Overcoming Downstream Development Challenges for Emerging Nucleic Acid Therapies
Nucleic acids are an important and exciting class of novel therapeutics with messenger RNA (mRNA) representing one of the most significant leaps in modern medicine. These molecules operate by new mechanisms of action that transform how treatments are designed, manufactured, and delivered. Their increasing popularity comes from breakthroughs achieved over the past decade in mRNA engineering, stabilization, delivery, and manufacturing scalability.
mRNA provides genetic instructions so the patient’s own cells can temporarily produce the desired protein. This mechanism can be used for cancer immunotherapy, infectious disease prevention, and transient gene-editing delivery. The advantages of mRNA include both its ability to enable more effective treatments and significantly simplified manufacturing compared to conventional biologic therapeutics. Production of mRNA is faster because it involves a cell-free chemical process, so there is no need for cell-line development and extensive cell culture process optimization. Process volumes are much smaller, supporting greater versatility.
Nucleic Acid Purification Challenges
Significant progress has been made in improving the efficiency of the upstream in vitro transcription process used to generate mRNA from plasmid DNA (pDNA), but there do still remain challenges to achieving cost-effective, efficient, high-yield purification of both mRNA and pDNA. Commonly used chromatographic resins and monoliths are long‑established in the bioprocessing industry, with extensive historical validation, regulatory familiarity, and broad platform experience. Their inherent strengths include strong binding interactions, reliable separation performance, and high resolution, helping manufacturers remove host‑derived contaminants, process‑related impurities, and unwanted isoforms.
The traditional approach is challenging as the large size of mRNA transcripts, particularly self‑amplifying RNA (saRNA, which is attracting increasing attention due to its enhanced antigen expression), create significant purification bottlenecks, as oversized molecules generate backpressure in traditional chromatography systems and reduce throughput. In addition, mRNA molecules are highly susceptible to shear stress and mechanical degradation throughout pumping, mixing, and filtration, and thus require extremely gentle, carefully optimized handling to preserve integrity. Purification is further complicated by inherently low yields and difficulties removing impurities such as double-stranded RNA (dsRNA) and truncated products, leading to lengthy multi‑step processes that strain consistency and cost. These factors together contribute to long processing times and reduced manufacturing agility.
pDNA production brings its own complexities, particularly in separating supercoiled plasmid — the preferred therapeutic isoform — from open circular and linear variants that have nearly identical properties and are notoriously difficult to resolve chromatographically. Achieving high purity at scale is further hindered by persistent contaminants such as host‑cell DNA (HCD), RNA, proteins, and endotoxins, all of which are challenging to remove without compromising plasmid topology
Resins and monoliths, while widely used still have notable limitations when applied to large and structurally complex biological molecules like mRNA, saRNA, and plasmid DNA. Packed-bed resins can be relatively slow because mass transfer relies on diffusion into small pores, causing long processing times and reduced throughput. These constraints become more pronounced as molecule size increases, leading to reduced binding efficiency, elevated backpressure, and compromised resolution for very large constructs. Monoliths offer improved convective flow, but they too face challenges in handling oversized nucleic acids at scale, including reduced flow rates under load, pressure sensitivity, and limited ability to process highly viscous or shear‑sensitive materials without compromising integrity.
These traditional formats, therefore, can struggle to balance speed, resolution, and scalability for next‑generation nucleic acid modalities. As a result, mRNA and pDNA manufacturing remain technically demanding, high‑variability processes that lack robust, scalable, platform‑ready solutions.
Membrane chromatography solution
Developers of nucleic acid therapies are increasingly turning to next‑generation membrane chromatography solutions as powerful alternatives for overcoming the size, speed, and scalability limitations of resins and monoliths. Membranes rely on convective flow through large, open pore structures, enabling extremely fast processing times — measured in minutes instead of hours — while maintaining high binding capacity for large biomolecules. Their architecture inherently accommodates oversized nucleic acids, including mRNA, saRNA, and pDNA, without inducing the high backpressure or slow diffusion seen in packed media.
The Purexa portfolio offers an efficient impurity removal solution. Featuring rapid cycle times, and robust recovery, users experience a streamlined, scalable path to higher productivity, improved purity, and more resilient manufacturing processes for emerging RNA and DNA therapeutics.
Unlike early generations of membrane chromatography products that exhibited significant practical and engineering limitations including performance issues linked to fouling, sub‑optimal operating conditions, and lack of large-scale options for manufacturing, Purexa membranes show performance (binding capacity, yield, and purity) on par or better than that of typical resins with minimal fouling. The inherently robust products can be inserted into most established processes without needing to adjust factors like buffer conditions and they are available from lab to commercial scale, the latter made possible with a stackable cassette device that can produce a working volume of over 200 mL per cycle.
Demand for pDNA continues to expand as growing numbers of RNA therapeutic candidates enter and advance through the clinic. The need for efficient, cost-effective downstream processing solutions for pDNA, mRNA, and saRNA will grow in response. Similarly, growing evidence of the ability of in vivo and ex vivo cell and gene therapies to address unmet medical needs will drive demand for more efficient upstream and downstream manufacturing solutions for viral vectors.
The scalable portfolio of Purexa membranes is continually evolving to meet diverse customer needs across all stages of development. Plans also include expanding the application of Purexa membrane technology beyond monoclonal antibodies and nucleic acids to other biotherapeutic modalities, including other complex, emerging therapies.
