Illustration of an mRNA molecule against a dark blue background.
Trending interest in mRNA technology across biopharma will ultimately broaden its reach and likely expand its use into chronic and rare diseases.
iStock, Artur Plawgo

Overcoming mRNA Process Challenges

For mRNA technology to reach its full potential, innovations in manufacturing are needed

Mar 30, 2022
Scott Ripley
Scott Ripley

Scott Ripley is the general manager of the nucleic acid therapeutics business for Cytiva, leading the global commercial go-to-market strategy. Scott has more than 20 years of experience across research and bioprocess businesses, including a recent focus on the mRNA domain.

mRNA is now a widely known technology, but a small group of dedicated scientists and researchers have been studying this technology for decades in the hopes of developing novel cancer therapeutics. Despite many challenges, the researchers persevered, and mRNA has changed the course of the coronavirus pandemic. Although the pandemic played a crucial role in “cracking the code” of mRNA technology, it may take years of research and recent learnings to help scientists discover the next breakthrough. Before that can be accomplished, the industry must make investments that will alleviate the bottlenecks and address the unique needs of mRNA-based product developers.

A closer look at key challenges of mRNA

The mRNA market is still in its infancy and to advance the capabilities of mRNA technology, the biopharma industry needs to establish a development toolbox that is fit for purpose, rather than relying on legacy methods designed for monoclonal antibodies (mAb) or traditional vaccines. Key material needs, development, and manufacturing steps that are currently contributing to bottlenecks in mRNA process development include the following:


An integral raw material for mRNA-based therapies and vaccines is plasmid DNA (pDNA), which acts as a template for the mRNA. pDNA is also used for the production of viral vector-based therapies?another growing area of biopharma. This has led to a significant strain on GMP-quality pDNA supply.

One possible solution lies in alternative cell-free technologies to generate pDNA, such as rolling circle DNA amplification approaches, which seem promising for reducing process timelines and improving product quality.

In Vitro Transcription

After pDNA is manufactured in an E. coli-based fermentation process, it is harvested, linearized, purified, and used as templates for the enzymatic in vitro transcription (IVT) process, yielding the desired mRNA molecule.

IVT is currently a major cost-driving step in mRNA process development due to its complexity and the fact that it requires the careful addition of multiple diverse components in addition to the DNA template (such as enzymes and nucleotides to synthesize the mRNA).

Currently, reactions are batch-based, but alternate reactor designs could be devised to reduce inventory of expensive raw materials, eventually even moving to a continuous reaction scheme. This may be hard to develop, but it could make a big difference in overall productivity.


Compounding raw material variability challenges is the impurity profile of mRNA molecules, which can vary with each project, requiring different purification steps on a case-by-case basis.

mRNA is a very large molecule (30 to 50 nanometers), which is far beyond the size of proteins and comparable to viral vectors. As a result, the mRNA molecules do not interact well with conventional chromatography resins, where you will likely get only surface adsorption.

The varying impurity profiles of mRNA from the IVT step calls for options in purification technologies that would allow process development scientists to mix and match media based on the specific characteristics of the molecule.


Another critical step in mRNA processing is encapsulation using lipid nanoparticles. The specialized lipids used for mRNA provide a delivery system that protects the nucleic acid from degradation as the drug makes its way through a patient’s body.

Prior to encapsulation, the lipids must be dissolved in an organic solvent, which is typically ethanol. Because ethanol is highly flammable, facilities must be properly equipped to ensure safe use of these materials. Companies often do not have these capabilities in house, and a limited number of contract development and manufacturing organizations (CDMOs) have experience in this area.

In addition, lipids currently being used for mRNA were originally developed to deliver small interfering RNA (siRNA) therapies, and there may be better lipid nanoparticle formulations or alternative delivery technologies that improve conditions required for storage stability.


Due to the sensitivity of mRNA, a cold chain is currently necessary to deliver this generation of COVID-19 vaccines across the world, with ultra-cold storage environments required for the majority. However, addressing limitations during process development could help minimize mRNA’s temperature requirements.

There's ample room for improvement, such as selecting appropriate additives and excipients to achieve storage stability at higher temperatures. In addition to alternate lipid and excipient formulations, we may be able to use other formulation technologies, such as lyophilization, to achieve better stability.

Improvements will help expand mRNA beyond COVID-19

Trending interest in mRNA technology across biopharma will ultimately broaden its reach and likely expand its use into chronic and rare diseases. But to successfully execute on its promise, innovations in manufacturing must also take place. Identifying and discussing key bottlenecks and priority areas is the first step in the process. Through effective collaboration, we can overcome these challenges to ensure that the needs of the scientific community are met and that patients ultimately reap the benefits of new and improved treatments.