Fig. 4: Structural probing of ligand-induced conformational changes. | Nature Communications

Fig. 4: Structural probing of ligand-induced conformational changes.

From: Rational development of FMN-based orthogonal riboswitch that functions in response to specific non-cognate ligand

Fig. 4

a PAGE analysis of in-line probing assays with 3’ Cy3-labeled Aptamer-LP and Aptamer-M15 RNA in the absence or presence of FMN and DHEF at a concentration of 10 μM. OH and T1 designate RNAs that have been partially digested with alkali or RNase T1, respectively (left panel). A schematic representation of a T-loop-like motif (right panel). b, c In-line probing gel images with lanes loaded with aptamer RNAs subjected to various concentrations of ligands with Aptamer LP and Aptamer M15, respectively, no reaction (NR). d, e The plot of the fraction of RNA cleaved versus the logarithm of the molar concentration of ligand of Aptamer LP with FMN and Aptamer M15 with DHEF, respectively. Fraction-cleaved values were estimated based on the extent of band intensity changes at site 1 in (b, c). Data are shown as mean  ±  standard deviation (SD) (n = 3 replicates). Source Data are provided as a Source Data file.

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