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Abstract
Regulatory processes in biology can be re-conceptualized in terms of logic gates, analogous to those in computer science. Frequently, biological systems need to respond to multiple, sometimes conflicting, inputs to provide the correct output. The language of logic gates can then be used to model complex signal transduction and metabolic processes. Advances in synthetic biology in turn can be used to construct new logic gates, which find a variety of biotechnology applications including in the production of high value chemicals, biosensing, and drug delivery. In this review, we focus on advances in the construction of logic gates that take advantage of biological catalysts, including both protein-based and nucleic acid-based enzymes. These catalyst-based biomolecular logic gates can read a variety of molecular inputs and provide chemical, optical, and electrical outputs, allowing them to interface with other types of biomolecular logic gates or even extend to inorganic systems. Continued advances in molecular modeling and engineering will facilitate the construction of new logic gates, further expanding the utility of biomolecular computing.
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Synthesis Strategy of Reversible Circuits on DNA Computers. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
DNA computers and quantum computers are gaining attention as alternatives to classical digital computers. DNA is a biological material that can be reprogrammed to perform computing functions. Quantum computing performs reversible computations by nature based on the laws of quantum mechanics. In this paper, DNA computing and reversible computing are combined to propose novel theoretical methods to implement reversible gates and circuits in DNA computers based on strand displacement reactions, since the advantages of reversible logic gates can be exploited to improve the capabilities and functionalities of DNA computers. This paper also proposes a novel universal reversible gate library (URGL) for synthesizing n-bit reversible circuits using DNA to reduce the average length and cost of the constructed circuits when compared with previous methods. Each n-bit URGL contains building blocks to generate all possible permutations of a symmetric group of degree n. Our proposed group (URGL) in the paper is a permutation group. The proposed implementation methods will improve the efficiency of DNA computer computations as the results of DNA implementations are better in terms of quantum cost, DNA cost, and circuit length.
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Teders M, Pogodaev AA, Bojanov G, Huck WTS. Reversible Photoswitchable Inhibitors Generate Ultrasensitivity in Out-of-Equilibrium Enzymatic Reactions. J Am Chem Soc 2021; 143:5709-5716. [PMID: 33844531 PMCID: PMC8154525 DOI: 10.1021/jacs.0c12956] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Ultrasensitivity
is a ubiquitous emergent property of biochemical
reaction networks. The design and construction of synthetic reaction
networks exhibiting ultrasensitivity has been challenging, but would
greatly expand the potential properties of life-like materials. Herein,
we exploit a general and modular strategy to reversibly regulate the
activity of enzymes using light and show how ultrasensitivity arises
in simple out-of-equilibrium enzymatic systems upon incorporation
of reversible photoswitchable inhibitors (PIs). Utilizing a chromophore/warhead
strategy, PIs of the protease α-chymotrypsin were synthesized,
which led to the discovery of inhibitors with large differences in
inhibition constants (Ki) for the different
photoisomers. A microfluidic flow setup was used to study enzymatic
reactions under out-of-equilibrium conditions by continuous addition
and removal of reagents. Upon irradiation of the continuously stirred
tank reactor with different light pulse sequences, i.e., varying the
pulse duration or frequency of UV and blue light irradiation, reversible
switching between photoisomers resulted in ultrasensitive responses
in enzymatic activity as well as frequency filtering of input signals.
This general and modular strategy enables reversible and tunable control
over the kinetic rates of individual enzyme-catalyzed reactions and
makes a programmable linkage of enzymes to a wide range of network
topologies feasible.
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Affiliation(s)
- Michael Teders
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Aleksandr A Pogodaev
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Glenn Bojanov
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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4
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Kaniewska K, Bollella P, Katz E. Implication and Inhibition Boolean Logic Gates Mimicked with Enzyme Reactions. Chemphyschem 2020; 21:2150-2154. [DOI: 10.1002/cphc.202000653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/14/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Klaudia Kaniewska
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
- Faculty of Chemistry Biological and Chemical Research Center University of Warsaw 101 Żwirki i Wigury Av. 02-089 Warsaw Poland
| | - Paolo Bollella
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
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5
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Katz E. Boolean Logic Gates Realized with Enzyme‐catalyzed Reactions – Unusual Look at Usual Chemical Reactions. Chemphyschem 2018; 20:9-22. [DOI: 10.1002/cphc.201800900] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699–5810 USA
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6
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Filipov Y, Zakharchenko A, Minko S, Katz E. Magneto‐Controlled Biocatalytic Cascades with Logically Processed Input Signals – Substrate Channeling versus Free Diffusion. Chemphyschem 2018; 19:3035-3043. [DOI: 10.1002/cphc.201800851] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Yaroslav Filipov
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
| | | | - Sergiy Minko
- Nanostructured Materials Lab University of Georgia Athens GA 30602 USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
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7
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Filipov Y, Gamella M, Katz E. Nano-species Release System Activated by Enzyme-based XOR Logic Gate. ELECTROANAL 2017. [DOI: 10.1002/elan.201700742] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yaroslav Filipov
- Department of Chemistry and Biomolecular Science
- Department of Physics; Clarkson University; Potsdam, NY 13699 USA
| | | | - Evgeny Katz
- Department of Chemistry and Biomolecular Science
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8
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Filipov Y, Domanskyi S, Wood ML, Gamella M, Privman V, Katz E. Experimental Realization of a High-Quality Biochemical XOR Gate. Chemphyschem 2017; 18:2908-2915. [PMID: 28745425 DOI: 10.1002/cphc.201700705] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 07/22/2017] [Indexed: 11/09/2022]
Abstract
We report an experimental realization of a biochemical XOR gate function that avoids many of the pitfalls of earlier realizations based on biocatalytic cascades. Inputs-represented by pairs of chemicals-cross-react to largely cancel out when both are nearly equal. The cross-reaction can be designed to also optimize gate functioning for noise handling. When not equal, the residual inputs are further processed to result in the output of the XOR type, by biocatalytic steps that allow for further gate-function optimization. The quality of the realized XOR gate is theoretically analyzed.
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Affiliation(s)
- Yaroslav Filipov
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA.,Department of Physics, Clarkson University, Potsdam, NY, 13699, USA
| | - Sergii Domanskyi
- Department of Physics, Clarkson University, Potsdam, NY, 13699, USA
| | - Mackenna L Wood
- Department of Physics, Clarkson University, Potsdam, NY, 13699, USA
| | - Maria Gamella
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, NY, 13699, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
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Agudelo J, Privman V, Halámek J. Promises and Challenges in Continuous Tracking Utilizing Amino Acids in Skin Secretions for Active Multi-Factor Biometric Authentication for Cybersecurity. Chemphyschem 2017; 18:1714-1720. [DOI: 10.1002/cphc.201700044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Juliana Agudelo
- Department of Chemistry, University at Albany; State University of New York; Albany NY 12222 USA
| | - Vladimir Privman
- Department of Physics; Clarkson University; Potsdam NY 13699 USA
| | - Jan Halámek
- Department of Chemistry, University at Albany; State University of New York; Albany NY 12222 USA
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10
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Enzyme‐Based Logic Gates and Networks with Output Signals Analyzed by Various Methods. Chemphyschem 2017; 18:1688-1713. [DOI: 10.1002/cphc.201601402] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Indexed: 01/16/2023]
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11
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Wood ML, Domanskyi S, Privman V. Design of High Quality Chemical XOR Gates with Noise Reduction. Chemphyschem 2017; 18:1773-1781. [DOI: 10.1002/cphc.201700018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Mackenna L. Wood
- Department of Physics; Clarkson University; Potsdam NY 13676 USA
| | - Sergii Domanskyi
- Department of Physics; Clarkson University; Potsdam NY 13676 USA
| | - Vladimir Privman
- Department of Physics; Clarkson University; Potsdam NY 13676 USA
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12
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Domanskyi S, Privman V. Modeling and Modifying Response of Biochemical Processes for Biocomputing and Biosensing Signal Processing. EMERGENCE, COMPLEXITY AND COMPUTATION 2017. [DOI: 10.1007/978-3-319-33921-4_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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13
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Katz E, Poghossian A, Schöning MJ. Enzyme-based logic gates and circuits-analytical applications and interfacing with electronics. Anal Bioanal Chem 2016; 409:81-94. [PMID: 27900435 DOI: 10.1007/s00216-016-0079-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 12/24/2022]
Abstract
The paper is an overview of enzyme-based logic gates and their short circuits, with specific examples of Boolean AND and OR gates, and concatenated logic gates composed of multi-step enzyme-biocatalyzed reactions. Noise formation in the biocatalytic reactions and its decrease by adding a "filter" system, converting convex to sigmoid response function, are discussed. Despite the fact that the enzyme-based logic gates are primarily considered as components of future biomolecular computing systems, their biosensing applications are promising for immediate practical use. Analytical use of the enzyme logic systems in biomedical and forensic applications is discussed and exemplified with the logic analysis of biomarkers of various injuries, e.g., liver injury, and with analysis of biomarkers characteristic of different ethnicity found in blood samples on a crime scene. Interfacing of enzyme logic systems with modified electrodes and semiconductor devices is discussed, giving particular attention to the interfaces functionalized with signal-responsive materials. Future perspectives in the design of the biomolecular logic systems and their applications are discussed in the conclusion. Graphical Abstract Various applications and signal-transduction methods are reviewed for enzyme-based logic systems.
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Affiliation(s)
- Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA.
| | - Arshak Poghossian
- Institute of Nano- and Biotechnologies, FH Aachen, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Mußmann-Str. 1, 52428, Jülich, Germany. .,Peter Grünberg Institute (PGI-8), Research Centre Jülich GmbH, 52425, Jülich, Germany.
| | - Michael J Schöning
- Institute of Nano- and Biotechnologies, FH Aachen, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Mußmann-Str. 1, 52428, Jülich, Germany. .,Peter Grünberg Institute (PGI-8), Research Centre Jülich GmbH, 52425, Jülich, Germany.
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Gorecki J, Gorecka JN, Nowakowski B, Ueno H, Yoshikawa K. How many enzyme molecules are needed for discrimination oriented applications? Phys Chem Chem Phys 2016; 18:20518-27. [PMID: 27405538 DOI: 10.1039/c6cp03860c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical reactions establish a molecular mechanism for information processing in living organisms. Here we consider a simple enzymatic reaction model that can be used to discriminate parameters characterizing periodic reagent inflow. Numerical simulations based on the kinetic equations show that there exist a range of inflow frequencies and amplitudes in which the time evolution of the system is very sensitive to small changes in the values of these parameters. However, the kinetic equations are derived for the thermodynamic limit, whereas in a real biological medium, like a cell, the number of enzyme molecules is an integer and finite. We use stochastic simulations to estimate discriminator reliability as a function of the number of enzyme molecules involved. For systems with 10 000 molecules the functionality predicted by kinetic equations is confirmed. If the number of molecules is decreased to 100, discrimination becomes unreliable.
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Affiliation(s)
- Jerzy Gorecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Joanna N Gorecka
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Bogdan Nowakowski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland. and SGGW, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Hiroshi Ueno
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
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15
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Verma A, Fratto BE, Privman V, Katz E. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications. SENSORS 2016; 16:s16071042. [PMID: 27399702 PMCID: PMC4969838 DOI: 10.3390/s16071042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 02/07/2023]
Abstract
We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.
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Affiliation(s)
- Arjun Verma
- Department of Physics, Clarkson University, Potsdam, NY 13699, USA.
| | - Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
| | - Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, NY 13699, USA.
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
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16
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Biocomputing — tools, aims, perspectives. Curr Opin Biotechnol 2015; 34:202-8. [DOI: 10.1016/j.copbio.2015.02.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 12/20/2022]
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17
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Notes on stochastic (bio)-logic gates: computing with allosteric cooperativity. Sci Rep 2015; 5:9415. [PMID: 25976626 PMCID: PMC5386197 DOI: 10.1038/srep09415] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/24/2015] [Indexed: 11/30/2022] Open
Abstract
Recent experimental breakthroughs have finally allowed to implement in-vitro reaction kinetics (the so called enzyme based logic) which code for two-inputs logic gates and mimic the stochastic AND (and NAND) as well as the stochastic OR (and NOR). This accomplishment, together with the already-known single-input gates (performing as YES and NOT), provides a logic base and paves the way to the development of powerful biotechnological devices. However, as biochemical systems are always affected by the presence of noise (e.g. thermal), standard logic is not the correct theoretical reference framework, rather we show that statistical mechanics can work for this scope: here we formulate a complete statistical mechanical description of the Monod-Wyman-Changeaux allosteric model for both single and double ligand systems, with the purpose of exploring their practical capabilities to express noisy logical operators and/or perform stochastic logical operations. Mixing statistical mechanics with logics, and testing quantitatively the resulting findings on the available biochemical data, we successfully revise the concept of cooperativity (and anti-cooperativity) for allosteric systems, with particular emphasis on its computational capabilities, the related ranges and scaling of the involved parameters and its differences with classical cooperativity (and anti-cooperativity).
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18
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Privman V, Domanskyi S, Mailloux S, Holade Y, Katz E. Kinetic Model for a Threshold Filter in an Enzymatic System for Bioanalytical and Biocomputing Applications. J Phys Chem B 2014; 118:12435-43. [DOI: 10.1021/jp508224y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | | | | | - Yaovi Holade
- Université de Poitiers, IC2MP, UMR-CNRS 7285, 4 rue Michel Brunet, B27 TSA 51106, 86073 Poitiers Cedex 9, France
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Mailloux S, Guz N, Zakharchenko A, Minko S, Katz E. Majority and minority gates realized in enzyme-biocatalyzed systems integrated with logic networks and interfaced with bioelectronic systems. J Phys Chem B 2014; 118:6775-84. [PMID: 24873717 DOI: 10.1021/jp504057u] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Biocatalytic reactions operating in parallel and resulting in reduction of NAD(+) or oxidation of NADH were used to mimic 3-input majority and minority logic gates, respectively. The substrates corresponding to the enzyme reactions were used as the input signals. When the input signals were applied at their high concentrations, defined as logic 1 input values, the corresponding biocatalytic reactions were activated, resulting in changes of the NADH concentration defined as the output signal. The NADH concentration changes were dependent on the number of parallel reactions activated by the input signals. The absence of the substrates, meaning their logic 0 input values, kept the reactions mute with no changes in the NADH concentration. In the system mimicking the majority function, the enzyme-biocatalyzed reactions resulted in a higher production of NADH when more than one input signal was applied at the logic 1 value. Another system mimicking the minority function consumed more NADH, thus leaving a smaller residual output signal, when more than one input signal was applied at the logic 1 value. The performance of the majority gate was improved by processing the output signal through a filter system in which another biocatalytic reaction consumed a fraction of the output signal, thus reducing its physical value to zero when the logic 0 value was obtained. The majority gate was integrated with a preceding AND logic gate to illustrate the possibility of complex networks. The output signal, NADH, was also used to activate a process mimicking drug release, thus illustrating the use of the majority gate in decision-making biomedical systems. The 3-input majority gate was also used as a switchable AND/OR gate when one of the input signals was reserved as a command signal, switching the logic operation for processing of the other two inputs. Overall, the designed majority and minority logic gates demonstrate novel functions of biomolecular information processing systems.
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Affiliation(s)
- Shay Mailloux
- Department of Chemistry and Biomolecular Science, Clarkson University , Potsdam, New York 13699-5810, United States
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Privman V, Zavalov O, Halámková L, Moseley F, Halámek J, Katz E. Networked Enzymatic Logic Gates with Filtering: New Theoretical Modeling Expressions and Their Experimental Application. J Phys Chem B 2013; 117:14928-39. [DOI: 10.1021/jp408973g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | | | - Lenka Halámková
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | | | - Jan Halámek
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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