Amino Allyl can be used to incorporate an active primary amino group onto the 5'-end of an oligonucleotide. This can then be conjugated to a NHS Activated ligand. The amino group then becomes internal to the 5' end ligand. The amino group is separated from the 5'-end nucleotide base by a 4-carbon spacer arm to reduce steric interaction between the amino group and the oligo.
The presence of the primary amino group allows the user to label the oligo with a variety of different ligands for affinity, reporter or protein moieties (as NHS esters or isothiocyanates), depending on the application. Examples include biotin, digoxigenin, and fluorescent dyes or quenchers, magnetic beads and enzymes (for example, alkaline phosphatase).
The primary amine labelled oligos can also be conjugated to carboxyl functional groups usually for solid supports applications using EDC mediated reaction as shown in the figure below.