Fig. 2

Structural probing of the 3′ UTR of WYMV RNA1 in the presence or absence of the NIb protein. a In-line probing of the WYMV RNA1 3′ UTR in the presence or absence of the NIb protein. L, ladder generated from treatment with NaOH, which cleaves at arbitrary nucleotides; T1, ladder generated from fragment denaturation and treatment with RNase T1, which cleaves at guanylates. InL: in-line cleavage products, which cleave bases at single-strand status. Base numbering is shown on the left hand side of the panel. Red and green solid triangles indicate strongly and weakly marked cleavage sites in the RNA1 3′ UTR, respectively. Green hollow triangles denote the weaker cleavage sites within the RNA1 3′ UTR in the presence of the NIb protein versus its absence. b RNA structure of the WYMV RNA1 3′ UTR in the presence or absence of the NIb protein. Black, green, and red nucleotides, respectively, indicate none or inapparent, marked, and strongly marked cleavage based on the in-line probing pattern. Green and red nucleotides indicate single-strand characteristics. Green hollow triangles denote the weaker cleavage sites within the RNA1 3′ UTR in the presence of the NIb protein versus its absence. H1, hairpin 1; H2, hairpin 2; H3, hairpin 3; H4, hairpin 4; H5, hairpin 5