Fig. 3. Interrogation of RNA features for high-affinity interaction with Sox2-HMG.

a Secondary structure of the Loop B RNA with the designated paired regions (P1 and P2), internal loop (blue dotted line), and terminal loop (green dashed line). Binding assessed to mutations b reducing paired region helix length, n = 8, c reducing the internal loop size, n = 8, d truncation of hairpins, n = 3 e removing the terminal loop, n = 6, f structured RNAs, xpt riboswitch and env4 Cbl riboswitch, n = 4, tRNA^Leu, n = 3, and g nucleic acid duplexes with n = 3 technical replicates each. Apparent binding affinity displayed as the average with s.e.m. reported.