Author: Sztuba-Solinska, Joanna; Teramoto, Tadahisa; Rausch, Jason W.; Shapiro, Bruce A.; Padmanabhan, Radhakrishnan; Le Grice, Stuart F. J.
Title: Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome Document date: 2013_3_26
ID: 1pbd4maf_29
Snippet: SHAPE analysis of PK2 Flip DENV-MINI mutant RNA indicated major reactivity changes within the 5 0 DB structure ( Figure 4 and Supplementary Figures S4 and S5) . The apical loop of the TL1-containing hairpin was rendered NMIA-sensitive with median reactivities for G470-U474 of 0.55, whereas the corresponding values for WT DENV-MINI were 0.05. The apex of the rightmost hairpin exhibited lower reactivity for residues G502-A506. In addition, the 'fli.....
Document: SHAPE analysis of PK2 Flip DENV-MINI mutant RNA indicated major reactivity changes within the 5 0 DB structure ( Figure 4 and Supplementary Figures S4 and S5) . The apical loop of the TL1-containing hairpin was rendered NMIA-sensitive with median reactivities for G470-U474 of 0.55, whereas the corresponding values for WT DENV-MINI were 0.05. The apex of the rightmost hairpin exhibited lower reactivity for residues G502-A506. In addition, the 'flipping' mutation of PK2 increased its susceptibility to acylation (C526-G530) validating disrupted TL1/PK2 base pairing. Other regions did not exhibit secondary structure rearrangements. Thus, data of Figure 4 and all subsequent illustrations representing RNA structures of DENV-MINI mutants present only the affected RNA motifs.
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