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Facile and diverse logic circuits based on dumbbell DNA-templated fluorescent copper nanoclusters and S1 nuclease detection. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Filipov Y, Bollella P, Katz E. Not-XOR (NXOR) Logic Gate Realized with Enzyme-Catalyzed Reactions: Optical and Electrochemical Signal Transduction. Chemphyschem 2019; 20:2082-2092. [PMID: 31233266 DOI: 10.1002/cphc.201900528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/19/2019] [Indexed: 11/06/2022]
Abstract
The studied enzyme-based biocatalytic system mimics NXOR Boolean logic gate, which is a logical operator that corresponds to equality in Boolean algebra. It gives the functional value true (1) if both functional arguments (input signals) have the same logical value (0,0 or 1,1), and false (0) if they are different (0,1 or 1,0). The output signal producing reaction is catalyzed by pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH), which is inhibited at acidic and basic pH values. Two other reactions catalyzed by esterase and urease produce acetic acid and ammonium hydroxide, respectively, shifting solution pH from the optimum pH for PQQ-GDH to acidic and basic values (1,0 and 0,1 input combinations, respectively), thus switching the enzyme activity off (output 0). When the input signals are not applied (0,0 combination) or both applied compensating each other (1,1 combination) the optimum pH is preserved, thus keeping PQQ-GDH running at the high rate (output 1). The biocatalytic cascade mimicking the NXOR gate was characterized optically and electrochemically. In the electrochemical experiments the PQQ-GDH enzyme communicated electronically with a conducting electrode support, thus resulting in the electrocatalytic current when signal combinations 0,0 and 1,1 were applied. The logic gate operation, when it was realized electrochemically, was also extended to the biomolecular release controlled by the gate. The release system included two electrodes, one performing the NXOR gate and another one activated for the release upon electrochemically stimulated alginate hydrogel dissolution. The studied system represents a general approach to the biocatalytic realization of the NXOR logic gate, which can be included in different catalytic cascades mimicking operation of concatenated gates in sophisticated logic circuitries.
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Affiliation(s)
- Yaroslav Filipov
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699 (USA)
| | - 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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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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Tavakoli J, Tang Y. Hydrogel Based Sensors for Biomedical Applications: An Updated Review. Polymers (Basel) 2017; 9:E364. [PMID: 30971040 PMCID: PMC6418953 DOI: 10.3390/polym9080364] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/10/2017] [Accepted: 08/12/2017] [Indexed: 02/07/2023] Open
Abstract
Biosensors that detect and convert biological reactions to a measurable signal have gained much attention in recent years. Between 1950 and 2017, more than 150,000 papers have been published addressing the applications of biosensors in different industries, but to the best of our knowledge and through careful screening, critical reviews that describe hydrogel based biosensors for biomedical applications are rare. This review discusses the biomedical application of hydrogel based biosensors, based on a search performed through Web of Science Core, PubMed (NLM), and Science Direct online databases for the years 2000⁻2017. In this review, we consider bioreceptors to be immobilized on hydrogel based biosensors, their advantages and disadvantages, and immobilization techniques. We identify the hydrogels that are most favored for this type of biosensor, as well as the predominant transduction strategies. We explain biomedical applications of hydrogel based biosensors including cell metabolite and pathogen detection, tissue engineering, wound healing, and cancer monitoring, and strategies for small biomolecules such as glucose, lactate, urea, and cholesterol detection are identified.
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Affiliation(s)
- Javad Tavakoli
- Medical Device Research Institute, College of Science and Engineering, Flinders University, Adelaide 5042, SA, Australia.
| | - Youhong Tang
- Institute for Nano Scale Science & Technology, College of Science and Engineering, Flinders University, Adelaide 5042, SA, Australia.
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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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Fratto BE, Guz N, Fallon TT, Katz E. An Enzyme-based 1:2 Demultiplexer Interfaced with an Electrochemical Actuator. Chemphyschem 2016; 18:1721-1725. [PMID: 27481283 DOI: 10.1002/cphc.201600799] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Indexed: 12/26/2022]
Abstract
An enzyme-based 1:2 demultiplexer is designed in a flow system composed of three cells where each one is modified with a different enzyme: hexokinase, glucose dehydrogenase and glucose-6-phosphate dehydrogenase. The Input signal activating the biocatalytic cascade is represented by glucose, while the Address signal represented by ATP is responsible for directing the Input signal to one of the output channels, depending on the logic value of the Address. The biomolecular 1:2 demultiplexer is extended to include two electrochemical actuators releasing entrapped DNA molecules in the active output channel. The modular design of the system allows for easy exchange and extension of the functional elements. The present demultiplexer can be easily integrated in various biomolecular logic systems, including different logic gates based on the enzyme- or DNA-based reactions, as well as containing different chemical actuators, for example, with a biomolecular release function.
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Affiliation(s)
- Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Nataliia Guz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Tyler T Fallon
- 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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Varghese S, Elemans JAAW, Rowan AE, Nolte RJM. Molecular computing: paths to chemical Turing machines. Chem Sci 2015; 6:6050-6058. [PMID: 28717447 PMCID: PMC5504628 DOI: 10.1039/c5sc02317c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/06/2015] [Indexed: 11/21/2022] Open
Abstract
In this perspective, we highlight some of the recent advances in the development of molecular and biomolecular systems for performing logic operations and computing. We also present a blueprint of a chemical Turing machine using a processive catalytic approach.
To comply with the rapidly increasing demand of information storage and processing, new strategies for computing are needed. The idea of molecular computing, where basic computations occur through molecular, supramolecular, or biomolecular approaches, rather than electronically, has long captivated researchers. The prospects of using molecules and (bio)macromolecules for computing is not without precedent. Nature is replete with examples where the handling and storing of data occurs with high efficiencies, low energy costs, and high-density information encoding. The design and assembly of computers that function according to the universal approaches of computing, such as those in a Turing machine, might be realized in a chemical way in the future; this is both fascinating and extremely challenging. In this perspective, we highlight molecular and (bio)macromolecular systems that have been designed and synthesized so far with the objective of using them for computing purposes. We also present a blueprint of a molecular Turing machine, which is based on a catalytic device that glides along a polymer tape and, while moving, prints binary information on this tape in the form of oxygen atoms.
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Affiliation(s)
- Shaji Varghese
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
| | - Johannes A A W Elemans
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
| | - Alan E Rowan
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
| | - Roeland J M Nolte
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
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Ma DL, He HZ, Chan DSH, Leung CH. Simple DNA-based logic gates responding to biomolecules and metal ions. Chem Sci 2013. [DOI: 10.1039/c3sc50924a] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Electrode interfaces switchable by physical and chemical signals for biosensing, biofuel, and biocomputing applications. Anal Bioanal Chem 2012; 405:3659-72. [DOI: 10.1007/s00216-012-6525-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 01/26/2023]
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Katz E, Bocharova V, Privman M. Electronic interfaces switchable by logically processed multiple biochemical and physiological signals. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm30172e] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Bocharova V, Katz E. Switchable electrode interfaces controlled by physical, chemical and biological signals. CHEM REC 2011; 12:114-30. [DOI: 10.1002/tcr.201100025] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Indexed: 11/10/2022]
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Pu F, Ren J, Yang X, Qu X. Multivalued Logic Gates Based on DNA. Chemistry 2011; 17:9590-4. [DOI: 10.1002/chem.201101140] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 05/27/2011] [Indexed: 11/09/2022]
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Zhou M, Wang F, Dong S. Boolean logic gates based on oxygen-controlled biofuel cell in “one pot”. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.01.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Silva-Rocha R, Tamames J, dos Santos VM, de Lorenzo V. The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol 2011; 13:2389-402. [PMID: 21410625 DOI: 10.1111/j.1462-2920.2011.02455.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The regulatory and metabolic networks that rule biodegradation of pollutants by environmental bacteria are wired to the rest of the cellular physiology through both transcriptional factors and intermediary signal molecules. In this review, we examine some formalisms for describing catalytic/regulatory circuits of this sort and advocate the adoption of Boolean logic for combining transcriptional and enzymatic occurrences in the same biological system. As an example, we show how known regulatory and metabolic actions that bring about biodegradation of m-xylene by Pseudomonas putida mt-2 can be represented as clusters of binary operations and then reconstructed as a digital network. Despite the many simplifications, Boolean tools still capture the gross behaviour of the system even in the absence of kinetic constants determined experimentally. On this basis, we argue that still with a limited volume of data binary formalisms allow us to penetrate the raison d'être of extant regulatory and metabolic architectures.
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Affiliation(s)
- Rafael Silva-Rocha
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, 28049, Spain
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Pita M, Privman V, Arugula MA, Melnikov D, Bocharova V, Katz E. Towards biochemical filters with a sigmoidal response to pH changes: buffered biocatalytic signal transduction. Phys Chem Chem Phys 2011; 13:4507-13. [DOI: 10.1039/c0cp02524k] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Digital biosensors with built-in logic for biomedical applications—biosensors based on a biocomputing concept. Anal Bioanal Chem 2010; 398:1591-603. [DOI: 10.1007/s00216-010-3746-0] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 04/11/2010] [Accepted: 04/12/2010] [Indexed: 11/29/2022]
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Katz E, Pita M. Biofuel Cells Controlled by Logically Processed Biochemical Signals: Towards Physiologically Regulated Bioelectronic Devices. Chemistry 2009; 15:12554-64. [DOI: 10.1002/chem.200902367] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Privman M, Tam TK, Pita M, Katz E. Switchable Electrode Controlled by Enzyme Logic Network System: Approaching Physiologically Regulated Bioelectronics. J Am Chem Soc 2008; 131:1314-21. [DOI: 10.1021/ja8088108] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marina Privman
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory, Clarkson University, Potsdam, New York 13699-5810, and Empire State College, State University of New York, Post Office Box 940, Black River, New York 13612-0009
| | - Tsz Kin Tam
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory, Clarkson University, Potsdam, New York 13699-5810, and Empire State College, State University of New York, Post Office Box 940, Black River, New York 13612-0009
| | - Marcos Pita
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory, Clarkson University, Potsdam, New York 13699-5810, and Empire State College, State University of New York, Post Office Box 940, Black River, New York 13612-0009
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory, Clarkson University, Potsdam, New York 13699-5810, and Empire State College, State University of New York, Post Office Box 940, Black River, New York 13612-0009
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Amir L, Tam TK, Pita M, Meijler MM, Alfonta L, Katz E. Biofuel Cell Controlled by Enzyme Logic Systems. J Am Chem Soc 2008; 131:826-32. [DOI: 10.1021/ja8076704] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liron Amir
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, New York 13699-5810, and Departments of Biotechnology Engineering and Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Tsz Kin Tam
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, New York 13699-5810, and Departments of Biotechnology Engineering and Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Marcos Pita
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, New York 13699-5810, and Departments of Biotechnology Engineering and Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Michael M. Meijler
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, New York 13699-5810, and Departments of Biotechnology Engineering and Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Lital Alfonta
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, New York 13699-5810, and Departments of Biotechnology Engineering and Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, New York 13699-5810, and Departments of Biotechnology Engineering and Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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