If you’re purifying therapeutic oligos you’ll need to clean the desalting resins afterwards in a far higher concentration of NaOH than the usual desalting resins will tolerate. This is how to solve the problem.
The purity requirements for therapeutic oligos are demanding and are often achieved using high resolution anion exchange chromatography. Oligos are then released in order of increasing length by raising salt concentration, and the salt can be removed using size exclusion chromatography (SEC).
Stringent purity requirements demand subsequent cleaning of the resins under harsh conditions. Commonly used desalting resins use dextran and only tolerate up to 0.2 M NaOH whereas cleaning-in-place (CIP) is preferentially performed with 1 M NaOH.
Pure agarose-based resins, on the other hand, with no dextran attached are alkali-stable in 1 M NaOH so if you use these instead, then you can achieve the required standard of CIP.
You can find many more details in our whitepaper where we’ve used a pure agarose-based SEC resin with a cut-off of 150 kDa to demonstrate desalting of two different oligos; a 20-nucleotide ssDNA (6.6 kDa) and a 45-nucleotide RNA (14.7 kDa).