Biocomputers: from test tubes to live cells

Benenson, Yaakov

doi:10.1039/b902484k

Cited by 142 publications

(115 citation statements)

References 113 publications

(168 reference statements)

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“…Through the mechanism of strand exchange, the concentration of an mRNA molecule can be formulated as a condition to determine the time of transition. This mechanism could be used as signal conversion to implement on the edge trigger (Benenson 2009). This is reserved as an open issue to be investigated.…”

Section: Practical Concernmentioning

confidence: 99%

Implementation of a genetic logic circuit: bio-register

2015

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We introduce an idea of synthesizing a class of genetic registers based on the existing sequential biological circuits, which are composed of fundamental biological gates. In the renowned literature, biological gates and genetic oscillator have been unveiled and experimentally realized in recent years. These biological circuits have formed a basis for realizing a primitive biocomputer. In the traditional computer architecture, there is an intermediate load-store section, i.e. a register, which serves as a part of the digital processor. With which, the processor can load data from a larger memory into it and proceed to conduct necessary arithmetic or logic operations. Then, manipulated data are stored back to the memory by instruction via the register. We propose here a class of bio-registers for the biocomputer. Four types of register structures are presented. In silicon experiments illustrate results of the proposed design.

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Section: Practical Concernmentioning

confidence: 99%

Implementation of a genetic logic circuit: bio-register

2015

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“…[1][2][3][4][5][6][7][8][9][10][11][12][13][14] Such multi-input reaction cascades are used in biosensing, biomolecular computing, and decision making devices and setups utilizing (bio)chemical processes with well-defined responses. [15][16][17][18][19][20] These systems require experimental design and theoretical understanding [21][22][23] of chemical and biochemical reactions that allow signal response modification and control.…”

Section: Introductionmentioning

confidence: 99%

“…The work on binary logic has used biomolecular processes involving proteins/enzymes, 9,66 DNA/RNA, [5][6][7][8][67][68][69] and bacterial cells. 70,71 Enzymatic processes are of great interest because they promise short-term development of new biosensing 19,20,24,27,[72][73][74] and bioactuating applications [75][76][77] with even moderate-complexity reaction cascades.…”

Section: Introductionmentioning

confidence: 99%

Kinetic Model for a Threshold Filter in an Enzymatic System for Bioanalytical and Biocomputing Applications

Privman¹,

Domanskyi²,

Mailloux³

et al. 2014

J. Phys. Chem. B

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A recently experimentally observed biochemical "threshold filtering" mechanism by processes catalyzed by the enzyme malate dehydrogenase is explained in terms of a model that incorporates an unusual mechanism of inhibition of this enzyme that has a reversible mechanism of action. Experimental data for a system in which the output signal is produced by biocatalytic processes of the enzyme glucose dehydrogenase are analyzed to verify the model's validity. We also establish that fast reversible conversion of the output product to another compound, without the additional inhibition, cannot on its own result in filtering.

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“…and biochemical [10][11][12][13][14] systems realizing binary logic gates and networks have been investigated for novel computational and signal processing designs. Biomolecular systems have included those based on proteins/enzymes, 14,15 DNA, 13,16 RNA 17 and even whole cells.…”

Section: Molecularmentioning

confidence: 99%

Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid “Filter” Response

et al. 2012

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We report the first realization of a biomolecular AND gate function with double-sigmoid response (sigmoid in both inputs). Two enzyme biomarker inputs activate the gate output signal which can then be used as indicating liver injury, but only when both of these inputs have elevated pathophysiological concentrations, effectively corresponding to logic-1 of the binary gate functioning. At lower, normal physiological concentrations, defined as logic-0 inputs, the liver-injury output levels are not obtained. High-quality gate functioning in handling of various sources of noise, on time scales of relevance to potential applications is enabled by utilizing "filtering" effected by a simple added biocatalytic process. The resulting gate response is sigmoid in both inputs when proper system parameters are chosen, and the gate properties are theoretically analyzed within a model devised to evaluate its noise-handling properties.

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Biocomputers: from test tubes to live cells

Cited by 142 publications

References 113 publications

Implementation of a genetic logic circuit: bio-register

Implementation of a genetic logic circuit: bio-register

Kinetic Model for a Threshold Filter in an Enzymatic System for Bioanalytical and Biocomputing Applications

Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid “Filter” Response

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