Enhanced RNase H activity with methylphosphonodiester/phosphodiester chimeric antisense oligodeoxynucleotides

Chimeric oligodeoxynucleotides, comprised of internal phosphodiester and terminal methylphosphonodiester sections, possess many beneficial characteristics as antisense effectors. We have investigated the effects of progressive replacement of phosphodiester by methylphosphonodiester linkages on hybrid stability with complementary RNA and DNA. The melting temperatures (Tms) of oligodeoxynucleotide/RNA heteroduplexes were found to decrease dramatically with increasing methylphosphonate substitution. In contrast, a smaller reduction in Tm was observed for comparable DNA heteroduplexes. This disparate reduction in hybrid stability was found with both the G + C-rich human c-myc and A + T-rich human c-Ha-ras sequences used, suggesting that methylphosphonate oligodeoxynucleotide analogues generally hybridize with less affinity to RNA than DNA. RNase H assays were employed to determine if the noted decreases in Tm impaired the ability of chimeric oligodeoxynucleotides to direct the degradation of RNA. Contrary to expectation, increasing methylphosphonate substitution gave rise to increasing rates of RNA degradation for both the c-myc and c-Ha-ras series. The present results suggest that chimeric oligodeoxynucleotide analogues may be of considerable utility as antisense agents in systems where RNase H is thought to make a major contribution to inhibition of gene expression.