There is dedicated de-salting kits , or at least PCR cleanup kits. But 10 bp is indeed small. Can you ask a company like Kilobaser how they purify their primers and RNAs? It's their daily business.

Are those valuable samples? Do you have enough to try things?

You could try running them in an agarose gel electrophoresis (preparative gel), cut out the "band" containing the DNA, put the agarose containing the DNA into a cut 1000 uL filter tip and centrifuge it into an eppendorf tube. This quick and dirty method should get rid of salts. The agarose stays in the filter of a filter tip, the liquid that comes through contains the DNA. in the TAE buffer.

Thanks! I am trying ethanol precipitation again, if that doesn't work I will try the agarose gel method you suggested.

Georgia Malcolm

To remove salts from a small sample of short oligonucleotides at the milligram scale, you can use one of the following methods:

1. Ethanol Precipitation:

• Add 2.5–3 volumes of cold ethanol and 0.1 volume of 3M sodium acetate (pH 5.2) to your oligonucleotide solution.
• Mix well and incubate at -20°C for 30 minutes to overnight.
• Centrifuge at high speed (e.g., 12,000–15,000 g) for 15–20 minutes to pellet the oligonucleotides.
• Wash the pellet with 70% ethanol, air-dry, and resuspend in water or buffer.

2. Desalting Columns:

• Use commercially available desalting columns (e.g., Sephadex G-25 or Glen-Pak cartridges).
• Load your oligonucleotide solution onto the column and follow the manufacturer's protocol to elute the desalted oligonucleotides.

3. Dialysis:

• Use a dialysis membrane with a molecular weight cutoff (MWCO) suitable for your oligonucleotides.
• Place the sample in the membrane and dialyze against a large volume of water or buffer to remove salts.

4. Solid-Phase Extraction (SPE):

• Use SPE cartridges designed for oligonucleotide purification.
• Load the sample onto the cartridge, wash with water or a low-salt buffer, and elute the purified oligonucleotides.

Tips to Avoid Issues:

• Ensure the oligonucleotides are not degraded during the process by working quickly and keeping the sample cold.
• If using ethanol precipitation, avoid over-drying the pellet, as it can be difficult to resuspend.

Let me know if it works

Thanks chatGPT

your welcome

Precipitation with 3x volume EtOH + 1 ul of 20 ug/ul GLYCOGEN (no salt). Extensive washing with 70% EtOH at room temperature.

HPLC (ammonium formate) would be your best option in my opinion. Then you can lyophilize your pure desalted sample. What salts do you want to remove exactly?

Andreas Stürmer at LSB/LNBio lab, we would synthesize these oligos in DMT-ON mode, and purify them with a reverse phase cartridge (like MicroPure II, QSP, Glen Pak, Oasis...).

Georgia Malcolm , as your oligos are already synthesized, probably DMT-OFF, the larger oligos (>10) can be desalted in sephadex G25 columns. As for the smaller, I'd do HPLC. If HPLC it is not a possibility, you can try to use a desalting column, but collect the end of the elution volume drop by drop, and analyse each drop (UV-VIS) to find the fractions with good enought DO at 260 and low enought salts (230).

The agarose gel tip (Andreas's) is one of my favorites quick dirty methods, but in your case, I guess it wouldn't do the job, since TAE has triethylamine, and one should never put this nasty salt inside the LCMS.

Please come back to tell us what you did, and if it worked!