Figure 2 | Scientific Reports

Figure 2

From: A 3′-end structure in RNA2 of a crinivirus is essential for viral RNA synthesis and contributes to replication-associated translation activity

Figure 2

SHAPE analysis of LCV RNAs 1 and 2.

Secondary structure models of the 3′ terminal region in: (a) wild-type (WT) LCV RNA1, (b) WT LCV RNA2, (c) ΔSL1 (LCV RNA2 with stem-loop [SL]1 deleted) and (d) ΔSL2 (LCV RNA2 with SL2 deleted). RNA secondary structures were generated from the RNAstructure software, with benzoyl cyanide (BzCN) reactivity incorporated as pseudo-free energy constraints. Each colored nucleotide corresponds to the level of BzCN reactivity for that particular nucleotide, with black, yellow and red representing unreactive (0–0.4), moderately reactive (0.4–0.85) and highly reactive (>0.85), respectively. Four digit numbers placed next to the sequence represent the positions of the nts in the LCV genome. “SL1” and “SL2” denote the right and the left apical stem-loops, respectively, of the Y-shape structure (YSS) in WT LCV RNAs 1 and 2. “S3” denotes the basal, closing stem of the YSS. The stop codon (UAG) encoding P4.8 in RNA2 is labeled “Stop”. Gray and blue nucleotides correspond to nucleotides for which information of BzCN reactivity was unavailable and nucleotides of the primer-binding site, respectively. The engineered 3′ linkers are as indicated.

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