Is irrelevant cleavage the price of antisense efficacy?

Antisense oligonucleotides are useful reagents for the suppression of gene expression. Their mechanism of action in eukaryotic cells appears to depend heavily on the activity of RNase H, a ubiquitous enzyme that cleaves the m RNA strand of an RNA-DNA duplex. However, the stringency requirements of RN ase H are very low, and as little as a 5-base complementary region of oligo mer to target may be sufficient to elicit RNase H activity. This would resu lt in scission of nontargeted mRNAs, or what is known as "irrelevant cleava ge." One strategy to reduce RNase H competency that has been employed is mo dification of the oligonucleotide backbone, replacing phosphodiester linkag es with uncharged methylphosphonates, which are not RNase H competent. Anot her strategy involves replacement of deoxyribonucleic acid with 2'-O-alkylr ibonucleic acid. A third strategy, eliminating RNase H dependency entirely, requires activation of RNase P. The relative merits of these strategies wi ll be discussed in the context of selective inhibition of gene function. (C ) 2000 Elsevier Science Inc. All rights reserved.