I'm running a conjugation reaction to label 20nt oligonucleotides with an NHS ester fluorophore. The oligos have a 3' amino group to anchor the ester.
I dissolved the NHS ester in 100% DMSO and the oligos in 0.1M sodium bicarbonate (pH 8.4), and added them together into a single tube for overnight reacting at 4˚C.
As soon as I added the NHS ester to the oligos, I noticed a bunch of small solid particles precipitate. Is this the DNA? Will this likely result in the reaction not proceeding or getting very little conjugated oligos? Any recommendations on dissolving this precipitate?
DNA probably is not soluble in DMSO, but whether it precipitates depends on how high the DMSO concentration is. The NHS ester of the fluorophore may not be soluble in the buffer, so you may be seeing that precipitate. Also, sodium bicarbonate is not soluble in DMSO, so that may also be precipitating.
If you can find the sulfosuccinimidy ester of your fluorophore, you can dissolve that in the buffer and avoid DMSO.
Dear Behnam Javidfar,
Kindly check the link attached herewith for the needful.
Article An easy and rapid DMSO-based method of extracting DNA from i...
I hope I have answered your question.
With Best Wishes,
Samir G. Pandya
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