Postsynthetic conjugation of protected oligonucleotides containing 3′-alkylamines

The expansion of a highly efficient, convergent method for synthesizing 3'-oligonucleotide conjugates is described. 3'-Oligonucleotide conjugates containing amide or urea linkages between the oligonucleotide portion and the conjugated species were obtained by reacting protected oligonucleotides containing 3'-alkylamines in aprotic organic solvents with carboxylic acid and isocyanate substrates, respectively. The protected oligonucleotides are obtained via standard automated synthesis on a photolabile solid-phase synthesis support. Excellent yields (83-100%) of bioconjugates were obtained using carboxylic acids and aryl isocyanates with as few as 5 molar equivalents of conjugation reagents relative to protected oligonucleotide. More moderate yields were obtained using alkyl isocyanates as substrates (70-88%). In addition, this method has proven to be useful for synthesizing complementary oligonucleotide-peptide conjugates from a single oligonucleotide, in which the polarity of the peptide with respect to the oligonucleotide is determined by the bond-forming process employed.