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5.3 Construction of RNA Nanoparticles with Integrated Logic Gate Operations Using Light‐Up Aptamers
ОглавлениеThis section is focused exclusively on the fluorogenic RNA aptamer‐based methods to fabricate responsive logic‐gated nanodevices. Based on the aforementioned properties, RNA‐based light‐up aptamers are ideal for binary logic system development. These systems can be programmed to respond to an input signal, inducing conformational change within the RNA aptamer's binding pocket that will further dictate binding strength of a fluorescent dye molecule. Various factors can serve as inputs. Nonspecific factors include temperature, pH, and ionic strength. Specific factors can include predesigned competitive short oligonucleotide strands, nonfluorescent molecule mimicking structures of the ligand dye, and RNA‐binding protein biomolecules, to name a few. The concentration of the inputs often needs to be fine‐tuned to display desirable outcomes and define the threshold between ON and OFF values. Short DNA oligonucleotides are commonly used as inputs because they are relatively inexpensive, are stable in aqueous solutions, and can hybridize with DNA as well as RNA strands to form RNA–DNA duplexes. When the inputs are present at a certain concentration, the overall fluorogenic aptamer structure can mimic a computer's function toggling between fluorescence (ON) and nonfluorescence (OFF) states. However, these can be achieved only when specific LOGICAL conditions are satisfied following Boolean algebra or function. The Boolean algebra is used to analyze and simplify the digital (logic) circuits and uses only the binary numbers 0 and 1. Other values include “YES and NO” or “ON and OFF,” and this type of notation is often referred to as a binary algebra. Logic gate plays a role as an elementary building block of digital circuits. Depending on the complexity of the operations and tasks, some circuits may have only a few logic gates, while others, such as microprocessors, have combinatorial circuits embedding millions of logic gates.