Fig. 6: Split-broccoli aptamer modified TC-RNA arrays for RNA sensing.

a Schematics of a single broccoli aptamer functionalized TC-RNA tiles-based array for RNA sensing. Array 5 is initially fluorescence OFF at state 1 because of the flexible configuration of the split-broccoli aptamer. After target RNA stabilizes the split-broccoli aptamer at state 2, the fluorescence turns ON. At state 3, DNA invaders displace the target RNA, and the split-broccoli aptamer switches OFF again. b–d AFM images of State 1(direct annealed control), State 1 to State 2, and State 2 (direct annealed control). The scale bar is 200 nm. The inset image size is 100 nm×100 nm. e The normalized fluorescence intensity of controls, State 1, State 1 to State 2, State 2 to State 3, State 1 to State 3, and State 2. f The kinetic comparison of the changes in fluorescence intensity in response to variations in the ratio between RNA target and DNA invader for Array 5. g The DFHBI-1T dye response curve of array 5. h The RNA target response curve of array 5. i The fluorescence intensity of Array 5 binding with different RNA targets. M0 is the original RNA target. M1 to M7 are mutant RNA targets. j Schematics of two broccoli aptamer functionalized TC-RNA tiles-based arrays for RNA detection. The fluorescence will turn on when the presence of target RNA is detected. k–m AFM images of State 1 (direct annealed control), State 2 (direct annealed control), and State 2 to State 3. The scale bar is 200 nm. n The normalized fluorescence intensities of controls, State 1, State 1 to State 3, State 2, State 2+RNA, State 2 to State 3, and State 3 (direct annealed control). Note, for each assembled array, the same amount of RNA strands (0.5 μM) was incubated with 40 mM HEPES (pH 7.4), 100 mM KCl, 1 mM MgCl₂, and 10 μM DFHBI-1T. AFM images were taken after a 2-h annealing program from 90 ^oC to 25 ^oC. The fluorescence intensities are calculated by the means ± SEs of n = 6 experiments (Ex = 470 nm and Em = 505 nm). The Array 5 state 2 in (e) is the same as the M0-0nt in (i). The fluorescence intensities were calculated by the means ± SEs of n = 12 experiments, which were the combination of two batches of 6 independent measurements.