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.

We have also provided a 3D model of the TL1/PK2 interaction using the recently reported program RNAComposer (40) . As noted in Figure 7 , the hybridized 5 0 -3 0 termini and the TL1/PK2 pseudoknot are located on opposite ends of the DENV-MINI RNA, suggesting an independent structural/regulatory character. Also, the fact that hybridization of LNA/DNA chimeras to either TL1 or PK2 failed to induce extensive structural changes within the interacting 5 0 -3 0 termini (Supplementary Figure S3) suggests the TL1/PK2 pseudoknot might indeed function as an autonomous element. In addition, TL2 of the 3 0 DB is spatially separated from other structural domains and linked to adjacent segments of the DENV-MINI RNA by relatively long single-stranded regions. It is possible that a second TL2/PK1 pseudoknot could be formed by rotation of the 3 0 DB, thereby bringing TL2 into proximity with PK1. However, such a rearrangement would also entail partial dissolution of the hybridized 5 0 -3 0 termini and perhaps even the TL1/PK2 interaction, such as might occur in the presence of viral proteins and/or host factors, or in the event the 5 0 terminal portion of the genome has been removed by ribonucleases (10) or is sequestered during translation. A similar hypothesis was proposed based on MPGAfold-directed secondary structure prediction of DENV MINI RNA, which indicated differences in the folding behavior of the two DBs (8) . In the lack of the 5 0 -3 0 communication, it was proposed that TL2 could be available to bind PK1 in the 3 0 DB to form the putative TL2/PK1 pseudoknot (8) .