Automated synthesis of branched oligodeoxynucleotide analogues using arabino-uridine as branching nucleotide

Abstract

Fully automated synthesis of branched oligodeoxynucleotides (branched ODNs) has been accomplished using 2′-O-levulinyl- or 5′-O-levulinyl-protected arabino-uridine derivatives as branching monomers. Selective removal of the levulinyl groups is accomplished using 0.5 M hydrazine hydrate in a pyridine–acetic acid–water (4∶3∶0.35, v/v/v) buffer. The affinity of the branched ODNs towards complementary DNA has been evaluated at 260 nm and 284 nm during thermal denaturing experiments. Enhanced affinity of a branched ODN compared with the corresponding linear reference is attributed to bimolecular triple helix formation.