DNA computing circuits using libraries of DNAzyme subunits

Elbaz, Johann; Lioubashevski, Oleg; Wang, Fuan; Remacle, Françoise; Levine, R. D.; Willner, Itamar

doi:10.1038/nnano.2010.88

Cited by 424 publications

(330 citation statements)

References 26 publications

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“…[16][17][18][19][20][21][22] Winfree, Stojanovic, Willner, Katz and their co-workers have, for example, developed optically reported 'AND' , 'OR' and 'SET-RESET' logic gate operations. 7,[23][24][25][26][27][28][29][30][31] Although the above examples serve as promising proofs of principle (see also refs 27-35), it remains necessary to create complex, multicomponent devices on a single biomolecular platform to achieve increased computational complexity and develop realistic DNAbased information processing systems. In this study, we fabricated and tested encoders and decoders based on a multiplex, DNA-based electrochemical biosensor that uses electronic (electrochemical) signals as its readout.…”

Section: Introductionmentioning

confidence: 99%

DNA biomolecular-electronic encoder and decoder devices constructed by multiplex biosensors

et al. 2012

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We fabricated and tested encoders and decoders based on a multiplex, DNA-based electrochemical biosensor that uses electronic (electrochemical) signals as its readout. These devices use two or more sequence-specific DNA probes, with each being modified with a distinct redox reporter. These probes, when interrogated together, serve as encoders and decoders, converting patterns that are encoded and decoded by the presence or absence of specific DNA sequences into specific electronic outputs. We demonstrated these multifunctional, bio-electrochemical devices, for example, 4-to-2 and 8-to-3 encoders and 1-to-2 and 2-to-3 decoders. Accordingly, these devices bridge the division between DNA-based devices and silicon-based electronics. NPG Asia Materials (2012) 4, e1; doi:10.1038/am.2012.1; published online 18 January 2012Keywords: biosensors; decoder; DNA-based; encoder; multiplex INTRODUCTIONIn recent decades, serious attempts have been made to implement computational approaches, models and paradigms that utilize the information transfer and processing abilities of naturally occurring and modified biomolecules. 1-11 A decade ago, for example, Adleman performed a now-classic experiment in which computations were conducted using DNA molecules, demonstrating that biology can provide new computing substrates. [12][13][14][15] In the decade since Adleman's invention, reports have been made of a wide and diverse range of DNA logic devices. [16][17][18][19][20][21][22] Winfree, Stojanovic, Willner, Katz and their co-workers have, for example, developed optically reported 'AND' , 'OR' and 'SET-RESET' logic gate operations. 7,[23][24][25][26][27][28][29][30][31] Although the above examples serve as promising proofs of principle (see also refs 27-35), it remains necessary to create complex, multicomponent devices on a single biomolecular platform to achieve increased computational complexity and develop realistic DNAbased information processing systems. In this study, we fabricated and tested encoders and decoders based on a multiplex, DNA-based electrochemical biosensor that uses electronic (electrochemical) signals as its readout. These devices uses two or more sequence-specific DNA probes that, when interrogated together, serve as encoders, converting patterns that are encoded and decoded by the presence or absence of specific DNA sequences into specific electronic outputs.

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Section: Introductionmentioning

confidence: 99%

DNA biomolecular-electronic encoder and decoder devices constructed by multiplex biosensors

et al. 2012

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“…7 This class of DNAzymes has been applied in nucleic acid detection, 8 metal ions sensing, 3,4,6,7,9−11 and molecular logic gate constructing. 4,12,13 The enzymatic activities play central roles in any extended analytical applications of DNAzymes. A number of biochemical and biophysical methods have been carried out for measuring DNAzyme activities, especially for RNA-cleaving DNAzymes.…”

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confidence: 99%

Nanoparticles-Free Fluorescence Anisotropy Amplification Assay for Detection of RNA Nucleotide-Cleaving DNAzyme Activity

Zhang

Zhao

et al. 2015

Anal. Chem.

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Fluorescence anisotropy is a homogeneous, sensitive, ratiometric, and real-time analytical technology. However, it is a great challenge to produce a large fluorescence anisotropy change upon the presence of target small molecules without nanoparticles-dependent amplification. This work reports a nanoparticle-free and multiple G-enhanced fluorescence anisotropy assay for detection of DNAzyme activity. A Pb 2+ -dependent GR-5 DNAzyme was used as a model. We hybridized the rA-cleavable substrate strand containing a TMR label at the 5′-end with the DNAzyme strand containing an extended three G bases at the 3′-end. By this design, we demonstrate that both fluorescence quenching and the enhanced DNAzyme activity contribute to a Pb 2+ -induced large fluorescence anisotropy change (|Δr| = 0.168). The limit of detection for Pb 2+ is estimated to be about 100 pM with a dynamic range from 200 pM to 100 nM. The interference from the other nine divalent metal ions of 1000-times excess amount is negligible. Moreover, we show an extended assay for evaluation of the interactions of Pb 2+ with cysteine and glutathione by the detection of GR5 DNAzyme activity. Collectively, we developed a novel fluorescence anisotropy amplification assay, enabling us to detect DNAzyme activity and associated cofactors and inhibitors and to characterize the Pb 2+ -chelation capability of free thiols.O ne class of functional nucleic acids with catalytic activity is DNAzymes, which have potential applications in diagnosis, therapeutics, and bioanalysis. 1−4 Various DNAzymes have been in vitro selected to catalyze a wide range of reactions, such as RNA cleavage, DNA cleavage, RNA ligation, DNA ligation, DNA phosphorylation, cleavage of the phosphoramidate bond, and porphyrin metalation. 5,6 One type of DNAzymes can cleave RNA. These RNA-cleaving DNAzymes are composed of a DNA enzyme strand and a DNA substrate strand containing a single RNA linkage (rA), which serves as the cleavage site. 7 This class of DNAzymes has been applied in nucleic acid detection, 8 metal ions sensing, 3,4,6,7,9−11 and molecular logic gate constructing. 4,12,13 The enzymatic activities play central roles in any extended analytical applications of DNAzymes. A number of biochemical and biophysical methods have been carried out for measuring DNAzyme activities, especially for RNA-cleaving DNAzymes. These methods include polyacrylamide gel electrophoresis (PAGE), 14 MALDI-TOF mass spectrometry, 15 fluorescence resonance energy transfer (FRET), 16,17 and fluorescence anisotropy (FA). 18−22 Among known techniques for detection of DNAzyme activity, FA has a number of advantages. It is a simple, realtime, and truly homogeneous analysis. Moreover, it does not require the separation of substrates and the cleaved products. This technique also presents several other attractive features, such as the requirement of only one fluorescent label and relative insensitivity to the photobleaching of the fluorophore and to instrument parameters due to its ratiometric nature. In fact, F...

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“…PB was also deposited on the driving cathode, and no color change was observed at pole IV (Sub 2 = '0'), as shown in Figure 2a Operation of a three-input concatenated logic circuit In addition to the frequently operated advanced logic devices, complicated concatenated logic circuits, which are usually difficult to fabricate at the molecular scale, connected by several logic devices can perform sophisticated multi-level logic computations. 10,14,45 Our bipolar electrochemistry-based universal logic platform can not only operate advanced logic devices but also perform concatenated logic computation. A three-input concatenated logic circuit with dual output was subsequently fabricated.…”

Section: Operation Of a 1-to-2 Demultiplexermentioning

confidence: 99%

Dual-electrochromic bipolar electrode-based universal platform for the construction of various visual advanced logic devices

et al. 2017

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A universal logic platform based on dual-electrochromic bipolar electrodes (BPEs) for the operation of various visual advanced logic devices was designed and constructed for the first time. Two BPEs separated by three reaction channels filled with different reaction solutions constituted the closed BPE system and were used as the initial state. Under different input combinations, the electrochemical oxidation of 2, 2′ -azinobis (3-ethylbenzthiazoline-6-sulfonic acid) and the electrodeposition of Prussian blue occurred at different poles simultaneously and triggered rapid color changes that could be easily visualized by the naked eye. By defining the color changes at the two specific poles as outputs, visual advanced logic devices, including an encoder, a decoder, a demultiplexer, a keypad lock and a three-input concatenated logic circuit with two outputs, were successfully constructed.

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DNA computing circuits using libraries of DNAzyme subunits

Cited by 424 publications

References 26 publications

DNA biomolecular-electronic encoder and decoder devices constructed by multiplex biosensors

DNA biomolecular-electronic encoder and decoder devices constructed by multiplex biosensors

Nanoparticles-Free Fluorescence Anisotropy Amplification Assay for Detection of RNA Nucleotide-Cleaving DNAzyme Activity

Dual-electrochromic bipolar electrode-based universal platform for the construction of various visual advanced logic devices

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