Figure 3.

Solution structures of free CDE1GG and CDE2GG RNAs. (A and B) Zoom-in of the assigned aromatic H1′ region of the ¹H,¹H-NOESYs of CDE1GG (A) and CDE2GG (B). The intraresidual H5/H6 cross peak assignment is shown in light grey. (C and D) The three dimensional structures of CDE1GG (blue) and CDE2GG (red) after refinement with the force-field RNA-ff1 (55) (see also Table 1). Two orientations for each CDE show the side-on view with the loops pointing into the direction of the viewer, and a top down view displaying the loop-orientation with respect to the helical main axis. Tri-loop residues are labeled in sequential order (orange, magenta and green respectively) to highlight differences in loop geometry. (E) NMR structure of the Tnf CDE (43). See also Supplementary Figures S3 and S4.