I want to couple 2 small molecules, one is a DNA oligo with an amine group and the other one a small molecule with with a carboxyl group.
I found protocols for EDC (https://en.wikipedia.org/wiki/1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide) coupling of amines and carboxylic acids, but they always refer to proteins (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017125_EDC_UG.pdf). My molecules are stable in a wide range of pH, what buffer conditions would work best for my coupling reaction?
The protocol you mentioned is really not suitable for oligonucleotides labeling. You may to use method that we have used for labeling of 5'-aminohexyl-functionalized (2'-5')-triadenylate (https://doi.org/10.1016/j.tetlet.2020.152227).
Please pay attention to solubility of small molecule active ester and oligonucleotide in solvent on conjugation step. We have needed to use high content of DMF (DMF:sodium bicarbonate buffer–2:1) since our label has low solubility in water. But we were able to use high content of DMF since trinucleotides are soluble in such water-organic mixture. Longer oligonucleotides may precipitate even at lower DMF content but mostly they are soluble in buffers with 40% DMF content. Another method of increasing water solubility of hydrophobic compounds is to use sulfo-N-hydroxysuccinimide or sodium 2,3,5,6-Tetrafluoro-4-hydroxybenzenesulfonate instead of HONHS or HOBt. Of course, EDC can be used instead of DCC. Also, conjugate purification may be performed by denaturing polyacrylamide gel electrophoresis or by RP-HPLC.
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