Our most popular 5'-amino-modifier is the C6 version, available with a monomethoxytrityl (MMT) or a trifluoroacetyl (TFA) protecting group. Which is appropriate for what set of circumstances?
If you wish to purify the 5'-amino-modified oligonucleotide, the MMT group is preferable since the oligo can be easily purified by reverse phase techniques. The MMT group is then removed with aqueous acid. Also, the MMT group can be removed by extended deblocking on the synthesizer, allowing a solid-phase conjugation of a tag containing an activated carboxylic acid. However, the conjugate must be stable to the subsequent conditions of cleavage and deprotection.
The base-labile TFA group is preferred if the amino-modified oligo is not going to be purified prior to the conjugation reaction. It is logical to assume that only the amino-modified oligo is full-length and, therefore, that the conjugation reaction will select for only the full-length oligo.