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. Author manuscript; available in PMC: 2017 Nov 29.
Published in final edited form as: Nat Chem Biol. 2017 May 29;13(7):807–813. doi: 10.1038/nchembio.2392

Figure 5.

Figure 5

Structure-based analysis of the RNA Mango-TO1-Biotin complex. (a) Effect on fluorophore-binding affinity of mutations in the ligand binding pocket (* Kds in panel (b) were measured using 31-nt RNA constructs with a 4 base pair duplex). (b) Effect on fluorophore-binding affinity of mutations in the tetraloop-like junction motif († measurements in this panel were with 39–40 nt RNA constructs each containing an 8 base pair duplex). (c) through (f), effect on Kd and relative fluorescence enhancement (FE‡) of circular permutation (CP) of the connectivity of RNA Mango by either moving the attachment point of the tetraloop-like junction in a full-length (FL) 39–40 nt construct, or by deleting the duplex and junction (Δ). Guanines of the three tiers are represented as squares, colored as in Fig. 1. The four guanine stacks are numbered as in Fig. 2a. The two adenosines that cover the two heterocycles of the TO moiety of the fluorophore are represented as yellow rectangles. All data are the mean of three independent trials ± s.d.