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.

 
 
 
 
 
 
 
 
 

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 chromatographic separation products 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 desalting products 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 chromatographic separation products 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 desalting products in our product finder.

 
 
 
 
 
 
 
 
 
 
 
 

Select publications using our products in oligonucleotide applications

 

  • Schick, C.; Martin, C.T..  Identification of Specific Contacts in T3 RNA Polymerase-Promoter Interactions: Kinetic Analysis using Small Synthetic Promoters, BioChemistry 1993, 32 (16), 4275-4280.  DOI: 10.1021/bi00067a016
  • Vu, H.; Majlessi, M.; Adelpour, D.; Russel, J. The use of 6-carboxynaphthofluorescein phosphoramidite in the automated synthesis of quencher-dye oligonucleotide probes (QDOPs), Tetrahedron Letters 2009, 50 (7), 737-740.  DOI: 10.1016/j.tetlet.2008.11.059 
  • Roussis, S.G.; Cedillo, I; Rentel, C.  Automated determination of early eluting oligonucleotide impurities using ion-pair reversed-phase liquid chromatography high resolution-mass spectrometry, Analytical Biochemistry 2020, 595, 113623.  DOI:  10.1016/j.ab.2020.113623
  • Hanson, G.J.; Zhou, M. Oligonucleotide Conjugates. US2020/0254109.
  • Akiyama, H; et al. Intraocular injection of an aptamer that binds PDGF-B: A potential treatment for proliferative retinopathies, Journal of Cellular Physiology 2006, 207, 407-412
 
 
 
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