Aldevron Breakthrough Blog

In Purification, One Size Does NOT Fit All

Downstream challenges in mRNA production

In my previous post, I brought up important questions that should be asked when beginning to design a scalable manufacturing process to meet specific use requirements. In this post, some of the difficulties encountered in process development are reviewed.

The downstream process design will be guided by the product’s intended use and release specifications, as well as its properties which can vary considerably from one mRNA construct to the next. Because of this, there is no one-size-fits-all purification process. In finding the process that fits best, general challenges must be addressed in all programs:

  • mRNA constructs for therapies and vaccines are inherently large and sensitive to shear stress and degradation. This is especially true for self-amplifying mRNA
  • Impurities such as dsRNA, abortive transcripts, and DNA template have properties similar to mRNA, which makes the removal of these difficult
  • Purification solutions for large-scale GMP manufacturing are limited, which necessitates reliance on suboptimal lab-scale methods and products that were not designed for mRNA

Manufacturing solutions to these challenges are emerging. Chromatography technologies such as monolithic columns provide scalable solutions for shear and slow adsorption, and fiber-based resins in development promise higher capacities and flow rates to reduce process times and costs and to better maintain mRNA integrity.

Contaminants and impurities can be further reduced using an affinity column such as oligo dT, which enriches full-length, polyadenylated transcripts in the final product. And for uses demanding the highest level of mRNA purity, polishing steps such hydrophobic interaction or reverse phase chromatography will further reduce levels of process enzymes, endotoxin and dsRNA.

Achieving the highest level of purity is costly and not always justified. In cases where impurities are relatively low in the upstream process and the end use doesn’t require the absolute highest purity, a simpler purification process such as multimodal or ion exchange chromatography in flow-through mode followed by tangential flow filtration can produce satisfactory results for a range of uses. Advantages to this approach include higher process recoveries and lower process times, which reduce production costs and loss of mRNA integrity.


To summarize this three-part post series, mRNA-based therapies and vaccines hold considerable promise that is being realized with the rapid development of vaccines against infectious diseases, and as novel, transformative medicines enter clinical stages of development. Although the advancement of manufacturing technologies specifically for mRNA production hasn’t kept pace, innovative and smart use of existing technologies is filling the gap as mRNA-specific manufacturing solutions emerge.

For more depth on manufacturing considerations for mRNA, please view my presentation, Self-amplifying and messenger RNA for Vaccines and Therapies: Manufacturing for clinical stages, presented at the TIDES USA conference in May 2022.

About the author

Latest posts

Nate Spangler, Ph.D.

Nate Spangler, Ph.D.

Nathan Spangler is Aldevron’s Senior Director of Innovation & Strategy. Located in Madison, Nathan was instrumental in planning and building Aldevron’s recombinant antibody and protein business. For nearly two decades, he has supported discovery and development of drugs through R&D and commercialization of tools and technologies, as well as the building and management of contract development and research businesses in the life sciences industry.

Topics: mRNA, Plasmid DNA, Clinical Grade Manufacturing/cGMP, Research Grade Manufacturing, Immunotherapy