The simplest approach to carboxy modification of oligos is to include the carboxylate NHS ester in the phosphoramidite to form the protected and activated carboxylate in situ. Both of our NHS ester carboxy-modifiers (5'-Carboxy-Modifier C10 and NHS-Carboxy-dT) use this approach. While the oligo is still fully protected and attached to the support, it can be reacted with amines on the synthesis column. The reaction is fast and specific while any precious excess amine can be recovered.
Deprotection with sodium hydroxide is a standard technique which can be used to deprotect oligos while hydrolyzing the carboxylate NHS ester to the carboxylate. Our Carboxy-dT also falls into this category in that the methyl ester protecting the carboxylate has to be hydrolyzed with sodium hydroxide.
An alternative approach to 5'-carboxy-modification is when the carboxylate is protected with a 2-chlorotrityl group. This protecting group is simply removed using the standard deblock cycle to generate a free carboxyl group on an otherwise fully protected oligonucleotide.