Fig. 1: smFRET analysis of the Bacillus cereus crcB fluoride riboswitch.
From: An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch
a Structure of the fluoride riboswitch in the absence and presence of fluoride. The circled nucleotides show the 3′ ends of the constructs used for smFRET. The positions of donor and acceptor are shown by green and red ovals labeled D and A, respectively. b Experimental smFRET setup. The RNA is immobilized through a biotinylated LNA capture probe. c The different lengths of RNA used for smFRET. The orange sequence at the 3′ end of the riboswitch is complementary to the CP LNA (or bubble DNA, in experiments performed with RNAP as shown in Fig. 4). The red and green segments are a guide to the eye to compare the riboswitch structure in the absence and presence of F-, analogous to the color scheme used in panel a. d Representative smFRET traces for RNA64 in the absence of Mg2+ and F- (left), in the presence of only Mg2+ (middle), and in the presence of both Mg2+ and F- (right). e Example of an RNA64 smFRET trace that transitions between all three FRET states (observed in 5–10% of traces in the presence of Mg2+ only and Mg2+ plus F-). The HMM fit is shown in red above the trace and the FRET distribution of the trace, fitted with three Gaussian peaks, is shown on the right.
