I have used C18 columns for standar oligonucleotides, but when it comes to dual-labeled oligos, as for instance a probe with FAM 5' and 3' BHQ1, it is not that straight forward.
I mean, when you run HPLC of that probe, you'll se a small peak for single labeled failures, and a good single peak next. But if you run that same sample in a CN column, that single peak will divide in some other peaks. We found that because we had problems in the aplication of the probe, and found later that it was due to poor separation in the probe. Using the CN column instead of the C18 solved the issue.
However, the CN columns we bought after late 2022 presented loss of resin when exposed to acetonitrile. Same oligos, same reagents, same procedure, same everything... and resin loss as soon as we connected the column to the HPLC and started ambienting the column. We tried 8 columns from 3 different brands, and in the end, one of those brands collected the columns back to study and confirmed that there is a problem with the CN columns.
And that it it. I need a good, really good columns to really purify dual-labeled probes, being a fluorophore and a non-fluorescent quencher. What columns do you use for analysis and purification of your standar and modified oligos and probes?
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