Oligonucleotide Purification with MCSGP: Higher Yield, Fewer IPCs

Bachem — a leading global peptide and oligonucleotide CDMO — integrated MCSGP into large-scale oligonucleotide API manufacturing at Bubendorf, Switzerland. A pharmaceutical company required multi-ton oligonucleotide API with high throughput and a reduced environmental footprint; Bachem delivered with MCSGP on their cGMP-qualified production systems.

Results vs. batch for a production-scale oligonucleotide:

• Batch baseline: 93.7% purity, 81.6% yield
• MCSGP: comparable purity, +8% yield, PMI of 1,300 kg per kg API
• Capacity with 2×45 cm columns: >1,500 kg oligonucleotide API per year
• Throughput scales with column diameter: >300 kg/yr (20 cm) → >700 kg/yr (30 cm) → >1.5 t/yr (45 cm) → >2.5 t/yr (60 cm)

Key GMP and industrial milestones:

• 2021: First two process-scale MCSGP systems (HPLC + AEX, 20 and 30 cm columns) installed and qualified at Bubendorf
• 2022: First GMP MCSGP purification completed for oligonucleotides — first ever at industrial scale
• 2023: First GMP batches of oligonucleotides released under MCSGP continuous chromatography

Quantitative results: Bachem AG — “Greener Purification at Large-Scale: An Oligonucleotide Case Study” (March 2023) GMP milestones: Bachem AG — “Greener Purification at Large-Scale: An Oligonucleotide Case Study” (updated 2025)

A landmark 2025 publication (Eisenhuth & Müller-Späth, Processes 13(12), 3950) provides the first regulatory-compliant Process Characterization and Performance Qualification (PPQ) framework for MCSGP — demonstrated on a 20-mer synthetic peptide and explicitly applicable to oligonucleotide manufacturers. Key outcomes: 96% reduction in IPC burden, 73% reduction in PMI, and full process robustness confirmed across 397 elutions. → See the Peptide Purification page for full details

Molecule: GalNAc-cluster-conjugated DNA-LNA gapmer antisense oligonucleotide (Roche) Chromatographic Mode: Reversed-phase HPLC Equipment: Contichrom CUBE

Key finding: The +38.8% absolute yield increase enables 42.5% downscaling of oligonucleotide synthesis — a massive cost reduction given that synthesis is the dominant cost driver in oligonucleotide manufacturing. Equipment, chemicals, and methodology are analogous to standard RP purification, allowing a “like for like” transition.

Weldon, R. et al. J. Chromatogr. A, 1663, 462734 (2022). DOI: 10.1016/j.chroma.2021.462734

Molecule: Sugar-conjugated sense strand of a therapeutic siRNA (J&J) Chromatographic Mode: Anion exchange (AIEX) Equipment: Contichrom CUBE 30

Key finding: MCSGP was successfully implemented for continuous AIEX purification of a conjugated siRNA therapeutic. The software-aided method development procedure enabled fast transfer from batch to continuous-mode chromatography. Given the very high costs of oligonucleotide synthesis, the 13% yield improvement alone represents substantial cost savings.

Weldon, R. et al. Org. Process Res. Dev., 29, 1400–1410 (2025). DOI: 10.1021/acs.oprd.4c00513

MCSGP continuously recycles the impure side-fractions that batch AIEX or IP-RP chromatography discards — recovering full-length oligonucleotide product without compromising purity. Published data on a GalNAc-conjugated gapmer showed yield increasing from 52.7% to 91.5%. For a conjugated siRNA, yield improved from 80% to 93%. Improvements of +13–74% are typical depending on crude purity and impurity complexity.

Yes. MCSGP uses the same anion exchange (AIEX), ion-pair reversed-phase (IP-RP), and reversed-phase (RP) stationary phases and eluent systems as your existing batch method. No change to your resin or buffer chemistry is needed — MCSGP process parameters are then developed from those existing conditions, typically within 1–2 weeks on the CUBE.

Oligonucleotides with complex impurity profiles see the largest gains — particularly phosphorothioate ASOs (broad diastereomer peaks), GalNAc-conjugated sequences (added conjugate complexity), and siRNAs (high-purity strand requirements). Even well-optimized 20-mer oligonucleotides show +50% absolute yield improvement.

Yes. MCSGP supports anion exchange (AIEX), ion-pair reversed-phase (IP-RP), and reversed-phase (RP) separations used for oligonucleotide purification. It uses the same stationary phases and eluent systems as the existing batch process, allowing established conditions to serve as the starting point for MCSGP process development. Published applications demonstrate the process in both AIEX and RP modes.

Yes. Bachem has run GMP MCSGP oligonucleotide purification since 2023 at their Bubendorf facility — the world’s first industrial-scale MCSGP for oligonucleotides. A December 2025 landmark publication (Müller-Späth et al., Processes 13(12), 3950) provides the first-ever Process Characterization and PPQ framework applicable to oligonucleotide MCSGP processes.

Yes. All Contichrom systems support batch, 2D/3D integrated batch, and continuous modes on the same hardware. The TWIN HPLC production systems are dual-mode (MCSGP + batch) on a single skid — so you can run both oligonucleotide purification processes without separate equipment.

Starting from an existing batch AIEX or IP-RP oligonucleotide method, the ChromIQ® MCSGP Wizard enables process design in as little as 15 minutes. A first MCSGP oligonucleotide run can be achieved within approximately one day. Full optimization typically takes 1–2 weeks.

AutoPeak® monitors the oligonucleotide elution profile in real-time via UV and conductivity, dynamically adjusting collection windows to compensate for crude feed variability, column aging, and retention time drift. Studies showed that without AutoPeak®, yields dropped to 20% under process variation — with AutoPeak®, consistent high yield is maintained automatically.

Oligonucleotide synthesis is the dominant cost driver. By boosting purification yield to 90%+, MCSGP enables proportional downscaling of upstream solid-phase synthesis — up to 42.5% less synthesis for the same final product output. Combined with elimination of re-chromatography and reduced QC burden, MCSGP delivers transformative process economics.

For oligonucleotide manufacturing, MCSGP delivers reduced solvent and buffer consumption per gram of purified product, smaller upstream synthesis campaigns (from higher yield), and dramatically fewer IPC analyses. The FDA actively encourages the shift to continuous manufacturing for pharmaceutical APIs, and MCSGP significantly improves Process Mass Intensity (PMI).