NMR characterization and ligand binding site of the stem–loop 2 motif from the Delta variant of SARS-CoV-2

(A) Determination of estimated K_D via ligand-detected ¹H-1D NMR titration. (B) RNA-based Euclidean distance plot to determine the binding site of P4C11 to s2m. The structural formula of the ligand is shown in the upper right corner. Internal loop residues are highlighted in green and loop residues are highlighted in magenta. A threshold of twofold the standard deviation was used. (C) ¹H, ¹³C HSQC spectra of the aromatic region of s2m Delta (100 µM) with 0 µM (black) and 500 µM (yellow) P4C11. Resonance assignments are annotated and the notation of nucleotides corresponds to the position in the genome −29,000. Loop resonances are labeled in magenta and internal loop resonances are labeled in green. (D) The secondary structure of s2m Delta is colored with HSQC-based chemical shift perturbation (CSP) heatmap (strong: red, weak: blue) and red corresponds to the maximum CSP detected. (E) Overview of values of different ligands for s2m SCoV-2 and s2m Delta.