Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome

Sztuba-Solinska, Joanna; Teramoto, Tadahisa; Rausch, Jason W.; Shapiro, Bruce A.; Padmanabhan, Radhakrishnan; Le Grice, Stuart F. J.

The model shows close association of the 5 0 -and 3 0 -UTRs ( Figure 7A and B), in agreement with previous studies, suggesting that efficient transfer of RNA-dependent RNA-polymerase from the 5 0 SLA to the 3 0 SL motif is essential for initiation of (À) strand RNA synthesis (12, 17) . In addition, positioning of the hybridized 5 0 -3 0 termini and the TL1/PK2 pseudoknot on opposite termini of the DENV-MINI RNA is consistent with the two domains playing independent structural/regulatory roles in DENV replication. TL2 of the 3 0 DB is likewise spatially separated from other structural motifs, suggesting a functional role for TL2 that does not involve interactions with other RNA elements in the context. The 3 0 DB itself is linked to adjacent segments of the DENV-MINI RNA by relatively long, presumably flexible segments of single-stranded RNA. It is conceivable that a second TL2/PK1 pseudoknot could be formed by rotation of the 3 0 DB motif, thereby bringing TL2 into proximity with PK1. However, such a rearrangement would also require partial dissolution of the hybridized 5 0 -3 0 termini. It is important to note, however, that there is no evidence that base pairing between TL2 and PK1 occurs in the DENV-MINI RNA in vitro. In general, although caution must be exercised in interpreting these 3D structural data, the model presented here serves to provide plausible insights into how RNA substructures may interact during DENV replication.