polymerase (for example, T7 RNA polymerase, T3 RNA polymerase, SP6 RNA polymerase) and mutant polymerases (for example, incorporating modified nucleic acids).
[0089] RNA polymerase in the transcription mixture is, in certain embodiments, at a final concentration of about 1000 to about 50,000 U/mL, in further embodiments, at a final concentration of about 1000 to about 12,000 U/mL. DNA template in the transcription mixture is, in certain embodiments, at a final concentration of about 1 to about 200 nM, in further embodiments, at a final concentration of about 5 to about 70 nM. Nucleotide triphosphates (NTPs) in the transcription mixture are, in certain embodiments, at a final concentration of about 0.5 to about 10 mM. Magnesium/magnesium ions and DTT (or some other reducing agent) are often included in transcription buffers. Magnesium in the transcription mixture is, in certain embodiments, at a final concentration of about 12 to about 60 mM. Buffer (for example, HEPES or Tris at a pH of about 7 to about 8.5) in the transcription mixture is, in certain embodiments, at a final concentration of about 10 to about 250 mM. Spermidine (or some other polyamine compound) in the transcription mixture is, in certain embodiments, at a final concentration of about 0.1 to about 5 mM. T7 RNA polymerase in the transcription mixture is, in certain embodiments, at a final concentration of about 1000 to about 10,000 U/mL. RNase inhibitor in the transcription mixture is, in certain embodiments, at a final concentration of about 500 to about 2000 U/mL. Pyrophosphatase in the transcription mixture is, in certain embodiments, at a final concentration of about 0.1 to about 10 U/mL.
[0090] The “starting reaction mixture” is the mixture in which the transcription reaction/preparation of RNA (for example, mRNA) takes place. The starting reaction mixture comprises, in certain embodiments, 50 ng/μL DNA plasmid template, rNTPs (5 mM), CleanCap AG (4 mM), reaction buffer (10× buffer: 400 mM HEPES (pH 7.2-7.5), 100 mM DTT, 20 mM spermidine, 0.02% triton X-100, 165 mM Mg2+), T7 RNA polymerase (about 4000 U/mL), RNase inhibitor (about 1000 U/mL), and inorganic pyrophosphatase (about 2 U/mL). In further embodiments, the starting reaction mixture is prepared in Rnase-free water. In still further embodiments, a chaotropic agent is added to the starting reaction mixture to get a final volume of about 40 μL.
Chaotropic Agents
[0091] Chaotropic agents generally create a denaturing environment for nucleic acids and proteins. Thus, it is contemplated herein to use chaotropic agents to reduce the nucleic acid interactions that cause the formation of dsRNA during in vitro transcription (IVT). Chaotropic agents contemplated for use in the methods, uses, and compositions of the disclosure include, without limitation, urea, formamide, sodium salicylate, ethanol, sodium perchlorate, arginine, n-butanol, thiourea, and 2-propanol. Additional chaotropic agents include, without limitation, guanidinium chloride/guanidine hydrochloride, guanidine thiocyanate, lithium perchlorate, lithium acetate, propylene glycol, phenol, and DMSO.
[0092] In specific embodiments of the invention, chaotropic agents are used at, without limitation, any of the concentrations: formamide (0.4 M, 0.8 M, 1.2 M, 1.6 M, 2.0 M, 2.4 M, or 2.8 M); sodium perchlorate (0.01 M, 0.025 M, 0.050 M, 0.075 M, 0.2 M, 0.8 M, or 1.6 M); sodium salicylate (0.005 M, 0.010 M, 0.020 M, 0.040 M, 0.1 M, 0.2 M, 0.3 M, or 0.4 M), arginine (0.010 M, 0.025 M, 0.050 M, 0.075 M, 0.2 M, 0.4 M, or 0.8 M); ethanol (0.4 M, 0.8 M, 1.2 M, or 1.6 M); thiourea (0.1 M, 0.2 M, 0.4 M, or 0.8 M); 2-propanol (0.4 M, 0.8 M, 1.2 M, or 1.6 M); n-butanol (0.08 M, 0.16 M, 0.24 M, or 0.32 M); guanidine hydrochloride (0.005 M, 0.010 M, 0.020 M, 0.040 M, 0.4 M, 0.8 M, 1.2 M, or 1.6 M); sodium dodecyl sulfate (SDS) (0.001735 M, 0.008675 M, 0.0347 M, or 0.1388 M); dimethyl sulfoxide (DMSO) (0.4 M, 0.8 M, 1.2 M, or 1.6 M); or propylene glycol (0.4 M, 0.8 M, 1.2 M, or 1.6 M).
[0093] The chaotropic agents evaluated herein include:
TABLE-US-00001 TABLE 1 list of chaotropic agents tested Agent Urea Formamide Guanidine HCl Sodium Salicylate DMSO Ethanol SDS Sodium Perchlorate Propylene Glycol Arginine n-butanol Thiourea 2-propanol
Compositions
[0094] The disclosure provides compositions comprising mRNA prepared according to the method of any one of the preceding claims, wherein the composition is substantially free of dsRNA. These compositions can be used for therapeutic purposes. In certain embodiments, these compositions can be further formulated for administration to a subject.
EXAMPLES
[0095] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the methods and compositions of the disclosure, and are not intended to limit the scope of what the inventors regard as their disclosure. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.
General Methods
[0096] Unless otherwise specified, standard in vitro transcription (IVT) was used in the examples. Standard IVT runs were prepared as a stock solution and aliquoted to mix with different chaotropic agents at various concentrations immediately or within a certain time frame. The IVT in the presence of chaotropic agents were usually kept for 2-3 hours at selected temperature, i.e., around 37° C. After DNase I was added to digest DNA plasmid, the mRNA samples were purified by spin column. Yield, dsRNA content, and mRNA integrity were assessed for the impact of the selected chaotropic agents at the tested concentration. dsRNA content was assessed by J2 anti-dsRNA mAb dot blot. HPLC-purified mRNA Drug Substance and dsRNA control sample were used to quantify dsRNA content. The results from different membrane should not be compared directly without referring to dsRNA control. Yield was evaluated by Nanodrop (UV/Vis) following manufacturer's instruction, and mRNA integrity was measured by Fragment Analyzer followed by manufacturer's instruction. 0.7% agarose gel was used to confirm that correct mRNA was produced and evaluate the yield visually.
In Vitro Transcription Recipe
[0097] The standard IVT recipe consisted of: 5 mM of each NTP, 50 ng/μL plasmid, 16.5 mM Mg2+, 40 mM HEPES, 10 mM DTT, 0.002% Triton X-100, RNase inhibitor (1 kU/mL), E. Coli Inorganic Pyrophosphastase (2 U/mL), and T7 RNA polymerase (4 kU/mL). CleanCap AG (4 mM) was used if a co-transcriptional manner was applied. Alternatively, Vaccinia Capping Enzyme (VCE) and 2′-O-methyltransferase were used for post-transcriptional capping. Whether modified NTP or not, whether CleanCap AG or VCE, and plasmid information are listed in each specific example, below.
J2 mAb Dot Blot
[0098] J2 mAb dot blot protocol: the same amount of purified mRNA was applied on each sample dot for a fair comparison, and the estimated dsRNA concentration was calculated based on 10 ng dsRNA control on the same membrane. More specifically, 1000 ng of each mRNA sample and 10 ng/2 ng dsRNA control sample were used for J2 mAb dot blot, unless otherwise specified. Drug Substance (DS) refers to HPLC-purified mRNA drug substance. After blocking the membrane with 3.3% non-fat milk in 1×TBST buffer for 1 h, J2 antibody was applied in 1×TBST buffer to incubate the membrane for 1 h. After washing 6 times, anti-mouse IgG-HRP antibody was applied to the membrane for 1 h. After washing 6 times, chemiluminescence was developed to show the intensity of the dsRNA.
Gel Electrophoresis
[0099] Gel electrophoresis protocol: the same volume (10 μL of 40-fold diluted IVT samples post-DNase I treatment) of mRNA samples prior to spin column purification were used, and 6000-nt RiboRuler RNA ladder was used to show the length of correct mRNA. 10000× diluted GelRed was used in a pre-stained manner to signal the bands. Gel was run at 100V for 1 h at room temperature and imaged by Amersham Imager 680.
[0100] For screening, 20-200 μL IVT was usually used for the convenience of spin column purification. Larger volume as specified was used to further demonstrate the broad application of chaotropic agents to reduce formation of dsRNA during IVT.
Example 1. Screening Chaotropic Agent Urea for dsRNA Reduction
[0101] Urea was tested for the purpose of dsRNA reduction during in vitro transcription (IVT). Glycogen debranching enzyme-encoding messenger RNA (mRNA) was synthesized by in vitro transcription of a linearized DNA plasmid template. 5′ capping structure was included through capping agent in a co-transcriptional manner, and 3′ polyA tail was encoded in the DNA plasmid. A mixture of 50 ng/μL DNA plasmid template, rNTPs (5 mM each, N1-methylpseudouridine (N1mΨ) used instead of UTP), CleanCap AG (4 mM), urea (X M), reaction buffer (10× buffer: 400 mM HEPES (pH 7.2-7.5), 100 mM DTT, 20 mM spermidine, 0.02% triton X-100, 165 mM Mg.sup.2+), T7 RNA polymerase (4000 U/mL), Rnase inhibitor (1000 U/mL), inorganic pyrophosphatase (2 U/mL) was prepared in Rnase-free water to get a final volume of 40 μL.
[0102] Urea concentrations from 0 M to 1.6 M were evaluated. The dot blot results indicated that increasing urea concentration effectively reduced dsRNA during IVT. mRNA integrity was slightly increased or comparable.
[0103] The results of IVT in the presence of different concentrations of urea are shown in Table 2, below. The impact of urea on mRNA yield and dsRNA is shown in
TABLE-US-00002 TABLE 2 Results of IVT in the presence of urea at different concentrations Urea Yield dsRNA dsRNA in Samples concentration (mg/mL) (ppt) Integrity DS (ppt) Earlier 0 M 2.824 6.43 N. D. Unable to quantify samples 0.1 M 2.923 5.25 N. D. dsRNA due to dark 0.2 M 2.930 4.69 N. D. background, but dsRNA 0.4 M 2.825 1.53 N. D. lower than that 0.8 M 2.458 1.44 N. D. of 0.8 M urea 0.4 M 2.830 4.05 N. D. Unable to quantify 0.8 M 2.763 2.40 N. D. dsRNA due to dark 1.2 M 2.525 1.23 N. D. background, but dsRNA 1.6 M N. D. N. D. N. D. higher than that of 1.2M urea 1 0 M 3.633 5.71 75.9% 3.14 2 1.2 M 2.647 2.44 77.1% 3 1.3 M 2.179 3.26 76.5% 4 1.4 M 1.542 2.20 75.8% 5 1.5 M 1.012 2.80 76.2%
Example 2. Screening Chaotropic Agent Formamide for dsRNA Formation Reduction
[0104] Given the benefits seen with the addition of the chaotropic agent urea, in vitro transcription of glycogen debranching enzyme-encoding mRNA was used as an example for the screening of the impact of additional chaotropic agents on the dsRNA reduction. A mixture of 50 ng/μL linearized DNA plasmid template, rNTPs (5 mM each, N1-methylpseduouridine used instead of UTP), CleanCap AG (4 mM), formamide (X M), reaction buffer (10× buffer: 400 mM HEPES (pH 7.2-7.5), 100 mM DTT, 20 mM spermidine, 0.02% triton X-100, 165 mM Mg2+), T7 RNA polymerase (4000 U/mL), Rnase inhibitor (1000 U/mL), inorganic pyrophosphatase (2 U/mL) was prepared in RNase-free water to get a final volume of 40 μL. The transcription mixture was incubated at about 37° C. for 2 h and 20 minutes, followed by DNase I treatment for 15 minutes. Synthesized mRNA was purified by silica membrane-based spin columns.
[0105] Formamide was tested for the purpose of dsRNA reduction during IVT. Formamide concentrations from 0 M to 2.8 M were evaluated. Formamide also effectively reduced dsRNA during IVT. mRNA integrity slightly increased or remained comparable.
[0106] The results of IVT in the presence of different concentrations of formamide are shown in Table 3, below. The impact of formamide on mRNA yield and dsRNA is shown in
TABLE-US-00003 TABLE 3 Results of IVT in the presence of formamide Formamide Yield dsRNA dsRNA in samples Concentration (mg/mL) (ppt) Integrity DS (ppt) 1 0 M 3.762 5.95 75.2% 2.04 2 0.4 M 4.037 5.12 74.0% 3 0.8 M 3.519 3.57 74.8% 4 1.2 M 3.860 2.66 75.7% 5 1.6 M 3.457 2.38 77.4% 6 0 M 3.633 5.71 75.9% 3.82 7 1.6 M 3.435 3.63 75.6% 8 2.0 M 2.427 4.06 76.4% 9 2.4 M N. D. N. D. N. D. 10 2.8 M N. D. N. D. N. D.
Example 3. Screening Chaotropic Agent Sodium Perchlorate for dsRNA Formation Reduction
[0107] Because of perchlorate's known chaotropic action, sodium perchlorate was tested for the purpose of dsRNA reduction during IVT. Sodium perchlorate concentrations from 0 M to 1.6 M were evaluated. Sodium perchlorate at low concentration effectively reduced dsRNA during IVT. mRNA integrity slightly increased.
[0108] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of sodium perchlorate are shown in Table 4, below. The impact of sodium perchlorate on mRNA yield and dsRNA is shown in
TABLE-US-00004 TABLE 4 Results of IVT in the presence of sodium perchlorate NaClO.sub.4 Yield dsRNA dsRNA in Sample Concentration (mg/mL) (ppt) Integrity DS (ppt) 1 0 M 3.579 4.25 74.6% 0.91 2 0.05 M 1.145 2.00 78.5% 3 0.2 M N. D. N. D. N. D. 4 0.8 M N. D. N. D. N. D. 5 1.6 M N. D. N. D. N. D. 6 0 M 3.633 5.71 75.9% 2.81 7 10 mM 4.204 3.72 77.4% 8 25 mM 4.202 3.83 76.3% 9 50 mM 3.082 3.34 77.5% 10 75 mM N. D. N. D. N. D.
Example 4. Screening Chaotropic Agent Thiourea for dsRNA Formation Reduction
[0109] Thiourea was tested for the purpose of dsRNA reduction during IVT. Thiourea concentrations from 0 M to 0.8 M were evaluated. Thiourea at low concentration moderately reduced dsRNA during IVT. At high concentrations, thiourea shut down IVT.
[0110] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of thiourea are shown in Table 5, below. The impact of thiourea on mRNA yield and dsRNA is shown in
TABLE-US-00005 TABLE 5 Results of IVT in the presence of thiourea dsRNA Thiourea Yield (ng/ug of dsRNA Sample concentration (mg/mL) mRNA) purity in DS 1 0 M 3.443 4.95 71.6% 3.75 2 0.1 M 3.829 4.43 74.3% 3 0.2 M 3.351 3.73 75.8% 4 0.4 M N. D. N. D. N. D. 5 0.8 M N. D. N. D. N. D.
Example 5. Screening Chaotropic Agent Sodium Salicylate for dsRNA Formation Reduction
[0111] Sodium salicylate was tested for the purpose of dsRNA reduction during IVT. Sodium salicylate concentrations from 0 M to 0.4 M were evaluated. Sodium salicylate at low concentration moderately reduced dsRNA during IVT. At high concentrations, IVT was aborted.
[0112] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of sodium salicylate are shown in Table 6, below. The impact of sodium salicylate on mRNA yield and dsRNA is shown in
TABLE-US-00006 TABLE 6 Results of IVT in the presence of sodium salicylate Sodium yield dsRNA dsRNA in samples salicylate Conc. (mg/mL) (ppt) Integrity DS (ppt) 1 0 M 3.762 5.95 75.2% 2.04 2 0.1 M N. D. N. D. N. D. 3 0.2 M N. D. N. D. N. D. 4 0.3 M N. D. N. D. N. D. 5 0.4 M N. D. N. D. N. D. 6 0 M 3.633 5.71 75.9% 3.31 7 5 mM 3.933 5.33 77.0% 8 10 mM 4.149 3.98 77.6% 9 20 mM 4.017 4.16 76.8% 10 40 mM 1.732 4.08 78.0%
Example 6. Screening Chaotropic Agent Arginine for dsRNA Formation Reduction
[0113] Arginine was tested for the purpose of dsRNA reduction during IVT. Arginine concentrations from 0 M to 0.8 M were evaluated. Arginine at low concentration moderately reduced dsRNA during IVT. At high concentrations, IVT was shut down.
[0114] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of arginine are shown in Table 7, below. The impact of arginine on mRNA yield and dsRNA is shown in
TABLE-US-00007 TABLE 7 Results of IVT in the presence of Arginine yield dsRNA dsRNA in samples Arginine Conc. (mg/mL) (ppt) Integrity DS (ppt) 1 Blank 3.579 4.34 74.6% 0.88 2 0.05 M arginine 1.391 1.62 78.0% 3 0.2 M arginine N. D. N. D. N. D. 4 0.4 M arginine N. D. N. D. N. D. 5 0.8 M arginine N. D. N. D. N. D. 6 Blank 3.633 5.71 75.9% 3.12 7 10 mM arginine 3.957 5.84 75.2% 8 25 mM arginine 3.387 5.19 74.1% 9 50 mM arginine 3.212 4.11 75.0% 10 75 mM arginine 1.740 4.15 78.3%
Example 7. Screening Chaotropic Agent Ethanol for dsRNA Formation Reduction
[0115] Ethanol was tested for the purpose of dsRNA reduction during IVT. Ethanol concentrations from 0 M to 1.6 M were evaluated. Ethanol at high concentration moderately reduced dsRNA during IVT.
[0116] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of arginine are shown in Table 8, below. The impact of arginine on mRNA yield and dsRNA is shown in
TABLE-US-00008 TABLE 8 Results of IVT in the presence of ethanol dsRNA Ethanol Yield dsRNA in DS Sample Concentration (mg/mL) (ppt) Integrity (ppt) 1 0 M 3.579 6.00 74.6% 0.81 2 0.4 M 2.256 5.70 77.6% 3 0.8 M 2.052 4.21 74.2% 4 1.2 M 1.282 3.59 78.3% 5 1.6 M N. D. N. D. N. D.
Example 8. Screening Chaotropic Agent 2-Propanol for dsRNA Formation Reduction
[0117] 2-propanol was tested for the purpose of dsRNA reduction during IVT. 2-propanol concentration from 0 M to 1.6 M was evaluated. 2-propanol at low concentration moderately reduced dsRNA during IVT. At high concentrations, 2-propanol aborted IVT.
[0118] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of 2-propanol are shown in Table 9, below. The impact of 2-propanol on mRNA yield and dsRNA is shown in
TABLE-US-00009 TABLE 9 Results of IVT in the presence of 2-propanol dsRNA 2-propanol Yield dsRNA in DS Sample concentration (mg/mL) (ppt) Integrity (ppt) 1 0 M 3.443 4.54 71.6% 3.18 2 0.4 M 3.537 4.01 67.4% 3 0.8 M N. D. N. D. N. D. 4 1.2 M N. D. N. D. N. D. 5 1.6 M N. D. N. D. N. D.
Example 9. Screening Chaotropic Agent n-Butanol for dsRNA Formation Reduction
[0119] n-butanol was tested for the purpose of dsRNA reduction during IVT. n-butanol concentrations from 0 M to 0.32 M were evaluated. n-butanol at low concentration moderately reduced dsRNA during IVT.
[0120] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of n-butanol are shown in Table 10, below. The impact of n-butanol on mRNA yield and dsRNA is shown in
TABLE-US-00010 TABLE 10 Results of IVT in the presence of n-butanol dsRNA n-butanol Yield dsRNA in DS Sample concentration (mg/mL) (ppt) Integrity (ppt) 1 0 M 3.443 4.41 71.6% 2.2 2 0.08 M 3.821 4.82 72.4% 3 0.16 M 3.230 4.05 73.9% 4 0.24 M 1.644 3.43 75.4% 5 0.32 M N. D. N. D. N. D.
Example 10. Screening Chaotropic Agent Guanidine Hydrochloride for dsRNA Formation Reduction
[0121] Guanidine hydrochloride was tested for the purpose of dsRNA reduction during IVT. Guanidine hydrochloride concentrations from 0 M to 1.6 M were evaluated. Guanidine hydrochloride at low concentration did not reduce dsRNA during IVT. At high concentrations, Guanidine hydrochloride shut down IVT.
[0122] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of guanidine hydrochloride are shown in Table 11, below. The impact of guanidine hydrochloride on mRNA yield and dsRNA is shown in
TABLE-US-00011 TABLE 11 Results of IVT in the presence of guanidine hydrochloride dsRNA Yield dsRNA in DS Samples Guanidine Conc (mg/mL) (ppt) Integrity (ppt) 1 0 M 3.762 5.95 75.2% 2.04 2 0.4 M N. D. N. D. N. D. 3 0.8 M N. D. N. D. N. D. 4 1.2 M N. D. N. D. N. D. 5 1.6 M N. D. N. D. N. D. 6 0 M 3.633 4.92 75.9% 3.03 7 5 mM 3.945 5.75 72.7% 8 10 mM 3.981 5.62 75.3% 9 20 mM 4.085 5.08 76.7% 10 40 mM 3.712 5.22 76.6%
Example 11. Screening Chaotropic Agent SDS for dsRNA Formation Reduction
[0123] SDS was tested for the purpose of dsRNA reduction during IVT. SDS concentrations from 0.05% (1.735 mM) to 4% (138.8 mM) were evaluated. SDS shut down IVT completely at all tested concentrations.
[0124] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of SDS are shown in Table 12, below. The impact of SDS on mRNA yield and dsRNA is shown in
TABLE-US-00012 TABLE 12 Results of IVT in the presence of SDS Yield dsRNA Sample SDS concentration (mg/mL) (ppt) Integrity 1 0 M (0%) 3.579 6.00 74.6% 2 0.001735 M (0.05%) N. D. N. D. N. D. 3 0.008675 M (0.25%) N. D. N. D. N. D. 4 0.0347 M (1%) N. D. N. D. N. D. 5 0.1388 M (4%) N. D. N. D. N. D.
Example 12. Screening Chaotropic Agent DMSO for dsRNA Formation Reduction
[0125] DMSO was tested for the purpose of dsRNA reduction during IVT. DMSO concentrations from 0 M to 1.6 M were evaluated. DMSO did not reduce dsRNA during IVT. Instead, an increase of dsRNA was detected.
[0126] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of DMSO are shown in Table 13, below. The impact of DMSO on mRNA yield and dsRNA is shown in
TABLE-US-00013 TABLE 13 Results of IVT in the presence of DMSO dsRNA DMSO yield dsRNA in DS samples concentration (mg/mL) (ppt) Integrity (ppt) 1 0 M 3.579 3.00 74.6% 0.79 2 0.4 M 3.605 3.27 75.9% 3 0.8 M 3.450 3.30 76.2% 4 1.2 M 2.915 3.85 76.6% 5 1.6 M 1.913 5.28 74.7%
Example 13. Screening Chaotropic Agent Propylene Glycol for dsRNA Formation Reduction
[0127] Propylene glycol was tested for the purpose of dsRNA reduction during IVT. Propylene glycol concentrations from 0 M to 1.6 M were evaluated. Propylene glycol did not reduce dsRNA during IVT. Instead, an increase of dsRNA was detected.
[0128] The same IVT composition used in Example 1, except chaotropic agent, was applied in the instant example. The results of IVT in the presence of different concentrations of propylene glycol are shown in Table 14, below. The impact of propylene glycol on mRNA yield and dsRNA is shown in
TABLE-US-00014 TABLE 14 Results of IVT in the presence of propylene glycol dsRNA Propylene glycol Yield dsRNA in DS Sample concentration (mg/mL) (ppt) Integrity (ppt) 1 0 M 3.579 2.21 74.6% 0.79 2 0.4 M 3.133 3.16 74.9% 3 0.8 M 2.258 4.41 77.6% 4 1.2 M 2.409 2.70 77.1% 5 1.6 M 1.588 3.89 76.8%
[0129] Among the chaotropic agents tested, urea (at a concentration of 0.1 M to 1.5 M) resulted in a decrease in dsRNA formation; formamide (at a concentration of 0.4 M to 2.8 M) resulted in a decrease in dsRNA formation; sodium perchlorate (at a concentration of 0.01 M to 0.075 M) resulted in a decrease in dsRNA formation; sodium salicylate (at a concentration of 0.005 M to 0.04 M) resulted in a decrease in dsRNA formation; arginine (at a concentration of 0.01 M to 0.075 M) resulted in a decrease in dsRNA formation; and ethanol (at a concentration of 0.4 M to 1.2 M) resulted in a decrease in dsRNA formation. Thiourea (at concentrations of 0.1 M and 0.2 M), 2-propanol (at a concentration of 0.4 M), and n-butanol (at concentrations of 0.16 M and 0.24 M) each resulted in a decrease in dsRNA formation. Other concentrations listed in Table 1, above, did not provide significant reduction in dsRNA formation or shut down the in vitro transcription. Meanwhile, guanidine hydrochloride, DMSO, propylene glycol, and SDS did not significantly reduce the formation of dsRNA, or shut down the in vitro transcription, at the concentrations listed.
Example 14. Temperature Effect on Urea in Reducing Formation of dsRNA
[0130] The effect of temperature on urea's reduction of dsRNA formation was investigated at concentrations of: 0 M (control), 0.4 M, 0.8 M, 1.2 M, and 1.6 M. For these five concentrations, the transcription mixture was incubated at about 34° C., 37° C., and 40° C., each for 2 hrs, followed by DNase I treatment for 20 minutes.
[0131] IVT runs with different urea concentrations were performed at 34, 37, and 40° C. The IVT reaction at higher temperature produced less dsRNA, but had lower tolerance for higher urea concentration. For example, 1.6 M urea at 40° C. completely aborted the IVT, whereas a slight product could be seen at 34 and 37° C. On the other hand, higher temperature also accelerated IVT dramatically. More specifically, at 0.8 M urea, IVT performed at 37° C. generated more mRNA than that at 34° C.
[0132] The same IVT composition used in Example 1, except chaotropic agent at different concentrations, was applied in the instant example. The results of IVT in the presence of different concentrations of urea at different temperatures are shown in Table 15, below. The impact of temperature and urea on mRNA yield and dsRNA is shown in
TABLE-US-00015 TABLE 15 Temperature and urea sample information table Lane 1-5 0, 0.4, 0.8, 1.2, 1.6 M urea 34° C., 2 h Lane 6-10 0, 0.4, 0.8, 1.2, 1.6 M urea 37° C., 2 h Lane 11-15 0, 0.4, 0.8, 1.2, 1.6 M urea 40° C., 2 h
Example 15. Chaotropic Agent dsRNA Formation Reduction Works on Both Modified NTP and Regular NTP
[0133] N1mΨ was used in the study above. To ascertain whether or not the chaotropic agents' relevant activity is affected by NTP chemistry, N1mΨ was compared with regular UTP. dsRNA was significantly reduced by urea during IVT regardless of whether the NTP was modified or regular.
[0134] The results of IVT for modified vs. regular NTP in the presence of urea and formamide are shown in Table 16, below. The impact of urea and formamide on IVT involving modified vs. regular NTP is shown in
TABLE-US-00016 TABLE 16 Modified NTP and regular NTP sample information table dsRNA Yield dsRNA in DS Sample Sample information (mg/mL) (ppt) Integrity (ppt) 1 N1mΨ used, no chaotropic agents 3.198 5.08 79.24% 1.90 2 N1mΨ used, 1 M urea 2.983 2.47 78.54% 3 N1mΨ used, 1.6 M formamide 2.937 2.21 75.48% 4 Regular UTP used, no chaotropic agents 4.477 13.30 75.38% 5 Regular UTP used, 1 M urea 4.247 4.29 75.43% 6 Regular UTP used, 1.6 M formamide 4.202 4.68 75.08%
Example 16. Urea to Reduce Formation of dsRNA in a Scale-Up IVT
[0135] To demonstrate the broad application of chaotropic agents for dsRNA reduction during IVT, the IVT process was scaled up to 8 mL and 600 mL, respectively. In each case, the same IVT composition and parameters were used to evaluate urea's dsRNA formation reduction activity at larger scales. IVT was done in water bath.
[0136] The results of IVT in the presence of urea and scaled up are shown in Table 17, below. The impact of urea on scaled-up IVT is shown in
TABLE-US-00017 TABLE 17 Scale-up IVT results in the presence of urea at different concentrations mRNA dsRNA IVT Volume Urea Conc. yield dsRNA in DS (mL) (M) (mg/mL) (ppt) Integrity (ppt) 8 1.0 3.56 0.60 85.4% 0.70 600 1.0 3.51 1.59 83.57% 1.08
Example 17. Urea to Reduce Formation of dsRNA in a Scale-Up IVT in a Bioreactor
[0137] To further demonstrate the application of chaotropic agents to reduce the formation of dsRNA independent of IVT scales, 600 mL IVT was performed in a more scalable wave reactor with a 2 L disposable sterile wave bag. Natural UTP and 1M urea were used, but no capping reagent was included in IVT. This also indicated that chaotropic agent to reduce formation of dsRNA during IVT was independent of capping method (co-transcriptional capping agent, or enzymatic capping, or no capping). The produced 5′-ppp mRNA was suitable for enzymatic capping (though not done in the instant example). Control sample (300 mL IVT with no urea) was done in the wave reactor too.
[0138] The results of IVT in the presence of urea and scaled up in a bioreactor are shown in Table 18, below. The impact of urea on scaled-up IVT in a bioreactor is shown in
TABLE-US-00018 TABLE 18 Bioreactor scale-up IVT results in the presence of urea at different concentrations IVT Urea mRNA mRNA integrity dsRNA Volume Conc. yield dsRNA prior to in DS (mL) (M) (mg/mL) (ppt) purification (ppt) 300 0 4.13 26.9 82.1% Unable to 600 1.0 3.86 3.45 78.1% determine
Example 18. Delayed Addition of Chaotropic Agent to Control the Levels of dsRNA
[0139] In certain embodiments of the disclosure, chaotropic agents can be added to the IVT reaction mixture at a later time. Thus potentially controlling the level of dsRNA could be beneficial, for example, when a certain level of immunogenicity is desired, for example, for mRNA vaccines. In the instant study, urea solution was added into a standard IVT mixture at an interval of 30 minutes, the amount of dsRNA was increased when urea was added at a later time point.
[0140] The same IVT composition as used in Example 1, with 1 M urea, was applied in this example. All transcriptions were kept at 37° C. for a total of 180 minutes, and all results were measured at the end of transcription. The results of IVT in the presence of urea added at different time points are shown in Table 19, below. The impact of adding urea at different time points on dsRNA is shown in
TABLE-US-00019 TABLE 19 Addition of urea into IVT mixture at different time points dsRNA Yield dsRNA in DS Samples addition time (mg/mL) (ppt) integrity (ppt) 1 0 min, urea added 2.77 1.70 70.7% 1.00 2 30 min, urea added 3.09 1.40 71.9% 3 60 min, urea added 3.47 2.19 72.3% 4 90 min, urea added 3.60 3.38 70.1% 5 120 min, urea added 3.93 4.79 71.5% 6 120 min, water added 4.30 5.36 71.8%
Example 19. Using More than One Chaotropic Agent at the Same Time to Reduce Formation of dsRNA
[0141] In some embodiments of the disclosure, more than one chaotropic agent is used to reduce dsRNA formation during IVT. In the instant study, a combination of two chaotropic agents was tested. The results indicated that dsRNA was effectively reduced during IVT.
[0142] The same IVT composition used in Example 1, except chaotropic agent(s) and N1mΨ, was applied in the instant example to study the use of more than one chaotropic agent to reduce formation of dsRNA. Natural UTP was used in this example instead of N1mΨ. The results of IVT in the presence of more than one chaotropic agent are shown in Table 20, below. The impact of using more than one chaotropic agent on dsRNA is shown in
TABLE-US-00020 TABLE 20 Use of more than one chaotropic agent to reduce formation of dsRNA dsRNA Yield dsRNA in DS Samples Chaotropic agents (mg/mL) (ppt) Integrity (ppt) 1 None 4.11 15.97 69.1% 0.33 2 1M urea 2.91 2.92 69.5% 3 1.6 M formamide 3.04 2.22 70.4% 4 50 mM NaClO.sub.4 4.22 4.41 72.1% 5 0.5 M urea 4.23 9.84 72.8% 6 0.8 M formamide 3.97 9.95 73.2% 7 25 mM NaClO.sub.4 4.99 6.25 71.2% 8 0.5 M urea + 0.8 M formamide 3.40 3.02 71.7% 9 0.5 M urea + 25 mM NaClO.sub.4 4.56 3.47 71.0% 10 0.8 M formamide + 25 mM 4.87 2.31 70.8% NaClO.sub.4
Example 20. Formamide to Reduce Formation of dsRNA in IVT with a Template Encoding ˜1300-Nt RNA
[0143] To demonstrate the broad application of chaotropic agents in reducing formation of dsRNA during IVT, the DNA template was extended to a different DNA template that encodes an about 1300-nt EGFP-related RNA. Regular NTPs were used for IVT, and 5′ cap1 was obtained through post-transcriptional enzymatic capping. 1.6 M formamide was used to reduce dsRNA. After spin column purification, the mRNA was subjected to vaccinia capping system to obtain Cap1 structure.
[0144] Vaccinia capping enzyme and 2′-O-methyltransferase were used to obtain Cap1 structure for the mRNA in the presence of 0.5 mM GTP and 0.2 mM SAM. mRNA was heated at 65° C. for 5 minutes and cooled on ice for 5 minutes followed by adding buffer, GTP, SAM, and the two enzymes. The reaction was incubated at 37° C. for 60 minutes, and the mRNA was purified by spin column. The results of IVT with a plasmid encoding a 1300 nt RNA in the presence of chaotropic agent formamide with respect to dsRNA formation and mRNA yield are shown in
[0145] Thus, numerous chaotropic agents were screened for their reduction of formation of dsRNA during IVT. Select chaotropic agents including urea and formamide additionally showed efficacy in scale-up IVT, IVT with regular NTP vs. modified NTP, IVT with different DNA templates, and IVT at different temperatures.
[0146] While chaotropic agents reduce formation of dsRNA during IVT by partially breaking down unwanted intermolecular or intramolecular nucleic acid interactions believed to be the causes of dsRNA formation during IVT, they can also denature enzymes and shut down IVT partially or completely, resulting in low or no mRNA yield. In certain embodiments, non-charged chaotropic agents such as urea and formamide are employed to reduce formation of dsRNA during IVT.
[0147] It is demonstrated herein that adding chaotropic agents into the IVT reaction is a simple and effective way to reduce the formation of dsRNA. Furthermore, the claimed methods and compositions may replace other existing dsRNA-removal technologies, such as RP-HPLC and CHT chromatography processes, and achieve higher mRNA integrity, resulting in potent and low immuno-stimulatory mRNA. Of note, the claimed methods and compositions greatly simplify the mRNA production process by reducing or entirely removing its reliance on purification methods, e.g., chromatography steps, for dsRNA reduction, in turn, eliminating scalability concerns. Therefore, the claimed methods and compositions significantly drive the production of mRNA therapeutics.
[0148] The present disclosure is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the disclosure in addition to those described herein will become apparent to those skilled in the art from the foregoing description and the accompanying figures. Such modifications are intended to fall within the scope of the appended claims. The above specification, examples and data provide a complete description of the composition, manufacture of the composition and use of the composition of the invention. Since many embodiments of the invention can be made without departing from the spirit and scope of the invention, the invention resides in the claims hereinafter appended.