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. 2019 Mar 6;9(3):378. doi: 10.3390/nano9030378

Figure 1.

Figure 1

Design and integration of the split-Spinach aptamer and RNA nanoring. (A) The central portion of the Spinach aptamer crystallized by Huang et al. (PDB ID: 3IVK) [42] was placed in the interior of the previously reported RNA nanoring and grafted onto two of the nanoring’s opposing helical struts. Based on initial placement, the Spinach aptamer was modeled to contain two short stems and single-stranded linkers with variable lengths. (B) 2D diagram resulting from initial modification and modeling of the split-Spinach aptamer into the RNA nanoring. (C) Stereoview of split-aptamer integrated into RNA nanoring. (D) The variable stem and single-stranded linker lengths were tested via fluorescent spectroscopy in the presence of the light-up chromophore DFHBI. The combination containing 5- and 6-bp stems and 6-nt linkers (5bp/6p/6nt) showed the highest response and was therefore chosen as the initial base model for further refinement.