The introduction of a primary Amine (NH2) at the 5’-position is used to functionalize the corresponding terminus of the nucleotide for conjugation with e.g. an activated NHS ester or isothiocyanate fluorescent label. Several spacers are available (C3; C6 and C12), all of them are hydrophobic. The available lengths of the spacers are 3, 6, or 12 methylene (CH2) groups between the terminal phosphate and the amino “moiety”.
The 3’-NH2 modification allows the prevention of the 3’>5’ exonuclease degradation of oligonucleotides in biological fluids such as cell culture medium.
C6-dT, dU, Propargyl-dU and Propargylcaproyl-dU amino modifiers are used in post-coupling reactions, for instance, for modifying oligonucleotides that will be printed onto microarrays.
dR-NH2 modification (deoxyribose-NH2) forms abasic sites in the oligonucleotide. It provides the possibility to add more than one label anywhere in the sequence or on either terminus after post-coupling reactions between the Amine group and an activated label. The label is linked to the deoxyribose via a 6-carbon atom spacer which reduces steric hindrance.