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Imbriano A, Tricase A, Macchia E, Torsi L, Bollella P. Self-powered logically operated fluorescent detection of hepatitis B virus (HBV). Anal Chim Acta 2023; 1252:341037. [PMID: 36935148 DOI: 10.1016/j.aca.2023.341037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
In this study, a novel sensing strategy based on double sensing/actuating pathway is demonstrated, being capable to trigger the DNA-based AND gate for the sensitive and selective detection of hepatitis B virus DNA (HBV-DNA). Such an approach encompasses an enzymatic machinery logically operated using the variation of physiologically relevant biomarkers for liver dysfunctions. Alanine aminotransferase (ALT) and lactate dehydrogenase (LDH) are used as inputs of an AND gate generating an output signal, namely lactate. In particular, lactate is oxidized back to pyruvate at the anodic electrode by lactate oxidase connected in mediated electron transfer through ferrocene moieties (creating an amplifying recycling mechanism). The anodic electrode is further connected with a Myrothecium verrucaria bilirubin oxidase (MvBOx) based biocathode modified with SiO2 nanoparticles (SiO2NPs) functionalized with phenyl boronic acid and trigonelline, triggering the release of quenching DNA (qDNA) upon local pH change at the electrode surface (notably, modified SiONPs gets negatively recharged upon local pH gradient releasing negatively charged DNA). Next, the released qDNA labeled with BHQ2 and detecting DNA (dDNA, labeled with FAM) are detecting HBV-DNA. The proposed biosensor can discriminate between the absence and presence of HBV-DNA setting the threshold at 0.05 fM in model buffer solutions and 1 fM in human serum. This enzymatic/DNA logic network can be of particular interest for future biomedical applications (e.g., early detection of liver cancer disease etc.). In the future development this technology could be easily integrated with a smartphone camera, allowing more user-friendly applications.
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Affiliation(s)
- Anna Imbriano
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy
| | - Angelo Tricase
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy
| | - Eleonora Macchia
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Faculty of Science and Engineering, Åbo Akademi University, 20500, Turku, Finland
| | - Luisa Torsi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Faculty of Science and Engineering, Åbo Akademi University, 20500, Turku, Finland
| | - Paolo Bollella
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy.
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Bollella P. Enzyme-based amperometric biosensors: 60 years later … Quo Vadis? Anal Chim Acta 2022; 1234:340517. [DOI: 10.1016/j.aca.2022.340517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/01/2022]
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Bollella P, Guo Z, Edwardraja S, Krishna Kadambar V, Alexandrov K, Melman A, Katz E. Self-powered molecule release systems activated with chemical signals processed through reconfigurable Implication or Inhibition Boolean logic gates. Bioelectrochemistry 2020; 138:107735. [PMID: 33482577 DOI: 10.1016/j.bioelechem.2020.107735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023]
Abstract
The Implication (IMPLY) and Inhibition (INHIB) Boolean logic gates were realized using switchable chimeric pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH-Clamp) containing a fused affinity clamp unit recognizing a signal-peptide. The second component of the logic gate was the wild-type PQQ-glucose dehydrogenase working cooperatively with the PQQ-GDH-Clamp enzyme. The IMPLY and INHIB gates were realized using the same enzyme composition activated with differently defined input signals, thus representing reconfigurable logic systems. The logic gates were first tested while operating in a solution with optical analysis of the output signals. Then, the enzymes were immobilized on a buckypaper electrode for electrochemical transduction of the output signals. The switchable modified electrodes mimicking the IMPLY or INHIB logic gates were integrated with an oxygen-reducing electrode modified with bilirubin oxidase to operate as a biofuel cell activated/inhibited by various input signal combinations processed either by IMPLY or INHIB logic gates. The switchable biofuel cell was used as a self-powered device triggering molecule release function controlled by the logically processed molecule signals.
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Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699, USA.
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane 4001, QLD, Australia
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane 4072, QLD, Australia
| | - Vasantha Krishna Kadambar
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699, USA
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane 4001, QLD, Australia.
| | - Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699, USA.
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699, USA.
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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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Mohammadniaei M, Park C, Min J, Sohn H, Lee T. Fabrication of Electrochemical-Based Bioelectronic Device and Biosensor Composed of Biomaterial-Nanomaterial Hybrid. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1064:263-296. [PMID: 30471039 PMCID: PMC7120487 DOI: 10.1007/978-981-13-0445-3_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of bioelectronics has paved the way for the development of biochips, biomedical devices, biosensors and biocomputation devices. Various biosensors and biomedical devices have been developed to commercialize laboratory products and transform them into industry products in the clinical, pharmaceutical, environmental fields. Recently, the electrochemical bioelectronic devices that mimicked the functionality of living organisms in nature were applied to the use of bioelectronics device and biosensors. In particular, the electrochemical-based bioelectronic devices and biosensors composed of biomolecule-nanoparticle hybrids have been proposed to generate new functionality as alternatives to silicon-based electronic computation devices, such as information storage, process, computations and detection. In this chapter, we described the recent progress of bioelectronic devices and biosensors based on biomaterial-nanomaterial hybrid.
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Affiliation(s)
- Mohsen Mohammadniaei
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, South Korea
| | - Chulhwan Park
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea
| | - Junhong Min
- School of Integrative Engineering Chung-Ang University, Seoul, South Korea
| | - Hiesang Sohn
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
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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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Li M, Wang Z, Liang J, Yao H, Shen L, Liu H, Fan L. A chemical/molecular 4-input/2-output keypad lock with easy resettability based on red-emission carbon dots-Prussian blue composite film electrodes. NANOSCALE 2018; 10:7484-7493. [PMID: 29637973 DOI: 10.1039/c8nr01258j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work, a resettable 4-input/2-output keypad lock system based on red-emission carbon dots (rCDs) and Prussian blue (PB) modified electrodes was developed. Electrochromic PB layers were first electrochemically deposited on the indium tin oxide (ITO) electrode surface. An admixture of rCDs and chitosan (Chi) was then cast on the surface of PB layers, forming rCDs-Chi/PB film electrodes. UV-vis absorption of the films was sensitive to the applied potential since the blue PB constituent of the films would be transformed to nearly colorless Prussian white (PW) at the reduction potential of -0.2 V and then from PW back to PB at the oxidation potential of 0.4 V, and the transformation between PB and PW would also influence the fluorescence emission of the rCD constituent in the films. The addition of cysteine (Cys) in the testing solution could reduce the PB in the films into PW and generate an amperometric electrocatalytic current at 0.4 V. Meanwhile, the addition of Fe3+ in solution could greatly quench the fluorescence from the rCD component in the films. Thus, the responses of UV-vis absorbance, fluorescence emission and amperometric current of the rCDs-Chi/PB film electrode system exhibited potential-, Cys- and Fe3+-responsive switching properties. Based on the aforementioned work, a combinational logic gate circuit with 3 inputs and 3 outputs was established. In particular, on the same platform, a novel chemical/molecular 4-input/2-output keypad lock with easy resettability was elaborately designed with amperometric current and fluorescence peak intensity as two different types of outputs, so that a higher security level could be achieved.
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Affiliation(s)
- Menglu Li
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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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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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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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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Computational Biosensors: Molecules, Algorithms, and Detection Platforms. MODELING, METHODOLOGIES AND TOOLS FOR MOLECULAR AND NANO-SCALE COMMUNICATIONS 2017. [PMCID: PMC7123247 DOI: 10.1007/978-3-319-50688-3_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Advanced nucleic acid-based sensor-applications require computationally intelligent biosensors that are able to concurrently perform complex detection and classification of samples within an in vitro platform. Realization of these cutting-edge computational biosensor systems necessitates innovation and integration of three key technologies: molecular probes with computational capabilities, algorithmic methods to enable in vitro computational post processing and classification, and immobilization and detection approaches that enable the realization of deployable computational biosensor platforms. We provide an overview of current technologies, including our contributions towards the development of computational biosensor systems.
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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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Label-free fluorescent enzymatic assay of citrate synthase by CoA-Au(I) co-ordination polymer and its application in a multi-enzyme logic gate cascade. Biosens Bioelectron 2016; 86:1038-1046. [PMID: 27501341 DOI: 10.1016/j.bios.2016.07.107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/20/2016] [Accepted: 07/29/2016] [Indexed: 01/13/2023]
Abstract
Citrate synthase (CS) is one of the key metabolic enzymes in the Krebs tricarboxylic acid (TCA) cycle. It regulates energy generation in mitochondrial respiration by catalysing the reaction between oxaloacetic acid (OAA) and acetyl coenzyme A (Ac-CoA) to generate citrate and coenzyme A (CoA). CS has been shown to be a biomarker of neurological diseases and various kinds of cancers. Here, a label-free fluorescent assay has been developed for homogeneously detecting CS and its inhibitor based on the in situ generation of CoA-Au(I) co-ordination polymer (CP) and the fluorescence signal-on by SYBR Green II-stained CoA-Au(I) CP. Because of the unique property of the CoA-Au(I) CP, this CS activity assay method could achieve excellent selectivity and sensitivity, with a linear range from 0.0033 U/μL to 0.264 U/μL and a limit of detection to be 0.00165 U/μL. Meanwhile, this assay method has advantages of being facile and cost effective with quick detection. Moreover, based on this method, a biomimetic logic system was established by rationally exploiting the cascade enzymatic interactions in TCA cycle for chemical information processing. In the TCA cycle-derived logic system, an AND-AND-AND-cascaded gate was rigorously operated step by step in one pot, and is outputted by a label-free fluorescent signal with visualized readout.
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Yoon J, Chung YH, Lee T, Kim JH, Kim J, Choi JW. A biomemory chip composed of a myoglobin/CNT heterolayer fabricated by the protein-adsorption-precipitation-crosslinking (PAPC) technique. Colloids Surf B Biointerfaces 2015; 136:853-8. [PMID: 26539811 DOI: 10.1016/j.colsurfb.2015.10.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/15/2015] [Accepted: 10/20/2015] [Indexed: 11/19/2022]
Abstract
In this study, a biomemory chip consisting of a myoglobin/carbon nanotube (CNT) heterolayer is fabricated via the protein-adsorption-precipitation-crosslinking (PAPC) technique for electrochemical signal enhancement, long-term stability, and improved memory function. The PAPC technique is used to fabricate a myoglobin/CNT heterolayer with a CNT core and a high-density myoglobin-shell structure to achieve efficient heterolayer formation and improved performance of the heterolayer. The fabricated myoglobin/CNT heterolayer is immobilized onto a Au substrate through a chemical linker. The surface morphology of the deposited heterolayer is investigated via transmission electron microscopy and atomic force microscopy. The redox properties of the myoglobin/CNT heterolayer are investigated by cyclic voltammetry, and the memory function of the heterolayer, including the "write step" and "erase step," is measured by chronoamperometry. Compared with the myoglobin monolayer without CNT, the myoglobin/CNT heterolayer fabricated by the PAPC technique exhibits greater electrochemical signal enhancement, long-term stability at room temperature, and improved memory function. The results suggest that the proposed myoglobin/CNT heterolayer produced via the PAPC technique can be applied as a platform for bioelectronic devices to achieve improved signal intensity and durability.
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Affiliation(s)
- Jinho Yoon
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 121-742, Republic of Korea
| | - Yong-Ho Chung
- Department of Chemical Engineering, Hoseo University, 20, Hoseo-ro 79 Beon-gil, Baebang-eup, Asan City, Chungnam 336-795, Republic of Korea
| | - Taek Lee
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 121-742, Republic of Korea
| | - Jae Hyun Kim
- Department of Chemical and Biological Engineering, Korea University, Anam 5-ga, Seoungbuk-gu, Seoul 136-701, Republic of Korea
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Anam 5-ga, Seoungbuk-gu, Seoul 136-701, Republic of Korea
| | - Jeong-Woo Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 121-742, Republic of Korea.
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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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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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Abstract
AbstractThe focus of this review paper is on the design and implementation of smart ‘Sense-and-Treat’ systems using enzyme-biocatalytic systems. These systems were used to perform biomolecular computing and they were functionally integrated with signal responsive materials aiming towards their biomedical use. Electrode interfaces, functionalized with signal-responsive materials, find applications in biocomputing, biosensing, and, specifically, triggered release of bioactive substances. ‘Sense-and-Treat’ systems require multiple components working together, including biosensors, actuators, and filters, in order to achieve closed-loop and autonomous operation. In general, biochemical logic networks were developed to process single biochemical or chemical inputs as well as multiple inputs, responding to nonphysiological (for concept demonstration purposes) and physiological signals (for injury detection or diagnosis). Actuation of drug-mimicking release was performed using the responsive material iron-cross-linked alginate with entrapped biomolecular species, responding to physical, chemical or biochemical signals.
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Mailloux S, Zavalov O, Guz N, Katz E, Bocharova V. Enzymatic filter for improved separation of output signals in enzyme logic systems towards ‘sense and treat’ medicine. Biomater Sci 2014; 2:184-191. [DOI: 10.1039/c3bm60197h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Gdor E, Katz E, Mandler D. Biomolecular AND Logic Gate Based on Immobilized Enzymes with Precise Spatial Separation Controlled by Scanning Electrochemical Microscopy. J Phys Chem B 2013; 117:16058-65. [DOI: 10.1021/jp4095672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Efrat Gdor
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Evgeny Katz
- Department
of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, United States
| | - Daniel Mandler
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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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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21
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Yamamoto K, Matsumoto T, Shimada S, Tanaka T, Kondo A. Starchy biomass-powered enzymatic biofuel cell based on amylases and glucose oxidase multi-immobilized bioanode. N Biotechnol 2013; 30:531-5. [DOI: 10.1016/j.nbt.2013.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/04/2013] [Accepted: 04/16/2013] [Indexed: 11/26/2022]
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22
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Privman V, Zavalov O, Simonian A. Extended Linear Response for Bioanalytical Applications Using Multiple Enzymes. Anal Chem 2013; 85:2027-31. [DOI: 10.1021/ac302998y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, New York 13699, United
States
| | - Oleksandr Zavalov
- Department of Physics, Clarkson University, Potsdam, New York 13699, United
States
| | - Aleksandr Simonian
- Materials Research
and Education
Center, Auburn University, Auburn, Alabama
36849, United States
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23
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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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24
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Biocatalytic Enzyme Networks Designed for Binary-Logic Control of Smart Electroactive Nanobiointerfaces. Top Catal 2012. [DOI: 10.1007/s11244-012-9894-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Zhou M, Wang J. Biofuel Cells for Self-Powered Electrochemical Biosensing and Logic Biosensing: A Review. ELECTROANAL 2012. [DOI: 10.1002/elan.201100631] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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26
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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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27
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Halámek J, Bocharova V, Arugula MA, Strack G, Privman V, Katz E. Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate. J Phys Chem B 2011; 115:9838-45. [DOI: 10.1021/jp2041372] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Halámek
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Vera Bocharova
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Mary A. Arugula
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Guinevere Strack
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Vladimir Privman
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
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28
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Gil B, Kahan-Hanum M, Skirtenko N, Adar R, Shapiro E. Detection of multiple disease indicators by an autonomous biomolecular computer. NANO LETTERS 2011; 11:2989-2996. [PMID: 21671655 DOI: 10.1021/nl2015872] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The promise of biomolecular computers is their ability to interact with naturally occurring biomolecules, enabling in the future the development of context-dependent programmable drugs. Here we show a context-sensing mechanism of a biomolecular automaton that can simultaneously sense different types of molecules, allowing future integration of biomedical knowledge on a broad range of molecular disease symptoms in the decision of a biomolecular computer to release a drug molecule.
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Affiliation(s)
- Binyamin Gil
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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29
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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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30
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Katz E. Processing electrochemical signals at both sides of interface: electronic vs. chemical signal processing. J Solid State Electrochem 2011. [DOI: 10.1007/s10008-011-1300-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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32
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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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33
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Sreejith S, Divya KP, Manojkumar TK, Ajayaghosh A. Multiple Analyte Response and Molecular Logic Operations by Excited-State Charge-Transfer Modulation in a Bipyridine Integrated Fluorophore. Chem Asian J 2010; 6:430-7. [DOI: 10.1002/asia.201000637] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Indexed: 11/06/2022]
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34
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Halámek J, Bocharova V, Chinnapareddy S, Windmiller JR, Strack G, Chuang MC, Zhou J, Santhosh P, Ramirez GV, Arugula MA, Wang J, Katz E. Multi-enzyme logic network architectures for assessing injuries: digital processing of biomarkers. MOLECULAR BIOSYSTEMS 2010; 6:2554-60. [PMID: 20953502 DOI: 10.1039/c0mb00153h] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A multi-enzyme biocatalytic cascade processing simultaneously five biomarkers characteristic of traumatic brain injury (TBI) and soft tissue injury (STI) was developed. The system operates as a digital biosensor based on concerted function of 8 Boolean AND logic gates, resulting in the decision about the physiological conditions based on the logic analysis of complex patterns of the biomarkers. The system represents the first example of a multi-step/multi-enzyme biosensor with the built-in logic for the analysis of complex combinations of biochemical inputs. The approach is based on recent advances in enzyme-based biocomputing systems and the present paper demonstrates the potential applicability of biocomputing for developing novel digital biosensor networks.
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Affiliation(s)
- Jan Halámek
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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35
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Tu Y, Zhou R, Fang H. Signal transmission, conversion and multiplication by polar molecules confined in nanochannels. NANOSCALE 2010; 2:1976-1983. [PMID: 20820644 DOI: 10.1039/c0nr00304b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The mechanism of signal transmission, conversion and multiplication at molecular level has been of great interest lately, due to its wide applications in nanoscience and nanotechnology. The interferences between authentic signals and thermal noises at the nanoscale make it difficult for molecular signal transduction. Here we review some of our recent progress on the signal transduction mediated by water and other polar molecules confined in nanochannels, such as Y-shaped carbon nanotubes. We also explore possible future directions in this emerging field. These studies on molecular signal conduction might have significance in future designs and applications of nanoscale electronic devices, and might also provide useful insights for a better understanding of signal conduction in both physical and biological systems.
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Affiliation(s)
- Yusong Tu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800, China
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36
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Privman V, Zhou J, Halámek J, Katz E. Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Signal Change. J Phys Chem B 2010; 114:13601-8. [DOI: 10.1021/jp107562p] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir Privman
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
| | - Jian Zhou
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
| | - Jan Halámek
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
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37
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Dadon Z, Samiappan M, Safranchik EY, Ashkenasy G. Light-Induced Peptide Replication Controls Logic Operations in Small Networks. Chemistry 2010; 16:12096-9. [DOI: 10.1002/chem.201001488] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Melnikov D, Strack G, Zhou J, Windmiller JR, Halámek J, Bocharova V, Chuang MC, Santhosh P, Privman V, Wang J, Katz E. Enzymatic AND Logic Gates Operated Under Conditions Characteristic of Biomedical Applications. J Phys Chem B 2010; 114:12166-74. [DOI: 10.1021/jp105912e] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitriy Melnikov
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Guinevere Strack
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Jian Zhou
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Joshua Ray Windmiller
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Jan Halámek
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Vera Bocharova
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Min-Chieh Chuang
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Padmanabhan Santhosh
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Joseph Wang
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Evgeny Katz
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
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39
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Halámek J, Windmiller JR, Zhou J, Chuang MC, Santhosh P, Strack G, Arugula MA, Chinnapareddy S, Bocharova V, Wang J, Katz E. Multiplexing of injury codes for the parallel operation of enzyme logic gates. Analyst 2010; 135:2249-59. [PMID: 20617272 DOI: 10.1039/c0an00270d] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of a highly parallel enzyme logic sensing concept employing a novel encoding scheme for the determination of multiple pathophysiological conditions is reported. The new concept multiplexes a contingent of enzyme-based logic gates to yield a distinct 'injury code' corresponding to a unique pathophysiological state as prescribed by a truth table. The new concept is illustrated using an array of NAND and AND gates to assess the biomedical significance of numerous biomarker inputs including creatine kinase, lactate dehydrogenase, norepinephrine, glutamate, alanine transaminase, lactate, glucose, glutathione disulfide, and glutathione reductase to assess soft-tissue injury, traumatic brain injury, liver injury, abdominal trauma, hemorrhagic shock, and oxidative stress. Under the optimal conditions, physiological and pathological levels of these biomarkers were detected through either optical or electrochemical techniques by monitoring the level of the outputs generated by each of the six logic gates. By establishing a pathologically meaningful threshold for each logic gate, the absorbance and amperometric assays tendered the diagnosis in a digitally encoded 6-bit word, defined as an 'injury code'. This binary 'injury code' enabled the effective discrimination of 64 unique pathological conditions to offer a comprehensive high-fidelity diagnosis of multiple injury conditions. Such processing of relevant biomarker inputs and the subsequent multiplexing of the logic gate outputs to yield a comprehensive 'injury code' offer significant potential for the rapid and reliable assessment of varied and complex forms of injury in circumstances where access to a clinical laboratory is not viable. While the new concept of parallel and multiplexed enzyme logic gates is illustrated here in connection to multi-injury diagnosis, it could be readily extended to a wide range of practical medical, industrial, security and environmental applications.
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Affiliation(s)
- Jan Halámek
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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40
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Xia F, Zuo X, Yang R, White RJ, Xiao Y, Kang D, Gong X, Lubin AA, Vallée-Bélisle A, Yuen JD, Hsu BYB, Plaxco KW. Label-free, dual-analyte electrochemical biosensors: a new class of molecular-electronic logic gates. J Am Chem Soc 2010; 132:8557-9. [PMID: 20527878 PMCID: PMC3082468 DOI: 10.1021/ja101379k] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An "XOR" gate built using label-free, dual-analyte electrochemical sensors and the activation of this logic gate via changing concentrations of cocaine and the relevant cDNA as inputs are described.
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Affiliation(s)
- Fan Xia
- Center for Polymers and Organic Solids, University of California, Santa Barbara, California 93106
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Xiaolei Zuo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Renqiang Yang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, P.R. China
| | - Ryan J. White
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Yi Xiao
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Di Kang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Xiong Gong
- Department of Physics, University of California, Santa Barbara, California 93106
| | - Arica A. Lubin
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Alexis Vallée-Bélisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Jonathan D. Yuen
- Center for Polymers and Organic Solids, University of California, Santa Barbara, California 93106
| | - Ben Y. B. Hsu
- Center for Polymers and Organic Solids, University of California, Santa Barbara, California 93106
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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41
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Arugula MA, Bocharova V, Halámek J, Pita M, Katz E. Enzyme-based multiplexer and demultiplexer. J Phys Chem B 2010; 114:5222-6. [PMID: 20350002 DOI: 10.1021/jp101101b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A digital 2-to-1 multiplexer and a 1-to-2 demultiplexer were mimicked by biocatalytic reactions involving concerted operation of several enzymes. Using glucose oxidase (GOx) and laccase (Lac) as the data input signals and variable pH as the addressing signal, ferrocyanide oxidation in the output channel was selectively activated by one from two inputs, thus mimicking the multiplexer operation. A demultiplexer based on the enzyme system composed of GOx, glucose dehydrogenase (GDH) and horseradish peroxidase (HRP) allowed selective activation of different output channels (oxidation of ferrocyanide or reduction of NAD(+)) by the glucose input. The selection of the output channel was controlled by the addressing input of NAD(+). The designed systems represent important novel components of future branched enzyme networks processing biochemical signals for biosensing and bioactuating.
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Affiliation(s)
- Mary A Arugula
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory, Clarkson University, Potsdam New York 13699-5810, USA
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42
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Wang YJ, Xin BJ, Duan XR, Xing GW, Wang S. Assembly of Anionic Conjugated Polymer with 6-O-Modified PNP-β-Galactoside for Fluorescence Logic-signal-based Multiplex Detections of Enzymes. Macromol Rapid Commun 2010; 31:1473-8. [PMID: 21567554 DOI: 10.1002/marc.201000165] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 04/15/2010] [Indexed: 11/08/2022]
Abstract
Anionic conjugated polymer (PFP-SO 3-) was assembled with a novel enzymatic substrate 6-O-modified PNP-β-galactoside (1) for sensitive multiplex enzyme detections. The PFP-SO 3-/1/lipase/β-galactosidase system has two chemical input signals which are Input 1 (lipase) and Input 2 (β-galactosidase), and output optical signals such as fluorescence emission at 416 nm or 450 nm. Four types of logic gates, including YES, INH, NAND and AND, were successfully constructed and utilized for multiplex detections of lipase and β-galactosidase in one tube.
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Affiliation(s)
- Ya-Juan Wang
- Department of Chemistry, Beijing Normal University, Beijing, 100875, China
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43
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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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44
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45
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46
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Halámek J, Kin Tam T, Strack G, Bocharova V, Pita M, Katz E. Self-powered biomolecular keypad lock security system based on a biofuel cell. Chem Commun (Camb) 2010; 46:2405-7. [DOI: 10.1039/b925484f] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Privman V, Pedrosa V, Melnikov D, Pita M, Simonian A, Katz E. Enzymatic AND-gate based on electrode-immobilized glucose-6-phosphate dehydrogenase: Towards digital biosensors and biochemical logic systems with low noise. Biosens Bioelectron 2009; 25:695-701. [DOI: 10.1016/j.bios.2009.08.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Revised: 08/03/2009] [Accepted: 08/07/2009] [Indexed: 11/16/2022]
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48
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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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49
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Bychkova V, Shvarev A, Zhou J, Pita M, Katz E. Enzyme logic gate associated with a single responsive microparticle: scaling biocomputing to microsize systems. Chem Commun (Camb) 2009; 46:94-6. [PMID: 20024304 DOI: 10.1039/b917611j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A microsize biocomputing system based on enzyme logic processing biochemical signals was developed. Optical transduction of pH signals generated in situ by the enzyme OR logic gate was achieved with the use of a single optode microparticle.
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Affiliation(s)
- Valeriya Bychkova
- Department of Chemistry, and NanoBio Laboratory, Oregon State University, Corvallis, OR 97331, USA
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50
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Switchable electrode controlled by Boolean logic gates using enzymes as input signals. Bioelectrochemistry 2009; 77:69-73. [DOI: 10.1016/j.bioelechem.2009.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 06/13/2009] [Accepted: 06/17/2009] [Indexed: 11/18/2022]
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