Fig. 1
From: Hierarchical mechanism of amino acid sensing by the T-box riboswitch
Single-molecule analysis of the B. subtilis glyQS T-box riboswitch. a General mechanism of transcriptional regulation by the T-box riboswitch. b Sequence and secondary structure of the glyQS T-box (core) riboswitch construct used in this study with key regions highlighted in color. The ΔDTM construct lacks the distal sequences in the boxed region and is capped by a UUCG tetraloop sequence (black). The sequence of the mutually exclusive terminator hairpin is also shown. The positions of the major in vitro and in vivo pause sites observed are marked by gray and red arrows, respectively. c Ribbon and surface representation of an Oceanobacillus iheyensis-derived Stem-I:tRNA crystal structure (PDB ID: 4LCK). Red spheres depict the Cy5 label at position 46 in the tRNA variable loop. Mg2+ ions bound near the dinucleotide bulge and the Specifier sequence are depicted as yellow spheres. d Schematic of the prism-TIRF-based single-molecule FRET setup showing an immobilized T-box:tRNA complex. e Schematic of the single-molecule fluorescence experiment to measure the binding kinetics in the presence of free Cy5-tRNAGly
