The presence of modifications obviously increases the complexity of the oligo synthesis. The synthesis of oligonucleotides containing modification in bases, sugars, fluorophores, linkers, etc., more and more is becoming the norm as researchers explore the variety available to them. Requests for oligonucleotides containing several modifications has become quite prevalent and great care has to be taken during synthesis, deprotection and purification to ensure that the oligo is isolated in pure form. Now that researchers are becoming interested in modified RNA oligos, the level of complexity will increase probably by an order of magnitude.
A wide range of products is available for conjugation using click chemistry
Glen Research offers a variety of products for the in situ synthesis of DNA analogs.
Large scale oligonucleotide synthesis is particularly challenging for a variety of reasons related obviously to synthesis scale. Novel high loading supports have had to be developed.
It has often been noted that longer the oligonucleotide, the more difficult it is to isolate a pure, biologically active product. if the long oligo synthesis has been carried out with the best efficiency possible, purification can be simply accomplished by DMT-ON purification.
Oligonucleotide synthesis is routinely carried out from the 3' to the 5' terminus for no other reason than the ease of synthesis of the monomer units. Glen Research offers phosphoramidites and supports for backwards oligonucleotide synthesis.
An alternative protecting scheme for the normal CE phosphoramidites should allow UltraMILD deprotection and should not react with a wider variety of tags and labels.