Chromatography Separation and Desalting in Oligonucleotide Purification

Reverse phase HPLC and adsorbent resins for the purification of oligonucleotide therapeutics and diagnostics.

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Solve difficult oligonucleotide purification challenges

The oligonucleotide market is growing rapidly due to the ability of oligonucleotides to alter (inhibit or augment) gene expression at the mRNA or DNA level. The largest class of therapies, AntiSense Oligonucleotides (ASO) therapies, works by silencing the production of mutated proteins that cause disease. The use of oligonucleotides is increasing in genetic research due to advances in CRISPR technology for DNA knockout studies. Growth in PCR-based diagnostics and microarray systems is increasing the demand for oligonucleotides as primers.

These oligonucleotide applications require precise targeting mechanisms for proper therapeutic or diagnostic function. Oligonucleotide synthesis is a complex process prone to errors in the base pair nucleic acid sequence. Oligonucleotide researchers and manufacturers need robust and selective purification strategies that are sensitive to minor differences in chemical and physical structure. We offer a range of chromatography resins to help companies optimize efficiency, resolution, and yield in oligonucleotide production, from benchtop to clinical trial to commercial scale.

NEW DuPont™ AmberChrom™ TQ1 Chromatography Resin

Learn more about our newest anion exchange resin, perfect for oligonucleotide and peptide purification and polishing steps.

NEWStudies on Anion Exchange DuPont™ AmberChrom™ TQ1 Chromatography Resin

Read a comprehensive application study that uses real-world drug feeds to validate performance characteristics.

NEWVersatility of Polymeric Resins for Oligonculeotide Purification

Explore the benefits of polymeric resins in challenging purifications across oligonucleotide modalities.

DuPont Resins for Downstream Drug Purification

Explore our comprehensive portfolio of reverse phase, adsorbent, and ion exchange resins for purification and separation in biopharma applications.

Resource Center

View all application studies, product data sheets, brochures, and other materials related to oligonucleotides in our resource center.

Chromatography purification of oligonucleotides

Learn more about the purification challenges that can be solved with AmberChrom™ chromatography resins. Chromatographic Separation Desalting

Design trityl-on and trityl-off oligonucleotide purification processes for high yield and high purity

Oligonucleotide synthesis can create many impurities that resemble the target sequence. Reverse Phase High Pressure Liquid Chromatography (RP HPLC) is a good way to get rid of impurities like failure sequences and base pair errors. It is an integral part of a downstream process that needs high recovery and high purity. Polymer RP HPLC resins are more durable than C18 silica resins and can withstand more extreme pH levels and aggressive cleaning protocols. DuPont™ AmberChrom™ chromatography resins can address these difficult oligonucleotide purification challenges:

Removal of phosphoramidite impurities
Separation of target oligonucleotide from failure sequences (N and N-1 separation)
Isolation and recovery based on end-capping state: DMT-on (trityl-on) or DMT-off (trityl-off) oligonucleotide purification

View all products for chromatographic separation in our product finder.

Desalting with adsorbent resins

Some oligonucleotides are purified in water with ion exchange resins, a process that leaves salt impurities in the oligonucleotide product stream. AmberChrom™ chromatography resins can be used as adsorbent resins in a salt polishing step as follows:

Bind oligonucleotide products
Wash out salts
Elute oligonucleotide product with aqueous ammonia

View all products for desalting in our product finder.

Chromatographic Separation+

Design trityl-on and trityl-off oligonucleotide purification processes for high yield and high purity

Oligonucleotide synthesis can create many impurities that resemble the target sequence. Reverse Phase High Pressure Liquid Chromatography (RP HPLC) is a good way to get rid of impurities like failure sequences and base pair errors. It is an integral part of a downstream process that needs high recovery and high purity. Polymer RP HPLC resins are more durable than C18 silica resins and can withstand more extreme pH levels and aggressive cleaning protocols. DuPont™ AmberChrom™ chromatography resins can address these difficult oligonucleotide purification challenges:
- Removal of phosphoramidite impurities
- Separation of target oligonucleotide from failure sequences (N and N-1 separation)
- Isolation and recovery based on end-capping state: DMT-on (trityl-on) or DMT-off (trityl-off) oligonucleotide purification
View all products for chromatographic separation in our product finder.
Desalting+

Desalting with adsorbent resins

Some oligonucleotides are purified in water with ion exchange resins, a process that leaves salt impurities in the oligonucleotide product stream. AmberChrom™ chromatography resins can be used as adsorbent resins in a salt polishing step as follows:
- Bind oligonucleotide products
- Wash out salts
- Elute oligonucleotide product with aqueous ammonia
View all products for desalting in our product finder.

Select publications using our products in oligonucleotide applications

Hanson, G.J. et al. (2022) Peptide Oligonucleotide Conjugates. US 202/0072143 A1 Google Patents US 2022/0072143 A1

Roussis, S.G. et al. (2020) Automated determination of early eluting oligonucleotide impurities using ion-pair reversed-phase liquid chromatography high resolution-mass spectrometry. Analytical Biochemistry 595: 113623-113623. DOI: https://doi.org/10.1016/j.ab.2020.113623

Vu, H. et al. (2009) The use of 6-carboxynaphthofluorescein phosphoramidite in the automated synthesis of quencher-dye oligonucleotide probes (QDOPs). Tetrahedron Letters 50 (7): 737-740. DOI: https://doi.org/10.1016/j.tetlet.2008.11.059

Akiyama, H. et al.(2006) Intraocular injection of an aptamer that binds PDGF-B: A potential treatment for proliferative retinopathies, Journal of Cellular Physiology 207(2): 407-412. DOI: https://doi.org/10.1002/jcp.20583

Schick, C. et al (1993) Identification of Specific Contacts in T3 RNA Polymerase-Promoter Interactions: Kinetic Analysis using Small Synthetic Promoters. BioChemistry 32(16): 4275-4280. DOI: https://doi.org/10.1021/bi00067a016