From precipitation to precision: designing crystallization for oligonucleotide purification
Nucleic Acid Insights 2026; 3(8), 517–525
DOI: 10.18609/nai.2026.066
The versatile application of oligonucleotides makes them a rapidly expanding system, but their manufacturing is constrained by costly and resource-intensive downstream purification. Current purification strategies rely predominantly on chromatographic techniques, which consistently deliver high-purity products but require large volumes of solvent, expensive stationary phases, lengthy processing times, and generate significant waste. This commentary proposes crystallization as an underexplored but promising alternative for oligonucleotide purification. Although oligonucleotides have historically been viewed as poor crystallization candidates, but this perception can be overcome through targeted strategies such as counterion selection, coformers, seeding, mixed-solvent systems, and temperature- or pH-controlled crystallization. Engineered crystallization could provide sequence-selective separation by exploiting differences in counterions, hydration, conformation, and backbone chemistry. This commentary further proposes practical development roadmap spanning sequence stratification, solubility mapping, nucleation control, selectivity optimization, solid-form characterization, and scale-up with process analytical technology. With continued development, crystallization has the potential to reduce process mass intensity, lower manufacturing costs, and enhance the sustainability of next-generation oligonucleotide production.