Supplementary Figure 2: NMR signal assignments and structural analysis of SL-K.
(a) Sequence and NMR-derived secondary structure of SL-K. Colors indicate the sequential assignment in (d). (b) Overlay of the Ade H2–C2, H8–C8, and H1′–C1′ regions of 1H-13C HMQC spectra of [13C,15N-Ade/Cyt] SL-K (red) and [13C,15N-Ade] J-K (black). Asterisks indicate signals due to heterogenous termini in the RNA transcript. (c) 1H-1H NOESY spectrum of the imino proton region and imino proton walk of SL-K that supports the secondary structure of SL-K. The lower and upper stem walks are shown with red and cyan lines, respectively. The NOE signals between upfield shifted imino protons from U738 and U759 indicate a non-canonical basepair formed by these residues. (d) Sequential walk of H1′–H6 (pyrimidine) or H1′–H8 (purine) connectivity for the assignments. Labels show the intraresidual H1′–H6 or H1′–H8 signals of each residue. Green, cyan, and purple lines represent the sequential walk of the segments shown in the same colors in (a). Asterisks indicate that the signals are below the threshold. (e, g) NOESY strips derived from 1H-1H NOESY spectrum of SL-K for the structural characterization of the bulges. (f, h, j) NOESY strips derived from 13C-edited HMQC-NOESY 3D spectra of [13C,15N-Ade/Cyt] or [13C,15N-Gua/Uri] labeled SL-K for the structural characterization of the bulges. The asterisk in (f) indicates that the signal is not in the same plane in the 13C dimension and not connected to the spin system. (i) The Gua H8–C8 region of 1H-13C HMQC spectrum of [13C,15N-Gua/Uri] SL-K.
