Oligonucleotides

More Oligo. Fewer IPCs. MCSGP for ASOs, siRNAs & GalNAc Conjugates.

In AIEX or IP-RP modes. Recover full-length product that batch chromatography discards in side-fractions, without changing your resin, gradient, or buffers.

Published case results: +50% yield (60→90%+) on 20-mer | +38.8 pp yield (52.7→91.5%) on GalNAc conjugate | +13 pp yield (80→93%) on conjugated siRNA AIEX

Sources: YMC ChromaCon Oligo Application Note; Weldon et al., J. Chromatogr. A 2022; Weldon et al., Org. Process Res. Dev. 2025

Talk to Our Oligonucleotide Specialists

Download the Application Note

Talk to Our Oligonucleotide Specialists

Download the Application Note

The Oligonucleotide Purification Bottleneck

Oligonucleotide therapeutics are surging — with 24 FDA-approved drugs, 200+ candidates in clinical trials, and blockbuster siRNAs driving demand to multi-kilogram scales. Purification by anion exchange (AIEX) or ion-pair reversed-phase (IP-RP) chromatography is the critical downstream bottleneck.

Batch chromatography forces a painful trade-off: high purity or high yield — not both. Oligonucleotide crude feeds contain hundreds of closely related impurities — N-1 shortmers, N+1 longmers, phosphodiester (PO) failures, depurination products, and phosphorothioate diastereomers — many differing by as little as 1 Da in a 7,000+ Da molecule. Achieving target purity requires a narrow center-cut, discarding valuable full-length product in side-fractions. Recovering that product means costly re-chromatography — with all the associated solvent, buffer, and QC burden.

For high-volume APIs demanded by cholesterol-lowering siRNAs, hepatitis B ASOs, and GalNAc-conjugated therapies, this inefficiency is unsustainable.

The Solution: MCSGP with AutoPeak® for Oligonucleotide Purification

MCSGP (Multi-column Countercurrent Solvent Gradient Purification) eliminates the purity-yield trade-off in oligonucleotide chromatography. Two identical columns continuously recycle impure side-fractions — recovering full-length oligonucleotide product that batch processes discard. It uses the same AIEX, IP-RP, and RP resins, buffers, and solvents as your existing batch oligonucleotide method.

AutoPeak® dynamic process control monitors oligonucleotide elution profiles in real-time via UV and conductivity, automatically adjusting collection windows to maintain consistent output quality — enabling robust, unattended 24/7 oligonucleotide purification. Without AutoPeak® control, studies have shown yields can drop to as low as 20% under process variability — AutoPeak® eliminates this risk.

Same chemistry. Better results. MCSGP works with the AIEX, IP-RP, and RP stationary phases and mobile phases already used in your oligonucleotide batch process — your existing resin and eluent conditions are the starting point for MCSGP development. No change to your chromatographic chemistry is needed.

Learn About MCSGP + AutoPeak®

Proven Results: MCSGP vs. Batch – Oligonucleotide Purification

+13–74%

Yield Increase

90%+

Typical MCSGP Yield

87% ↑

Throughput Increase

Zero

Re-chromatography Runs

42.5% ↓

Synthesis Scale Reduction

2×

Productivity Gain

Commercial GMP manufacturing: Bachem AG

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)

First MCSGP Process Validation Framework Published (Dec 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

Case Study 1: GalNAc-Conjugated DNA-LNA (RP)

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

Parameter	Batch	MCSGP
Yield	52.7%	91.5% (+73.6% relative)
Purity	Comparable	Comparable
Productivity	Baseline	2× higher
Buffer consumption	Baseline	Comparable

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

Case Study 2: siRNA Sense Strand (AIEX)

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

Parameter	Batch (Pilot Scale)	MCSGP
Yield	80%	93% (+13% absolute)
Purity	~95% (target >95%)	95.4%
Throughput	Baseline	+87% higher
Product elutions	Single batch	27 elutions over 13 cycles

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

Oligonucleotide Purification Comparison Table:

Parameter	Batch Oligonucleotide Chromatography	MCSGP with AutoPeak®
Purity-Yield Trade-off	Inherent — narrow cuts sacrifice yield	Eliminated — high purity AND yield simultaneously
Product Yield	50–80%	90–95% (+13–74% absolute)
Re-chromatography	Required for side-fractions	Eliminated — internal recycling
Buffer/Solvent Consumption	High	Comparable or reduced per gram product
IPC/QC Burden	Testing every side-fraction, every batch	Massively reduced — one sample per MCSGP cycle
Throughput	Limited by re-chromatography cycles	Up to 87% higher (continuous 24/7)
Process Control	Manual monitoring	Automated (AutoPeak® UV-based PAT)
Robustness	Sensitive to drift and crude feed variability	AutoPeak® dynamically compensates
Operator Requirement	Requires supervision	Designed for unsupervised operation
Upstream Synthesis Impact	Fixed synthesis scale	Higher yield enables up to 42.5% synthesis downscaling
Stationary Phase / Eluents	Standard AIEX / IP-RP / RP	Same — no change required

The Contichrom® Platform: From Oligonucleotide Development to Production

All Contichrom® systems support twin-column continuous chromatography with AIEX, IP-RP, and RP resins used in oligonucleotide purification (particle sizes ≥10 µm). Methods scale predictably from CUBE → PILOT 300X → TWIN HPLC.

Systems Overview

Contichrom® CUBE

The essential platform for chromatography process development. This versatile 100-bar benchtop FPLC system runs batch, integrated batch, and continuous chromatography — including MCSGP and CaptureSMB — out of the box. Develop purification processes for mAbs, peptides, oligonucleotides, ADCs, and viral vectors, with verified scale-up at over 100× to pilot and production systems.

Contichrom® PILOT

Scale peptide and oligonucleotide purification to pilot and clinical GMP manufacturing. This 100-bar preparative HPLC system features MCSGP with AutoPeak® to eliminate the yield-purity trade-off — delivering +10–50% absolute yield increase at target purity and significantly less solvent than batch HPLC. ATEX Zone 2 / Class I Div 2 certified for organic solvents. Flow rates up to 300 mL/min.

Contichrom® TWIN HPLC

Produce peptides and oligonucleotides at commercial GMP scale. This 80-bar industrial HPLC system uses MCSGP with AutoPeak® to eliminate the yield-purity trade-off — increasing recovery to >90% while reducing solvent consumption compared to batch. ATEX Zone 2 / Class I Div 2 certified for organic solvents, and flow rates up to 36 L/min.

Systems Overview

Oligonucleotide Applications

Antisense Oligonucleotides (ASOs)

ASOs with phosphorothioate (PS) backbones generate complex diastereomer mixtures and broad chromatographic peaks that make batch purification especially challenging. MCSGP continuously recovers full-length product from overlapping PS impurity shoulders — delivering yields of 90%+ at target purity with AIEX or IP-RP chromatography.

Small Interfering RNAs (siRNAs)

siRNA sense and antisense strands require high-purity individual strand purification before duplex annealing. Published MCSGP data on a conjugated siRNA sense strand showed yield improvement from 80% to 93% with AIEX, with 87% higher throughput — critical for the multi-kilogram scales demanded by cholesterol-lowering and hepatitis therapies.

GalNAc-Conjugated Oligonucleotides

GalNAc conjugation enables liver-targeted delivery and is used in the latest FDA-approved oligonucleotide therapies. The bulky GalNAc cluster adds purification complexity. MCSGP with RP-HPLC demonstrated +73.6% relative yield improvement for a GalNAc-DNA-LNA gapmer, enabling 42.5% synthesis downscaling.

Oligonucleotide Applications Continued….

Multi-Step Oligonucleotide Purification (AIEX + IP-RP / RP-AEX)

Combine orthogonal oligonucleotide purification steps — AIEX for charge-based separation and IP-RP for hydrophobicity-based separation — in a single automated 2D integrated batch workflow. RP-AEX sequence eliminates the need for in-line dilution and produces the sodium counterion form required for formulation.

Oligonucleotide Impurity Isolation & Characterization (N-Rich)

ICH-required oligonucleotide impurity characterization (N-1, N+1, PO failures, depurination products) typically takes weeks of repetitive analytical runs. N-Rich automated on-column enrichment isolates milligram quantities of target oligonucleotide impurities up to 80× faster.

Getting Started with Oligonucleotide MCSGP

See the Contichrom® platform in action before you commit, assess MCSGP suitability computationally or experimentally using your own sequence and resin, develop your continuous method at lab scale on a Contichrom CUBE, then scale to GMP production on the TWIN HPLC — the same platform behind Bachem’s first GMP-validated continuous oligonucleotide process (2023).

See It First — Free Demo or Webinar

Not yet familiar with the Contichrom® platform? Start here. YMC ChromaCon offers no-charge demonstrations and introductory webinars tailored to your team.

On-site in Zurich (half day, 2–4 hours): see the CUBE in person, run ChromIQ® live, discuss your oligonucleotide purification challenge with YMC ChromaCon application scientists
Remote webinar (1–3 hours): interactive live session covering MCSGP, N-Rich, ChromIQ® software, and the full Contichrom® ecosystem
Sessions cover MCSGP process design for AEX and IP-RP separations, the ChromIQ® MCSGP Wizard, and scale-up to TWIN HPLC

→ Request a free demo or introductory webinar

Modeling Assessment for Oligonucleotides

Predict how MCSGP will perform on your oligonucleotide molecule and resin before running a single continuous experiment. YMC ChromaCon builds a calibrated mechanistic model from your existing batch data.

Submit linear gradient batch chromatography runs with fraction collection and analytical purity data (AEX or IP-RP; from any HPLC or FPLC system — no Contichrom® required)
YMC ChromaCon calibrates and validates the model, simulates MCSGP operating points, and delivers a predicted batch vs. MCSGP performance comparison (yield, purity, productivity) with initial scale-up parameters
AutoPeak® dynamic control impact is included in the simulation
Typical timeline: 3–5 weeks from receipt of data; no material shipment required

→ MCSGP Process Modeling Service

Experimental Feasibility Study — Your Oligo, Your Resin

Your oligonucleotide is purified on YMC ChromaCon’s Contichrom® platform at our facility in Zurich. We reproduce your batch AEX or IP-RP method as a benchmark and run ≥ 3 MCSGP experiments side-by-side.

Ship starting material to Zurich — typically ≥ 20× a single preparative batch run, scaled to 1 cm i.D. columns
We reproduce your analytical HPLC method, establish the batch benchmark, and run MCSGP experiments using your resin and buffer system
Deliverable: side-by-side batch vs. MCSGP comparison with real chromatographic data from your sequence and resin, plus fractions for your independent purity verification
Typical timeline: 4–6 weeks after receipt of starting material and purchase order

→ YMC ChromaCon Feasibility Studies

Develop at Lab Scale — Rent or Purchase a CUBE

MCSGP method development is performed on the Contichrom CUBE using your existing AEX or IP-RP resin and buffer system. Available for rental or purchase.

ChromIQ® MCSGP Wizard designs the initial MCSGP operating point from a single batch chromatogram — method setup completed in as little as 15 minutes
Your current batch gradient conditions are the starting point — no new resin or method development required
AutoPeak® dynamic process control adjusts collection windows in real-time based on the UV elution profile, compensating for feed variability and column aging
The CUBE supports both MCSGP and N-Rich on the same platform

→ Contichrom CUBE Rental Program

→ Purchase a Contichrom CUBE

Scale to GMP Production — PILOT 300X or TWIN HPLC

The MCSGP method developed on the CUBE transfers directly to larger Contichrom systems for pilot and manufacturing-scale production. YMC ChromaCon provides scale-up consulting and GMP documentation support.

PILOT 300X (up to 300 mL/min, 100 bar, ATEX Zone 2) for pilot-scale and clinical supply batches
TWIN HPLC for GMP production — the same platform used for Bachem’s first GMP-validated continuous oligonucleotide purification process (2023)
Scale-up is driven by column diameter — bed height, gradient conditions, and AutoPeak® control logic are preserved across scales
Four TWIN HPLC system sizes cover lab through full production scale
GMP documentation support (IQ/OQ/PQ) and scale-up consulting available

→ Scale-Up Consulting and Training

01 / 05

Ready to Transform Your Oligonucleotide Purification?

Book a CUBE Rental Register for the Continuous Chromatography Workshop

How does MCSGP improve oligonucleotide purification yield?

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.

Does MCSGP work with my existing oligonucleotide batch method?

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.

Which oligonucleotide types benefit most from MCSGP?

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.

Can MCSGP handle both AIEX and IP-RP oligonucleotide purification modes?

Yes. MCSGP has been demonstrated with all major oligonucleotide chromatographic modes: anion exchange (AIEX) for charge-based separation of N-1/N+1 shortmers and longmers, and ion-pair reversed-phase (IP-RP) and standard reversed-phase (RP) for hydrophobicity-based purification. Published case studies cover both AIEX and RP modes.

Has MCSGP been validated for GMP oligonucleotide manufacturing?

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.

Can Contichrom systems also run standard batch oligonucleotide chromatography?

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.

How quickly can I transfer my oligonucleotide batch method to MCSGP?

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.

How does AutoPeak® handle oligonucleotide process variability?

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.

How does MCSGP reduce overall oligonucleotide manufacturing cost?

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.

How does continuous oligonucleotide purification improve sustainability?

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).