Selected article for: "apical loop and capsid protein gene"
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_21
    Snippet: Our secondary structure determination of DENV-MINI RNA was furthermore validated by single-strandspecific Pb 2+ ion-induced hydrolysis (23) (Supplementary Figure S2) . The observed cleavage pattern correlated with SHAPE-predicted single-stranded regions. The 5 0 -UTR regions highly sensitive to Pb 2+ cleavage included the vicinity of SLA internal loop (C14-G15), SLA SSL (U48-A49) and the polyU tract (U71-U80). The SLA TL (C30-U34), as well as the.....
    Document: Our secondary structure determination of DENV-MINI RNA was furthermore validated by single-strandspecific Pb 2+ ion-induced hydrolysis (23) (Supplementary Figure S2) . The observed cleavage pattern correlated with SHAPE-predicted single-stranded regions. The 5 0 -UTR regions highly sensitive to Pb 2+ cleavage included the vicinity of SLA internal loop (C14-G15), SLA SSL (U48-A49) and the polyU tract (U71-U80). The SLA TL (C30-U34), as well as the apical loop of cHP (A121-A127), was hydrolyzed weakly, agreeing with previous studies showing that in most cases, bulges and internal loops were more readily cleaved with Pb 2+ ions than apical loops (23) . The 5 0 -3 0 CS (U134-G144) and dsUAR (A88-G96) were resistant to cleavage, as they were predicted to be double-stranded. In addition, the two hairpins formed within the sequence of the 5 0 -end of the capsid protein gene (A152-G153 and A174-C175) were moderately sensitive to hydrolysis, whereas the following single-stranded region was hydrolyzed readily (C199-A205).

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