A general strategy to inhibiting viral -1 frameshifting based on upstream attenuation duplex formation

Hu, Hao-Teng; Cho, Che-Pei; Lin, Ya-Hui; Chang, Kung-Yao

One possible explanation of the observed opposite effects in attenuation activity modulation between the two antisense oligonucleotides is that the accessibility for trans-duplex formation is different between the two sides of the refolding hairpin stem in the presence of a nearby ribosome. Alternatively, the opposite effects may have been caused by the difference in spacing from the slippery site between the two antisense-mediated RNA-DNA duplexes, given that proximity plays an important role in the attenuation efficiency of a cis-formed attenuator hairpin (29) . Consistent with the later explanation, addition of an antisense DNA (restore DNA), with sequences complementary to the 3 -stem of an impaired attenuator hairpin (6BPGC5 WT) (Supplementary Figure S1B ), led to enhanced attenuation of −1 PRF efficiency of a reporter (6BPGC5 WT-SARSPK1) containing 6BPGC5 -WT in a dose-dependent manner ( Figure 1C and D). As the impaired attenuator hairpin shares the same 3 -stem sequences to those of 6BPGC, this result also rules out the accessibility issue. Thus, these findings indicate that an upstream duplex needs to be proximal to the slippery site for efficient −1 PRF attenuation and suggest that the duplex in a proximal upstream hairpin stem is the functional unit responsible for −1 frameshifting attenuation.