Synthesis of 2 '-modified oligodeoxynucleotides via on-column conjugation

Oligodeoxynucleotides modified at the 2'-position of 2'-amino-2'-deoxyuridi ne or uridine were prepared in high yield and purity using phosphoramidites 2 and 3, respectively. Oligodeoxynucleotide conjugates were prepared on th e solid-phase synthesis support following selective unmasking of the nucleo phile incorporated in these phosphoramidites. Synthesis of oligodeoxynucleo tides modified at the 2'-position of an internal nucleotide provides molecu les that are complementary to those previously prepared via a similar appro ach using CS-substituted pyrimidines. The efficiency of functionalization o f the 2'-O-alkylamino-uridine derived from 3 in a protected oligodeoxynucle otide was less susceptible to steric hindrance than the 2'-amino-2'-deoxyur idine in the same polymeric substrate. However, the greater reactivity of t he 2'-O-alkylamine containing nucleotide gave rise to undesired acetamide f ormation resulting from nucleophilic attack on the 5'-terminal acetate in c apped failure sequences. This problem was overcome by using 2,2,2-trimethyl acetyl anhydride as a capping agent during the automated synthesis cycles. Finally, the efficiency of the photochemical unmasking of the support bound alkylamine on a 1 mu mole scale was improved by using two 20 min photolysi s cycles, coupled with removing reaction byproducts between cycles.