[Synthesis and properties of mixed ribodeoxyribooligonucleotide duplexes containing an internucleotide trisubstituted...

Fragments of double-stranded RNAs and mixed double-stranded ribo/deoxyribooligonucleotides containing an internucleotide trisubstituted pyrophosphate bond in a predetermined position of the sugar-phosphate backbone were synthesized. The modified internucleotide bond was created between synthetic oligonucleotides by chemical ligation with carbodiimide. The chemical ligation conditions were optimized for a series of duplexes that differed in the content and mutual arrangement of ribo- and deoxyribonucleotide blocks. The yield of oligonucleotides containing the trisubstituted internucleotide pyrophosphate bond was 90% in an all-deoxy duplex and 15-68% in ribooligonucleotide-containing duplexes. The modified duplexes thus obtained are relatively stable in an aqueous solution at pH 5.5-7.5, whereas the modified internucleotide bond is cleaved by amines to form phosphamide derivatives of the corresponding oligonucleotides. Automated solid-phase synthesis of oligonucleotide 3'-ethylphosphates is described.