Fig. 2: Design and characterization of a TNT-sensing riboswitch.
From: An autonomous microbial sensor enables long-term detection of TNT explosive in natural soil
A The Riboswitch Calculator model predicted mRNA structures of the RS14 riboswitch before and after induction with 35 µM of TNT. The “OFF” state (state 1) shows the mRNA structure and translation initiation rate calculated when TNT is unbound (rTL,OFF). The “ON” state (state 4) shows the change in mRNA structure and translation rate when both TNT is fully bound to its aptamer and the ribosome is bound to the mRNA (rTL,35mM). Nucleotides are color-coded based on their interactions, (light blue) the TNT aptamer sequence, (green) the Shine-Dalgarno sequence (SD), (dark blue) the last 9 nucleotides of the 16S ribosomal RNA, and (pink) the start codon for mRFP1. The orange bar is the ribosomal footprint for initiation. For riboswitch characterizations, we added a strong B. subtilis promoter upstream to measure (B) the mRFP1 fluorescence levels and (C) the growth rates (doubling time in minutes) of the TNT-RS14 riboswitch strain (purple dots) and mRFP1-only control (yellow squares) in response to varied concentrations of TNT, up to 35 µM. Data points and error bars are the mean and standard deviation of N = 3 biological replicates. RFU is a relative fluorescence unit.
