Protocols For Oligonucleotide Conjugates: Synthesis And Analytical Techniques

Protecting Groups in Oligonucleotide Synthesis Etienne Sonveaux 1. Introduction A biopolymer is synthesized by assembling monomeric or oligomerit blocks. Each block features at least a nucleophilic and an electrophilic function, i.e., the a-amino and the carboxylic functions for peptides, the S-OH and the 3’-function (phosphate, phosphoramidite, or phosphonate), for n&leotides. The nucleophilic and electrophilic sites are linked together at the coupling step. Protection is a necessity. It guarantees the chemoselectivity of coupling and the solubility of synthons in organic solvents. There are two classes of protecting groups: persistent and transient. The persistent protections remain on the biopolymer during all the synthesis. They are cleaved at the very end. They cap the functions of the aglycone residue of nucleotides, or of the side chains of amino acids in peptide synthesis. They also cap the phosphate oxygen of oligonucleotides. The transient protections block the functions to be coupled at a given time of the synthesis. They are specifically cleaved before each coupling. When the synthesis is performed on a solid support, the first monomer of a hundred-mer has to survive to a hundred cleavages of a transient protecting group. The yield of successful removal is thus as limiting asthe coupling yield. This is also true for the final deprotection. If each monomeric unit is only 90% deprotected, the yield of a dimer of correct structure is g2%, of a trimer g3/10%, and of a n-mer 9V10”-2%. From Methods m Molecular Edited by. S