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

Secondary structure, imino proton assignment, and transfer to aromatic protons of s2m Delta. The assignment is annotated in each spectrum. The numbering of nucleotides corresponds to the position in the genome −29,000. Additionally, introduced terminal G-C base pairs are annotated as G−1/2 or C + 1/2, respectively. Nucleotides labeled in gray belong to the lower stem and nucleotides labeled in magenta belong to the upper stem. (A) ¹H, ¹H NOESY spectrum of the imino proton region. (B) ¹H, ¹⁵N BEST-TROSY of base-paired region of s2m Delta. A schematic representation of the secondary structure is shown in the lower right corner. (C) HCCNH spectrum showing H1-C6 and H3-C8 correlations for base-paired Us and Gs. (D) ¹H, ¹³C HSQC of the aromatic region showing C6-H6 and C8-H8 correlations for base-paired Us and Gs, respectively. Resonances that could be assigned in the HCCNH spectrum are annotated.