Fig. 2: Identification of the binding site by cgSHAPE-seq. | Nature Communications

Fig. 2: Identification of the binding site by cgSHAPE-seq.

From: Chemical-guided SHAPE sequencing (cgSHAPE-seq) informs the binding site of RNA-degrading chimeras targeting SARS-CoV-2 5’ untranslated region

Fig. 2

a cgSHAPE-seq probe (C30-FAI) synthetic route. Reaction conditions: (i) 4 Å molecular sieves, Et3N, dry CH2Cl2, room temperature; ii) dry CDCl3, room temperature. b cgSHAPE-seq mutational profiling analysis of the SL5 sequence in total RNA extract treated with C30-FAI (0.1 mM). Δmutation rate (FAI-N3 – DMSO) indicates the background structure-based differential acylation. ΔΔmutation rate [(C30-FAI – DMSO) – (FAI-N3 – DMSO)] indicates the proximity-based differential acylation. The cgSHAPE-seq experiments were performed with three replicates (n = 3). c Scatter plot of –LogP vs ΔΔmutation rate. P values were calculated from one-sided t-test. d Comparison of the Δmutation rates of G174 and on average in RNAs treated with different concentrations of C30-FAI or FAI-N3. Experiments were performed with three replicates (n = 3). Sequencing data were analyzed by ShapeMapper 2 to obtain the mutation rate and SD of each nucleotide. Data are presented as mean values ± SD. Source data are provided in the Source Data file.

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