Properties of base-pairing in the stem region of hairpin antisense oligonucleotides containing 2'-methoxynucleosides.

We have designed a new type of antisense oligodeoxyribonucleotide. These oligonucleotides are able to form hairpin loop structures at the 3'-ends. The stability to nuclease degradation was observed by incubation of these hairpin oligonucleotides with snake venom phosphodiesterase, DNA polymerase, and fetal bovine serum. Of particular interest is the hairpin antisense oligonucleotide containing 2'-methoxynucleosides with base-pairing in the stem region at the 3'-end, which has increased nuclease resistance.