mRNA Synthesis for the Development of Vaccines and Therapeutics

Section Overview

• How mRNA Vaccines Induce Immunity
• Advantages of mRNA as a Vaccine Modality
• Plasmid DNA (pDNA) Preparation for mRNA Synthesis
• mRNA In Vitro Transcription and Capping
• mRNA Synthesis Reagents for In Vitro Transcription (IVT)
• Purification and Analysis of mRNA
• Removal of dsRNA During mRNA Synthesis

The potential for synthetic mRNA to recapitulate the function of mature mRNA has elevated its potential for a spectrum of biopharmaceutical applications. These therapeutics include in vivo delivery of mRNA for protein replacement, stem cell induction, or cancer immunotherapies. Recent significant pharmaceutical uses include novel approaches for vaccines against infectious disease, most notably the mRNA-based vaccines that protect against SARS-CoV-2.

This technical article focuses on pDNA and mRNA preparation for lab-scale applications. For a complete overview of our products and solutions suitable for GMP manufacturing, visit our mRNA Manufacturing and Formulation page.

How mRNA Vaccines Induce Immunity

Messenger RNA (mRNA)-based vaccines are derived from the central dogma that mRNA encodes for proteins. This vaccine modality is straightforward, inducing an immunological response by delivering a genetic element that codes for all (or part) of an antigenic protein in a “translation-ready” molecule. This process is facilitated when the mRNA encoding the target antigen is taken up by antigen-presenting cells and translated into the target protein. This in turn induces an immune response, closely mimicking the natural process by which viruses infect cells.

Advantages of mRNA as a Vaccine Modality

Generally, mRNA vaccines are produced by in vitro synthesis through an enzymatic process. The development and manufacture of mRNA vaccines are relatively simple compared to more traditional modalities and can be accomplished in a shorter time period. These attributes make them suitable for accelerated development and scaleup, and are critical for emergent public health scenarios. Future innovations in mRNA vaccine design, formulation, and enhanced thermostability (beyond cold-chain distribution) would further reduce production costs and enhance global accessibility of mRNA as a modality.

Plasmid DNA (pDNA) Preparation for mRNA Synthesis

For mRNA-based vaccine design, in vitro transcription of a plasmid DNA (pDNA) template is typically used to produce functional synthetic mRNA. The plasmid vector may contain the following elements: an upstream promoter exclusively recognized by T7, SP6, or T3 RNA polymerase, all of which are derived from bacteriophages; 5' UTR; cDNA; 3' UTR; a downstream poly A-tail; and a unique cleavage site downstream of the poly A-tail. Preparation of the pDNA template often involves PCR amplification and gel purification of your target DNA, followed by restriction digestion (of both insert and plasmid backbone) and ligation using enzymes such as T4 DNA Ligase. Selection of proper transformation reagents (BL21 competent cells, SOC broth, and LB-agar plates with selection antibiotics) and purification techniques (GenElute™ Plasmid Miniprep Kit) are all considerations as researchers optimize conditions for template generation.

Figure 1. Plasmid generation for in vitro transcription (IVT). Following gene synthesis, cloning of the target DNA uses a plasmid vector (pDNA). The pDNA is expanded in bacterial culture, then purified using nucleic acid purification methods, such as silica-based membranes in spin columns.

mRNA IN VITRO TRANSCRIPTION AND CAPPING

Bacteriophage RNA polymerase is normally used to transcribe linearized plasmid DNA. The pDNA is first linearized with the selected unique restriction site enzyme. After digestion, the linearized pDNA may be purified using methods such as the phenol-chloroform protocol or the GenElute™ PCR Clean-Up Kit. For large scale purification, tangential flow filtration (TFF) is often advisable as it can be easily scaled up. Following linearization, in vitro transcription and capping is performed in a mixed solution of recombinant RNA polymerase (T7, SP6 or T3) and nucleoside triphosphates (ATP, CTP, GTP, UTP), plus a cap analog such as CleanCap^® Reagent or ARCA (Anti-Reverse Cap Analog). A modified nucleoside such as N1-Methylpseudouridine-5'-Triphosphate (N1-Methylpseudo-UTP, 1-Methylpseudo-UTP) can be used instead of GTP to suppress the innate immune system and is used in the current mRNA vaccines. The efficiency of capping mRNA with ARCA is ~70-80% on average because it competes with GTP, while the yield of mRNA is reduced by about one-fourth compared to standard mRNA synthesis. In comparison, the CleanCap^® reagent has been shown to work at 94% capping efficiency without affecting the yield of mRNA production. Capping may also be achieved post-transcriptionally, without a cap analog, by employing the vaccinia virus-encoded capping complex (Vaccinia capping enzyme, 2'-O-Methyltransferase, GTP, and S-adenosyl methionine (SAM)). Capping efficiency will depend on the secondary structure of the mRNA of interest. Finally, the length of the poly A tail of the template pDNA (up to 150 bases) can be extended by use of poly A enzyme when necessary.

Plasmid Preparation Reagents

Product No.	Product Name	Description
PLN70 PLN350	GenElute™ Plasmid Miniprep Kit	Simple, rapid, and cost-effective isolation of plasmid DNA from E. coli using silica-binding spin column technology. 1-5 mL of culture processed in less than 30 minutes for up to 15 μg purified plasmid. For Discovery work.
NA0150 NA0160	GenElute™ HP Plasmid Miniprep Kit	Simple, rapid, and cost-effective isolation of plasmid DNA from E. coli using silica-binding with convenience of spin or vacuum format. 1-5 mL of culture processed in approximately 30 minutes for up to 25 μg purified plasmid. For Discovery work.
PLD35	GenElute™ Plasmid Midiprep Kit	Simple, rapid, and cost-effective isolation of plasmid DNA from E. coli using silica-binding spin column technology. 20-40 mL of culture processed in approximately 45 minutes. For Discovery work.
NA0200	GenElute™ HP Plasmid Midiprep Kit	Simple, rapid, and cost-effective isolation of plasmid DNA from E. coli using silica-binding with convenience of spin or vacuum format. 50 mL of culture processed in approximately 30 minutes for up to 350 μg purified plasmid. For Discovery work.
PLED35	GenElute™ Endotoxin-free Plasmid Midiprep Kit	Simple, rapid, and cost-effective isolation of plasmid DNA from E. coli using silica-binding spin column technology with ≤0.1 EU/μg DNA for high efficiency transfection. 20-40 mL of culture processed in approximately 45 minutes for up to 250 μg of purified plasmid. For cell work.
PLEX15	GenElute™ Endotoxin-free Plasmid Maxiprep Kit	Simple, rapid, and cost-effective isolation of plasmid DNA from E. coli using silica-binding spin column technology with ≤0.1 EU/μg DNA for high efficiency transfection. 20-250 mL of culture processed for up to 1.2 mg of purified plasmid. For cell work.
NA0400 NA0410	GenElute™ HP Endotoxin-free Plasmid Maxiprep Kit	Simple and rapid isolation of plasmid DNA from E. coli using silica-binding vacuum format technology with ≤0.1 EU/μg DNA for high efficiency transfection. 150 mL of culture processed for up to 1.2 mg of purified plasmid in about 40 minutes.  For cell work.
NA0600	GenElute™ HP Endotoxin-free Plasmid Megaprep Kit	Simple, rapid, and cost effective isolation of plasmid DNA from E. coli using silica-binding vacuum technology. 200-1000 mL of culture processed in less than 1.5 hours for up to 5 mg of purified plasmid. For cell work.

Figure 2. mRNA synthesis is completed by linearization of pDNA, in vitro transcription (IVT) of mRNA using cell-free methods, and capping of the mRNA using cap analog or virus-encoded capping complex.

mRNA Synthesis Reagents for In Vitro Transcription (IVT)

Transcription Buffers

PURIFICATION AND ANALYSIS OF mRNA

The first step in mRNA purification is to remove the linearized pDNA template using deoxyribonuclease, or DNase. The mRNA is then precipitated with lithium chloride (LiCl), and washed with 75% ethanol. The resulting mRNA pellet can be resuspended with water or resuspension buffer. However, this precipitation method should be avoided during scale-up given the overall difficulty and use of hazardous solvents, which should be avoided under GMP production. As a standardized solution, the GenElute™ mRNA Miniprep Kit is recommended for smaller scale purification.

mRNA Purification Reagents

REMOVAL OF dsRNA DURING mRNA SYNTHESIS

Double-stranded RNA (or dsRNA) is a transcriptional by-product and a major concomitant of mRNA synthesis. The dsRNA can stimulate innate immune responses that counteract and reduce the translation efficiency of delivered mRNA. When mRNA is synthesized for vaccine development, dsRNA should therefore be removed. Cellulose-based purification using cellulose fibers can be applied for the removal of dsRNA at various scales via chromatography.

Reagents for Post Transcription Cleanup and Purification of mRNA

Reagents for Analysis of Synthetic mRNA