Sensing of UO<sub>2</sub><sup>2+</sup> and Design of Logic Gates by the Application of Supramolecular Constructs of Ion-Dependent DNAzymes

Moshe, Michal; Elbaz, Johann; Willner, Itamar

doi:10.1021/nl803887y

Cited by 133 publications

(95 citation statements)

References 36 publications

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“…Furthermore, the biocatalytic nature of many utilized biomolecular processes, offers certain advantages for analog noise control in the binary-gate circuit design paradigm. [17] Proteins/enzymes [5][6][7][8][9][10][11][12][14][15][16][17][19][20][161][162][163][164][165] and DNA/RNA/DNAzymes [6,7,[166][167][168][169][170][171][172][173][174][175][176][177][178][179][180][181][182] have been extensively used for gates, for realizing small networks and computational units, and for systems motivated [183] by applications.…”

Section: Introductionmentioning

confidence: 99%

Control of Noise in Chemical and Biochemical Information Processing

Privman

2011

Israel Journal of Chemistry

103

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Abstract:We review models and approaches for error-control in order to prevent the buildup of noise when gates for digital chemical and biomolecular computing based on (bio)chemical reaction processes are utilized to realize stable, scalable networks for information processing.Solvable rate-equation models illustrate several recently developed methodologies for gatefunction optimization. We also survey future challenges and possible new research avenues.

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Section: Introductionmentioning

confidence: 99%

Control of Noise in Chemical and Biochemical Information Processing

Privman

2011

Israel Journal of Chemistry

103

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“…In the presence of target, the DNAzyme cleaves the RNA, fragmenting the sequence into two parts, which destabilize the complex and enable the formation of an activated G4-DNAzyme. By making use of this strategy, the Willner group successfully developed colorimetric assays that can sensitively and specifically detect Pb 2+ , l -histidine, UO 2 2+ or Mg 2+ [130,131]. They further proved that the constructs can be applied to perform the “AND” and “OR” logic gate operations [131].…”

Section: Peroxidase-mimicking Dnazyme (G4-dnazyme) As Colorimetricmentioning

confidence: 99%

Integrating Deoxyribozymes into Colorimetric Sensing Platforms

Chang

Zakaria

Deng

et al. 2016

Sensors

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Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.

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“…The current gates are relatively slow, which is a common problem for many nucleic-acid-based logic gates. [7,9,12,29] As increasingly larger gates are constructed, speed becomes a limiting factor. [29] The kinetic response of hybridization or strand displacement of DNA could be optimized by changing the reaction conditions and selecting proper lengths of DNA.…”

Section: Wwwchemeurjorgmentioning

confidence: 99%

Multivalued Logic Gates Based on DNA

Pu¹,

Ren²,

Yang³

et al. 2011

Chemistry A European J

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Binary logic is the basis of modern computers, in which every bit is coded by 0 or 1, corresponding to a low or high signal, respectively. Simple Boolean logic gates receive one or more binary (0, 1) input signals and produce a single binary output signal. The principles of binary logic can be applied to the signal transduction operated by molecular switches.[1] In the past decade, molecular systems capable of performing Boolean logic operations have been attractive for the construction of molecular-level devices and machines. [1,2] Various materials, such as organic molecules, [2] protein, [3] nucleic acids, [4][5][6][7][8][9][10][11][12] enzymatic biochemical network, [13,14] supramolecular hydrogel, [15] and polymer-ligand interactions [16,17] have been used to process chemical signals, mimicking Boolean logic operations. These logic gates show great promise, but at the same time face substantial challenges.With the development of biological computing and quantum computing, the dominance of binary logic is challenged and multi-valued logic gates attract intense interest for research. Boolean binary logic has only two states that are true and false, or on and off. However, quite often, the logic gates suffer a certain degree of uncertainty and imprecision. In these cases, it is difficult to process information based on binary logic. Multi-valued logic is likely to play an increasingly important role in the conception and design of a molecular computer, since it would be able to deal with uncertain information. Multi-valued logic is defined as a nonbinary logic and involves the switching between more than two states. The number of distinguishable states increases, which allows for higher information densities.[18] The common application of a multi-valued variable is coding. The Morse code, which uses three different symbols, is probably the best known. The more different symbols there are, the shorter the code words.[19] A ternary or three-valued logic function is one that has two inputs that can assume three states (say 0, 1 and 2) and generates one output signal that can have one of these three states. Thus ternary logic is the extension of predominating binary logic. Recently, a multi-valued logic function was realized by using a nanofluidic diode based on conical nanopores functionalized with polyprotic acid chains.[20] The low, medium, and high pH values constitute the inputs, and the conductance values constitute the outputs. Pischels group has reported a tristable molecular fluorescent switch of the fluorophore 1 -spacer-receptor-spacer-fluorophore 2 dyad.[21] A careful assignment of the logic operation yielded a ternary NOR logic gate. In addition, Cervera et al. reported a multi-valued XOR logic gate implemented with metallic nanoparticles and organic ligands.[22] However, until now, the description of a ternary logic gate operation based on nucleic acids remains rare. Nucleic acids exhibit many advantages in comparison with organic molecules, such as easy synthesis with high reproducibility and purity,...

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Sensing of UO₂²⁺ and Design of Logic Gates by the Application of Supramolecular Constructs of Ion-Dependent DNAzymes

Cited by 133 publications

References 36 publications

Control of Noise in Chemical and Biochemical Information Processing

Control of Noise in Chemical and Biochemical Information Processing

Integrating Deoxyribozymes into Colorimetric Sensing Platforms

Multivalued Logic Gates Based on DNA

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Sensing of UO22+ and Design of Logic Gates by the Application of Supramolecular Constructs of Ion-Dependent DNAzymes

Cited by 133 publications

References 36 publications

Control of Noise in Chemical and Biochemical Information Processing

Control of Noise in Chemical and Biochemical Information Processing

Integrating Deoxyribozymes into Colorimetric Sensing Platforms

Multivalued Logic Gates Based on DNA

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Sensing of UO₂²⁺ and Design of Logic Gates by the Application of Supramolecular Constructs of Ion-Dependent DNAzymes