SHAPE-restrained secondary structure of free STMV RNA with a tRNA-like fold at the 3′ end.

<p>This alternate model of the STMV RNA was obtained by combining the SHAPE-restrained secondary structure predicted separately for nucleotides 1–727 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054384#pone-0054384-g002" target="_blank">Figure 2</a>) with the Gultyaev <i>et al.</i> prediction <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054384#pone.0054384-Gultyaev1" target="_blank">[10]</a> for nucleotides 728–1058 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054384#pone-0054384-g005" target="_blank">Figure 5</a>). Nucleotides are colored according to their SHAPE reactivity (see scale). The extended central domain (nucleotides 64–720) is identical to that of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054384#pone-0054384-g002" target="_blank">Figure 2</a>.