Fig. 5
Two-color ACE-Scan of TBA DAs. a Upper, secondary structure of the TBA construct used here, with 5ʹ and 3ʹ extensions colored in gray, TT loops colored in green, and proximal and distal G-quadruplex tetrads colored in yellow and orange, respectively. Lower, 3D view of the interaction of native TBA with human alpha thrombin exosite I (PDB 4DIH37). Colored surface shows the APBS-predicted electrostatic potential molecular surface of thrombin, purple sphere represents a sodium ion. b–d ACE-Scan generated (b) DA hybridization affinity landscape, (c) buffer-only koff landscape, and (d) thrombin-induced k*off,2 µM landscape. e Heat map of the Cy3-normalized signal of AF647-labeled thrombin molecules bound to surface-based TBA DAs after incubation with 2 µM thrombin for 1 h. f k*off,2 µM landscape for DAs engineered with single mismatched 11-mer ACEs. Left-hand column represents perfect match 10-mer ACEs. g Linear mapping of the mismatched 11-mer ACE induced fit landscape onto the TBA sequence (Methods section)
