Switch-MaP models of the SreA aptamer and full-length SreA riboswitch. (A) Switch-MaP SHAPE-informed secondary structures of the SreA aptamer (left) and full-length SreA riboswitch (right). P1–4 helices of the expected four-way junction are labeled. In the full-length construct (right), the expression platform is modeled with a terminator helix. (B) Similar pseudo-free energy alternative models of SreA full-length RNA. (C) Pairing probability arc plots of aptamer (top) and riboswitch (bottom) generated from Switch-MaP. The riboswitch plot is inverted and manually aligned to the aptamer plot. Normalized SHAPE reactivities are also plotted as colored bars for every nucleotide. Two 3′ terminal U nucleotides of the riboswitch are grayed out due to high background mutation rates (common during MaP of homopolymeric regions like this one).
