Selected article for: "alternative conformation and locally fold"
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_35
    Snippet: Further alternations were noted within the 3 0 -UTR, where the 3 0 SL became a part of extended hairpin (A641-U719) proceeded by short hairpin (sHP) (C627-G640) containing moderately reactive GNn/RA hexaloop ( Figure 5 and Supplementary Figures S7 and S8 ) (23, 38) . The sHP was shown previously to fold locally in the linear conformation of the DENV RNA, governing the balance between alternative DENV RNA structures (39) . The 3 0 UAR, which no l.....
    Document: Further alternations were noted within the 3 0 -UTR, where the 3 0 SL became a part of extended hairpin (A641-U719) proceeded by short hairpin (sHP) (C627-G640) containing moderately reactive GNn/RA hexaloop ( Figure 5 and Supplementary Figures S7 and S8 ) (23, 38) . The sHP was shown previously to fold locally in the linear conformation of the DENV RNA, governing the balance between alternative DENV RNA structures (39) . The 3 0 UAR, which no longer interacts with the 5 0 UAR, now formed both the rightmost side of the sHP and the leftmost side of the 3 0 SL (C638-U650), whereas the 3 0 DAR became a leftmost part of the sHP (C625-G630). As the 'flipping' PK1 mutation affects the secondary structure of neither the 3 0 nor the 5 0 DB, this result likely ruled out the existence of the previously proposed TL2/PK1 pseudoknot interaction (13, 16) . The VR region was not affected (C232-U448), with the exception of a short helical region (A190-U194 and A443-U448) that in DENV-MINI RNA linked both DBs and VR domains, and now was predicted to be single-stranded and NMIA reactive.

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