Fig. 2: Aptamers and ligands used in this study. | Nature Communications

Fig. 2: Aptamers and ligands used in this study.

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

Fig. 2

a Chemical structures of synthetic and natural analogs of FMN used in this study, wherein the black part represents the preserved moiety and the red part denotes the modified ribityl chain. b Sequence alignment of aptamers from Lactobacillus plantarum (LP), Pseudomonas fluorescens (PF), and Fusobacterium nucleatum (FN), the color code is given as per the structure of FMN aptamer in Fig. 1a. c The predicted secondary structure of aptamer LP. d, e Relative fluorescence intensity of FMN and DHEF after the addition of Aptamer LP (0-5 μM) and Aptamer M15 (0-5 μM), respectively (n = 3 replicates). f The predicted secondary structure of aptamer PF. The nucleotides involved in stacking interactions are highlighted in blue, and the position of mutated nucleotides is shown in red (Fig. 2c, f). g, h Relative fluorescence intensity of FMN and DHEF after the addition of Aptamer PF (0-3 μM) and Aptamer MPF (0-10 μM), respectively (n = 3 replicates) in a buffer containing 50 mM MOPS (pH-7.5), 100 mM NaCl, 2 mM MgCl2, 0.05% Tween-20, and 3% DMSO. For all relevant panels, data are shown as mean  ±  standard deviation (SD). Source Data are provided as a Source Data file.

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