A comparative study of ion exchange vs. ion pair chromatography for preparative separation of oligonucleotides (2025)

Introduction Oligonucleotides are essential molecules in modern therapeutics and diagnostics, playing a key role in genetic research, drug development, and disease diagnostics. However, the purification of these molecules presents significant challenges, particularly in large-scale production. Two widely used chromatographic techniques—Ion Exchange Chromatography (IEX) and Ion-Pair Reversed-Phase Liquid Chromatography (IP-RPLC)—offer different benefits and limitations. Our latest research, conducted in collaboration with leading experts in the field, provides a comprehensive comparison of these methods, evaluating their efficiency, cost-effectiveness, and environmental impact.

A comparative study of ion exchange vs. ion pair chromatography (2025)
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The Study: A Comparative Analysis

Our study, published in the Journal of Chromatography A, focused on the preparative purification of a 20-mer oligonucleotide. We systematically compared IEX and IP-RPLC under various conditions, examining key factors such as:

  • Purification Efficiency: The ability of each method to separate oligonucleotides from impurities.
  • Productivity: The amount of purified oligonucleotide obtained per unit time and per unit column volume.
  • Solvent Consumption: The volume of solvents required for each technique, affecting both cost and environmental impact.

By varying column load and gradient slopes, we assessed the performance of each technique at different purity levels, ranging from 95% to 99%.

Key Findings

  1. IEX Offers Superior Productivity: At 95% purity, IEX delivered more than twice the productivity of IP-RPLC. At 99% purity, the difference was even more pronounced, with IEX proving seven times more productive than IP-RPLC.
  2. Lower Solvent Usage with IEX: Solvent consumption was significantly lower in IEX, ranging from one-third to one-tenth of the amount required for IP-RPLC. This makes IEX a more cost-effective and environmentally friendly option.
  3. Differences in Elution Profiles: IEX followed an anti-Langmuirian elution behavior, which allowed for more efficient impurity separation. In contrast, IP-RPLC exhibited a Langmuirian elution profile, which resulted in lower yields at high purity levels.
  4. Loadability and Cycle Time: While IEX had longer cycle times, its higher loadability compensated for this, making it the preferred method for large-scale oligonucleotide purification.

Broader Industry Implications

These findings have significant implications for pharmaceutical and biotech industries involved in oligonucleotide synthesis and purification. The choice of purification method can impact overall production efficiency, cost, and sustainability:

  • For large-scale applications, IEX offers clear advantages, particularly for companies seeking to maximize throughput while minimizing solvent use.
  • For small-scale laboratory use, IP-RPLC remains a valuable option due to its ability to achieve high resolution in analytical settings.
  • Environmental considerations favor IEX due to its significantly lower solvent consumption and the absence of hazardous organic reagents.

Spotlight on Cecilia Unoson’s Contribution We are proud to highlight the contributions of our very own Cecilia Unoson, who was a co-author of this groundbreaking study. As a key member of the research team, Cecilia played an instrumental role in the study’s methodology, data analysis, and overall execution. Her expertise in chromatography and oligonucleotide purification was invaluable in shaping the study's findings and ensuring its relevance to industrial applications. Her work continues to drive innovation in the field, and we are thrilled to have her as part of our team at Bio-Works.

Conclusion

For companies involved in oligonucleotide production, transitioning to IEX can lead to substantial benefits, including cost reductions, increased efficiency, and improved sustainability. The findings of this study highlight the importance of method selection in optimizing purification workflows, particularly in large-scale operations where productivity and environmental impact are critical factors.

Acknowledgment of Authors

This study was conducted in collaboration with:

  • Martin Enmark (Karlstad University)
  • Cecilia Unoson (Bio-Works)
  • Marek Leśko (Karlstad University)
  • Olof Stålberg (QIAGEN DNA Synthesis)
  • Kathrin Stavenhagen (AstraZeneca)
  • Manasses Jora (AstraZeneca)
  • Tomas Leek (AstraZeneca)
  • Linda Thunberg (AstraZeneca)
  • Kayla Borland (AstraZeneca)
  • Jörgen Samuelsson (Karlstad University)
  • Torgny Fornstedt (Karlstad University)

This research was published in Journal of Chromatography A and supported by funding from the Swedish Knowledge Foundation.

If you’d like to learn more about how these findings apply to your purification processes, feel free to reach out to our team. We’d be happy to discuss how our insights can support your operations.

Source: https://www.sciencedirect.com/science/article/pii/S0021967325001384?via%3Dihub

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