Figure 3.

Structural details of the apical loop. (A) {¹H},¹³C-hetNOE of the aromatic pyrimidine H6C6 and the purine H8C8 moieties (bottom) and aliphatic H1’C1’ moieties (top) of 5_SL4sh. Residues of the loop region (gray) are highlighted in different colors according to the color scheme in Figure 2. A dashed line indicates the threshold for flexible residues (1.2). (B-C) NMR structural bundle of the apical loop. The loop closing base pair is used for structure alignment. The RNA is shown as a cartoon representation in two different orientations turned by 180° in respect to each other. The loop residues shown in different colors according to the color scheme in Figure 2 and assigned. (D) Aliphatic ¹H,¹³C-HSQC of 5_SL4sh. Resonances of U104 (green), G105 (red), C106 (blue) and A107 (magenta) are assigned in the respective colors. Gray spheres mark the canonical regions of the spectrum and characteristic ¹³C chemical shift regions are indicated to the right of the graph. (E) Overlay between the apical loop region of the NMR bundle of 5_SL4 and the lowest target function NMR structure of the cUUCGg tetraloop in a 14-nt RNA stem-loop (PDB entry 2koc). The C-G closing base pairs are used for alignment of the loops. The 5_SL4 RNA is shown as a cartoon representation using the color scheme shown in Figure 2. The UUCG tetraloop residues are colored accordingly. (F) Schematic representation of the transient structural features of the 5_SL4 apical loop. Residues are highlighted in different colors according to the color scheme in Figure 2 and assigned. Hydrogen bonds are shown as dashed lines and stacking interactions as gray ellipses. The Z-step with its lone pair...π stacking contact is indicated.