In nature, DNA is formed in the 5’–3’ direction. Early efforts in DNA synthesis were based on biological synthesis, and thus the first synthetic oligonucleotides were produced in the 5’–3’ direction. Har Gobind Khorana, a University of Wisconsin biochemist who won the 1968 Nobel Prize in Physiology or Medicine, led the group that developed the early 5’–3’ synthesis technique using a polystyrene solid support and three different protecting groups. Though this technique led to important breakthroughs, it was eventually replaced in the 1980s by much a more efficient synthesis method using phosphoramidite monomers (phosphoramidites are nucleotides with protection groups which are removed after synthesis). The growing oligonucleotide is connected to the solid support, a controlled pore glass bead via the 3’ carbon, and thus synthesis proceeds in the 3’–5’ direction.
Beaucage SL and Caruthers MH (1981) Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Letters 22: 1859–1862.
Author: Martin Whitman is a Technical Support Representative at IDT.