Mechanisms of the inhibition of reverse transcription by unmodified and modified antisense oligonucleotides

We have demonstrated that the synthetic oligonucleotides, either unmodified or phosphorothioates, prevent cDNA synthesis by the AMV or HIV reverse transcriptases. The RNA was truncated at the antisense oligonucleotide-RNA duplex during the reverse transcription. Th blockage involves the degradation of the RNA fragment bound to the antisense oligonucleotide by the reverse transcriptase associated RNase H activity. However, in the case of phosphorothioate oligomer, the production of cDNA would be inhibited by a hybrid formed between the AMV RT and phosphorothioate oligomer than arrested elongation of the cDNA strands, whereas arrest of a growing cDNA strand by HIV RT can be blocked by an oligonucleotide complementary to a region downstream from the primer.