The chemical synthesis of DNA using the phosphoramidite method proceeds in a 3’ to 5’ direction principally as a consequence of the use of building blocks activated as 3’-O-phosphoramidites. The primary 5’-OH group is significantly more reactive than the secondary 3’-OH (or 2’-OH) group, making it straightforward to protect with the DMTr group leaving the 3’-OH available to form the phosphoramidite. In contrast, ‘reverse’ oligonucleotide synthesis (i.e. in a 5’ to 3’ direction) has not been utilised to nearly the same extent. Nevertheless, there are several classical applications of this chemistry such as parallel-stranded oligonucleotides (hairpins) and nuclease resistant lilnkages. Newer applications such as DNA-chip technology are also coming to the fore.
Link Technologies offers a full set of reverse phosphoramidites and solid supports. These have standard heterocyclic base protection groups and are used with conventional automated synthesis protocols.