Overlay of SHAPE reactivities onto a secondary structure model portraying a 76 nt mlf-2-dG aptamer RNA. The color code serves to distinguish reactive (and thus unconstrained) nucleotides in B–E. An absence of markings denotes unanalyzable nucleotides. The lightest gray denotes nucleotides with the highest SHAPE reactivity, while the darkest gray indicates the lowest reactivity. (A) Secondary structure of 2′dG sensing riboswitch from M. florum in the ligand-bound state. P1 helix is considered a regulatory helix. Crystal structure indicates G41 and G42 are forming a long-range tertiary interaction (or PK) with C64 and C65. C76 is the binding site for 2′dG. (B) 0 mM Mg2+ without 2′-dG; (C) 0 mM Mg2+ with 20 µM 2′-dG; (D) 5 mM without 2′-dG; and (E) 5 mM with 20 µM 2′-dG.
