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Enzyme-Based Logic Systems: Composition, Operation, Interfacing, and Applications

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Encyclopedia of Complexity and Systems Science

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Abstract

Biomolecular systems for information processing have recently received great attention in the general framework of unconventional computing. While DNA biocomputing systems have been studied by many researchers and have already reached a high level of complexity, enzyme-based cascades mimicking Boolean logic operations are a relatively new subfield that is rapidly progressing. This chapter reviews recent progress in the enzyme-based information processing systems and suggests applications in biosensing, rather than computation. This chapter overviews various methods for analysis of output signals generated by enzyme-based logic systems. The considered methods include different optical techniques (optical absorbance, fluorescence spectroscopy, surface plasmon resonance), electrochemical techniques (cyclic voltammetry, potentiometry, impedance spectroscopy, conductivity measurements, use of field-effect transistor devices, pH measurements), and various mechano-electronic methods (using atomic force microscope, quartz crystal microbalance). While each of the methods is already well known for various bioanalytical applications, their use in combination with the biomolecular logic systems is rather new and sometimes not trivial. Many of the discussed methods have been combined with the use of signal-responsive materials to transduce and amplify biomolecular signals generated by the logic operations. Interfacing of biocomputing logic systems with electronics and “smart” signal-responsive materials allowed for extending logic operations to actuation functions, for example, stimulating molecular release and switchable features of bioelectronic devices, such as biofuel cells. The purpose of this chapter is to emphasize broad variability of the bioanalytical systems applied for the signal transduction in biocomputing processes. All bioanalytical systems discussed in the article are exemplified with specific logic gates and multi-gate networks realized with enzyme-based biocatalytic cascades.

This chapter is based partially on recently published review articles (Katz 2015, 2017; Katz et al. 2017) with the copyright permissions from Elsevier, Wiley-VCH, and Springer. The compiled text was updated and edited.

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Abbreviations

Abs:

Optical absorbance

ABTS:

2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (chromogenic substrate used to follow peroxidase activity)

ABTSox :

Oxidized ABTS (colored product)

Ac:

Acetic acid

AcCh:

Acetylcholine

AcChE:

Acetylcholinesterase (enzyme; EC 3.1.1.7)

ADH:

Alcohol dehydrogenase (enzyme; EC 1.1.1.1)

ADP:

Adenosine 5′-diphosphate

AFM:

Atomic force microscope (microscopy)

AGS:

Amyloglucosidase (enzyme; EC 3.2.1.3)

Ala:

Alanine (amino acid)

Ald:

Acetaldehyde

ALT:

Alanine transaminase (enzyme; EC 2.6.1.2)

Asc:

Ascorbic acid

ATP:

Adenosine 5′-triphosphate

BuCh:

Butyrylcholine

ChO:

Choline oxidase (enzyme; EC 1.1.3.17)

CK:

Creatine kinase (enzyme; EC 2.7.3.2)

CN:

4-Chloro-1-naphthol

CN-ox:

CN insoluble oxidized product

Crt:

Creatine

DC:

Direct current

DHA:

dehydroascorbic acid (product of oxidation of ascorbic acid)

Diaph:

Diaphorase (enzyme; EC 1.8.1.4)

DNA:

Deoxyribonucleic acid

EIS:

Electrolyte–insulator–semiconductor

Et-O-Ac:

Ethyl acetate

EtOH:

Ethanol

FET:

Field-effect transistor

Frc:

Fructose

G6PDH:

Glucose 6-phosphate dehydrogenase (enzyme; EC 1.1.1.49)

GDH:

Glucose dehydrogenase (enzyme; EC 1.1.1.47)

Glc:

Glucose

Glc6P:

Glucose-6-phosphate

Glc6PA:

Gluconate-6-phosphate acid (product of Glc6P oxidation)

GlcA:

Gluconic acid

Glu:

Glutamate (amino acid, salt form)

GluOx:

Glutamate oxidase (enzyme; EC 1.4.3.11)

GOx:

Glucose oxidase (enzyme; EC 1.1.3.4)

HK:

Hexokinase (enzyme; EC 2.7.1.1)

HRP:

Horseradish peroxidase (enzyme; EC 1.11.1.7)

Inv:

Invertase (enzyme; EC 3.2.1.26)

Ip :

Peak current (measured with cyclic voltammetry)

IR:

Infrared

ITO:

Indium tin oxide (electrode)

Lac:

Lactate

LDH:

Lactate dehydrogenase (enzyme; EC 1.1.1.27)

LSPR:

Localized surface plasmon resonance

Luc:

Luciferase (enzyme from ATP assay kit, Sigma-Aldrich)

Lucif:

Luciferin

MP-11:

Microperoxidase-11

MPh:

Maltose phosphorylase (enzyme; EC 2.4.1.8)

NAD+ :

Nicotinamide adenine dinucleotide

NADH:

Nicotinamide adenine dinucleotide reduced

NPs:

Nanoparticles

O/W:

Oil-in-water Pickering emulsion

P2VP:

Poly(2-vinylpyridine)

P4VP:

Poly(4-vinylpyridine)

PB:

Prussian blue

PEO:

Poly(ethylene oxide)

PEP:

Phospho(enol)pyruvic acid (or phosphoenolpyruvate in the form of salt)

Pi:

Inorganic phosphate

PK:

Pyruvate kinase (enzyme; EC 2.7.1.40)

Ppy:

Polypyrrole

Ppy-ox:

Polypyrrole-oxidized state

Ppy-red:

Polypyrrole-reduced state

PQQ:

Pyrroloquinoline quinone

PS:

Polystyrene

Pyr:

Pyruvate

QCM:

Quartz crystal microbalance

R:

Reflectance measured by SPR

Rcell :

Ohmic resistance measured in a bulk solution in an electrochemical cell

RE:

Reference electrode

Ret :

Electron transfer resistance (measured by Faradaic impedance spectroscopy)

RNA:

Ribonucleic acid

SPR:

Surface plasmon resonance

TBI:

Traumatic brain injury

TMB:

3,3′,5,5′-Tetramethylbenzidine (chromogenic substrate used to follow peroxidase activity)

UV:

Ultraviolet

Va :

Alternative voltage applied between the conducting support and reference electrode of the EIS devise

Vbias :

Constant (bias) voltage applied between the conducting support and reference electrode of the EIS devise

VFB :

Flat band voltage of the EIS device

W/O:

Water-in-oil Pickering emulsion

α-KTG:

α-Ketoglutaric acid

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Authors and Affiliations

  1. Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA

    Evgeny Katz

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    Robert A. Meyers

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Katz, E. (2017). Enzyme-Based Logic Systems: Composition, Operation, Interfacing, and Applications. In: Meyers, R. (eds) Encyclopedia of Complexity and Systems Science. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-27737-5_681-1

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