Light-Controlled, Toehold-Mediated Logic Circuit for Assembly of DNA Tiles

Abstract

Inspired by cytoskeletal structures that respond sensitively to environmental changes and chemical inputs, we report a strategy to trigger and finely control the assembly of stimulus-responsive DNA nanostructures with light under isothermal conditions. The strategy is achieved via integrating an upstream light-controlled, toehold-mediated DNA strand displacement circuit with a downstream DNA tile self-assembly process. By rationally designing an upstream DNA strand module, we further transform the upstream DNA strand displacement circuit to an “AND gate” circuit to control the assembly of DNA nanostructures. This example represents the demonstration of the spatial and temporal assembly of DNA nanostructures using a noninvasive chemical input. Such a light-controlled DNA logic circuit not only adds a new element to the tool box of DNA nanotechnology but also inspires us to assemble complex and responsive nanostructures.

DNA nanostructure-based nucleic acid probes: construction and biological applications

“…4B ), which allow the disassembly and reorganization of nanotubes to be controlled through invader and complementary anti-invader molecules. In addition, a variety of input signals (such as ultraviolet light, 53 pH, 54 transcription signal, 55 etc. ) can activate the disassembly or recombination of the DNA-based nanotubes.…”

Logic devices based on nucleic acid self‐assembly

“…In 2020, Xing et al designed a DNA tile self-assembly system mediated by light-controlled, toehold-mediated DNA circuits (Figure 3B). 100 In the upstream light-controlled circuit, the initial structures were photocleavable nitrobenzyl linker modified DNA hairpins (Pc-Hairpin). After irradiation by UV light, the Pc-Hairpin groups were cleaved and "hidden toehold" sticky ends were exposed.…”

“…(B) A light-controlled DNA tile self-assembly system. Reproduced with permission: Copyright 2020, American Chemical Society100…”

Development of a neuron model based on DNAzyme regulation

“…In the absence of input signals, Curve (1) had almost no increase in uorescent signals that could be observed. Curve (2) to Curve (4), the added input signals were X 3 , X 2 , X 1 . In the case of adding a signal, the uorescent started to rise and roughly rising to the same level.…”

“…Thanks to the rapid development of DNA nanotechnology, DNA molecules have become reliable programming materials due to their great parallel computing power, excellent data storage capacity, and predictable base pairing. 1,2 DNA-based logic gates have been used as the elementary building components of computing systems, each of which implements a Boolean function. These blocks were combined to realize the transformation process from abstract information to concrete data.…”