Synthesis and properties of new antisense oligodeoxynucleotides containing benzylphosphonate linkages

Synthetic antisense oligonucleotides are widely used as inhibitors of gene expression in cultured cells and have been proposed as potential therapeutic agents. In recent years, a great deal of effort has been directed toward the synthesis of analogs with an altered phosphodiester linkage to improve the stability of duplex formation, to improve the cellular uptake, and to decrease the rate of degradation of oligonucleotides by nucleases that cleave the phosphodiester linkage. We report here on the synthesis of oligonucleotides containing benzylphosphonate linkages. For this purpose, we prepared four fully protected benzylamidites and incorporated them into oligonucleotides using an automated DNA synthesizer. Compared with unmodified oligonucleotides and methylphosphonates, the benzylphosphonates are more stable against nucleases and exhibit a higher lipophilicity. Incorporation of benzylphosphonate linkages only slightly weakens the thermal stability of the duplex. The 18-mer oligonucleotide 5' A*T*GTT*GCCC*CATC*ATA*AA 3' with seven benzylphosphonate linkages (*) directed against the start of the pre-S-region of duck hepatitis B virus resulted in a 40% inhibition of viral replication at a concentration of 1.5 mumol.