ANTISENSE OLIGONUCLEOTIDES CONTAINING AN INTERNAL, NON-NUCLEOTIDE-BASED LINKER PROMOTE SITE-SPECIFIC CLEAVAGE OF RNA

We have designed and synthesized a series of novel antisense methylpho sphonate oligonucleotide (MPO) cleaving agents that promote site-speci fic cleavage on a complementary RNA target. These MPOs contain a non-n ucleotide-based linking moiety near the middle of the sequence in plac e of one of the nucleotide bases. The region surrounding the unpaired base on the RNA strand (i.e. the one directly opposite the non-nucleot ide-linker) is sensitive to hydrolytic cleavage catalyzed by ethylened iamine hydrochloride. Furthermore, the regions of the RNA comprising h ydrogen bonded domains are resistant to cleavage compared with single- stranded RNA alone. Several catalytic moieties capable of supporting a cid/base hydrolysis were coupled to the non-nucleotide-based linker vi a simple aqueous coupling chemistries. When tethered to the MPO in thi s manner these moieties are shown to catalyze site-specific cleavage o n the RNA target without any additional catalyst.