DNA Logic Gate Based on Metallo-Toehold Strand Displacement

Deng, Wei; Xu, Huaguo; Ding, Wei; Liang, Haojun

doi:10.1371/journal.pone.0111650

Cited by 15 publications

(12 citation statements)

References 50 publications

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“…After the basic operation of the CRN for DNA-based Boolean logic computing, the outlet DNAs extracted from the MPU chip were dyed with SYBR gold and run through the polyacrylamide gel for detection. The calculated DNA complexes have different structures. ,− Figure e shows a diagram of gel-based DNA Boolean logic detection. The decision (“True (1)” or “False (0)”), which is the result of the logic operation, is indicated by the band states of the DNA complex.…”

Section: Resultsmentioning

confidence: 99%

Programmable DNA-Based Boolean Logic Microfluidic Processing Unit

Lee

Lim

et al. 2021

ACS Nano

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As molecular computing materials, information-encoded deoxyribonucleic acid (DNA) strands provide a logical computing process by cascaded and parallel chain reactions. However, the reactions in DNA-based combinational logic computing are mostly achieved through a manual process by adding desired DNA molecules in a single microtube or a substrate. For DNA-based Boolean logic, using microfluidic chips can afford automated operation, programmable control, and seamless combinational logic operation, similar to electronic microprocessors. In this paper, we present a programmable DNA-based microfluidic processing unit (MPU) chip that can be controlled via a personal computer for performing DNA calculations. To fabricate this DNA-based MPU, polydimethylsiloxane was cast using double-sided molding techniques for alignment between the microfluidics and valve switch. For a uniform surface, molds fabricated using a three-dimensional printer were spin-coated by a polymer. For programming control, the valve switch arms were operated by servo motors. In the MPU controlled via a personal computer or smartphone application, the molecules with two input DNAs and a logic template DNA were reacted for the basic AND and OR operations. Furthermore, the DNA molecules reacted in a cascading manner for combinational AND and OR operations. Finally, we demonstrated a 2-to-1 multiplexer and the XOR operation with a three-step cascade reaction using the simple DNA-based MPU, which can perform Boolean logic operations (AND, OR, and NOT). Through logic combination, this DNA-based Boolean logic MPU, which can be operated using programming language, is expected to facilitate the development of complex functional circuits such as arithmetic logical units and neuromorphic circuits.

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Section: Resultsmentioning

confidence: 99%

Programmable DNA-Based Boolean Logic Microfluidic Processing Unit

Lee

Lim

et al. 2021

ACS Nano

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“…Would a single metal-mediated base pair be able to initiate a stranddisplacement reaction (Figure 1b)? This concept is fundamentally different from previous investigations of embedded metal-mediated base pairs within natural base pairs to regulate the strand displacement, [49][50][51] as those studies still basically rely on the conformational switch of nucleic acid structures induced by metal ions. In this new scenario, however, the metal-ligand complexation is not integrated into the nucleic acid structure, but functions as an independent toehold.…”

Section: Introductionmentioning

confidence: 90%

Controllable DNA strand displacement by independent metal–ligand complexation

et al. 2021

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“…208, 209 Such metallo-base pairs have been successfully used in a wide range of applications, such as DNA biosensors for detection of metal ions, construction of DNA nanomachines and fabrication of logic gates. 210-212 …”

Section: Functional Nucleic Acid-based Hydrogels and Their Bioanalmentioning

confidence: 99%

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

et al. 2016

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Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels.

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DNA Logic Gate Based on Metallo-Toehold Strand Displacement

Cited by 15 publications

References 50 publications

Programmable DNA-Based Boolean Logic Microfluidic Processing Unit

Programmable DNA-Based Boolean Logic Microfluidic Processing Unit

Controllable DNA strand displacement by independent metal–ligand complexation

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

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