A primary amino function can be incorporated during oligonucleotide synthesis at either the 5’or 3′ end or internally using an amino-modified dA, dC, dG, or dT reagent.
In order to successfully conjugate haptens or fluorophores to the primary amino group, it is necessary to ensure that the oligonucleotide has sodium as the counter-ion rather than ammonium, since the latter may interfere with the conjugation reaction. Oligonucleotides purchased from Oligos will either be in the sodium or ammonium form, depending on the type of purification. Gel filtration (GF) Grade and Reverse Phase (RP) HPLC Grade oligonucleotides will be in the ammonium salt form. Anion Exchange (AE) HPLC Grade and PAGE Grade oligonucleotides will be in the sodium salt form.
If an oligonucleotide is the ammonium salt form, it can be exchanged to the sodium salt form quite simply. The lyophilized oligonucleotide should be resuspended in a small volume of 0.2 M NaCl. The excess salt can then be removed by gel filtration on Sephadex G25 or by ethanol precipitation of the oligonucleotide.