Molecular logic gate operations using one-dimensional DNA nanotechnology

Rana, Muhit; Augspurger, Erik E.; Hizir, Mustafa Salih; Alp, Esma; Yigit, Mehmet V.

doi:10.1039/c7tc04957a

Cited by 20 publications

(14 citation statements)

References 32 publications

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“…In a similar scenario, we recently modified this nanotechnology for the development of colorimetric AND and OR logic gates using Hg 2+ and Ag + as the input signals. 206 HCR has also been used in combination with silver nanowires to detect Hg 2+ and hemin/G-quadruplex nanowires to detect Ag + . 207,208 Furthermore, the detection of copper, 209 lead, 210 and uranyl ions 211 has also been demonstrated using HCR.…”

Section: Acs Sensorsmentioning

confidence: 99%

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Chemical and Biological Sensing Using Hybridization Chain Reaction

2018

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Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

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Section: Acs Sensorsmentioning

confidence: 99%

“…The nanosensor was also tested for the detection of the targets in biological and environmental samples. In a similar scenario, we recently modified this nanotechnology for the development of colorimetric AND and OR logic gates using Hg 2+ and Ag + as the input signals …”

Section: Metal Ion Detectionmentioning

confidence: 99%

Chemical and Biological Sensing Using Hybridization Chain Reaction

2018

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“…Among these computing materials, DNA has been considered as an ideal biocomputing substrate since the first demonstration of solving the seven‐city Hamiltonian path problem in 1994 . The reliable prediction of DNA hybridization reaction based on the Watson–Crick base‐pairing principle is indispensable in the construction of biocomputing systems . Its simple synthesis method, predictable molecular behavior, and good biocompatibility can largely reduce operating cost, facilitate practical operations in vivo and in vitro, and also provide the potential for the construction of information processing systems .…”

Section: Introductionmentioning

confidence: 99%

Programmable DNA Nanoindicator‐Based Platform for Large‐Scale Square Root Logic Biocomputing

Zhou

Geng

Wang

et al. 2019

Small

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The prospect of programming molecular computing systems to realize complex autonomous tasks has advanced the design of synthetic biochemical logic circuits. One way to implement digital and analog integrated circuits is to use noncovalent hybridization and strand displacement reactions in cell‐free and enzyme‐free nucleic acid systems. To date, DNA‐based circuits involving tens of logic gates capable of implementing basic and complex logic functions have been demonstrated experimentally. However, most of these circuits are still incapable of realizing complex mathematical operations, such as square root logic operations, which can only be carried out with 4 bit binary numbers. A high‐capacity DNA biocomputing system is demonstrated through the development of a 10 bit square root logic circuit. It can calculate the square root of a 10 bit binary number (within the decimal integer 900) by designing DNA sequences and programming DNA strand displacement reactions. The input signals are optimized through the output feedback to improve performance in more complex logical operations. This study provides a more universal approach for applications in biotechnology and bioengineering.

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“…With the reliable prediction of hybridization behavior based on the Watson-Crick base-pairing principle, DNA is endowed with excellent advantages for the construction of biomolecular computing systems [6–8]. Its simple synthesis method, predictable molecular behavior, and good biological compatibility can largely reduce operating costs, facilitate practical operations in vivo and in vitro, and also provide the potential for the construction of information processing systems [9, 10].…”

Section: Introductionmentioning

confidence: 99%

Probe computing model based on small molecular switch

Wang

Zhang

et al. 2019

BMC Bioinformatics

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Background DNA is a promising candidate for the construction of biological devices due to its unique properties, including structural simplicity, convenient synthesis, high flexibility, and predictable behavior. And DNA has been widely used to construct the advanced logic devices. Results Herein, a molecular probe apparatus was constructed based on DNA molecular computing to perform fluorescent quenching and fluorescent signal recovery, with an ’ ON/OFF’ switching function. In this study, firstly, we program the streptavidin-mediated fluorescent quenching apparatus based on short-distance strand migration. The variation of fluorescent signal is acted as output. Then DNAzyme as a switching controller was involved to regulate the fluorescent signal increase. Finally, on this base, a cascade DNA logic gate consists of two logic AND operations was developed to enrich probe machine. Conclusion The designed probe computing model can be implemented with readout of fluorescence intensity, and exhibits great potential applications in the field of bioimaging as well as disease diagnosis.

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Molecular logic gate operations using one-dimensional DNA nanotechnology

Abstract: Hybridization chain reaction is programmed for DNA-based molecular logic gate operations using specific initiators and metal ion combinations.

Cited by 20 publications

References 32 publications

Chemical and Biological Sensing Using Hybridization Chain Reaction

Chemical and Biological Sensing Using Hybridization Chain Reaction

Programmable DNA Nanoindicator‐Based Platform for Large‐Scale Square Root Logic Biocomputing

Probe computing model based on small molecular switch

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