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has simplified RNA imaging in mammalian, yeast, and bacterial cells [44,84–87].

      5.3.1 Implementation of MG‐Binding RNA Aptamer to Design Binary Logic Gates

Common binary logic gate symbols and truth tables. The six most common binary logic gates include AND, OR, XOR, NAND, NOR, and XNOR; the OR logic gate yields 1 output when at least one of the inputs equals 1. Image described by caption.

      Source: (Panel b) Adapted from Goldsworthy et al. [46].

      The NAND and NOR gates were designed slightly differently. The extensions at the 5′‐ and 3′‐ends of the core MG‐binding aptamer region were shorter (18 nt at the 5′‐end and 17 nt at the 3′‐end). These are non‐interfering ends; thus they do not cause disruption of the MG‐binding pocket. Therefore, in the absence of both inputs, 0‐0, the output is 1 (Figure 5.4b). In NAND logic, the non‐interfering ends must be able to bind inputs A or B without changing the structure of the MG‐binding pocket. However, when both A and B are presented, the conformation of the aptamer needs to be sufficiently distorted to achieve OFF state. In NOR logic, the presence of either inputs significantly disrupts the conformation of the RNA molecule, rendering MG binding impossible. Hence, the output was “1” only in the absence of both potential DNA inputs.

      Programs such as NUPAC and mfold are often used to design DNA–RNA aptamers with MG‐binding potential. Unfortunately, these programs cannot analyze stability of hybrid RNA–DNA interactions. Since the overall design relies primarily on the strand displacement reaction between RNA–RNA and RNA–DNA interactions, the folding predictions might be inaccurate. To overcome this, various concentrations of RNA gates and DNA inputs should be explored to gain better ON and OFF separation threshold.

      5.3.2 Implementation of MG‐Binding RNA Aptamer and Broccoli RNA Aptamer to Design Half‐Adder Circuit

Image described by caption.
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