Synthesis and triple helix formation by alternate strand recognition of oligonucleotides containing 3′-3′ phosphodiester bonds

ODNs containing a 3'-3' phosphodiester junction have been conveniently synthesized through a solid phase procedure involving only 3'-phosphoramidite nucleosides, starting from a modified support linking the first nucleotide through the base. Thermal denaturation studies showed that 16-mers with this inversion of polarity cooperatively bound to 5'-(purine)(m)(pyrimidine)(n)-3'-type duplexes by specific recognition of the oligopurine domains alternately on the two DNA strands. The nature of the 3'-3' junction and nearest neighbors affected the stability of the resulting triplexes.