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Srivastava R, Bagh S. A Logically Reversible Double Feynman Gate with Molecular Engineered Bacteria Arranged in an Artificial Neural Network-Type Architecture. ACS Synth Biol 2023; 12:51-60. [PMID: 36384003 DOI: 10.1021/acssynbio.2c00520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Reversible logic gates are the key components of reversible computing that map inputs and outputs in a certain one-to-one pattern so that the output signals can reveal the pattern of the input signals. One of the main research foci of reversible computing is the implementation of basic reversible gates by various modalities. Though true thermodynamic reversibility cannot be attained within living cells, the high energy efficiency of biological reactions inspires the implementation of reversible computation in living cells. The implementation of synthetic genetic circuits is mostly based on conventional irreversible computing, and the implementation of logical reversibility in living cells is rare. Here, we constructed a 3-input-3-output synthetic genetic reversible double Feynman logic gate with a population of genetically engineered E. coli cells. Instead of following hierarchical electronic design principles, we adapted the concept of artificial neural networks (ANN) and built a single-layer artificial network-type architecture with five different engineered bacteria, named bactoneurons. We used three extracellular chemicals as input signals and the expression of three fluorescence proteins as the output signals. The cellular devices, which combine the input chemical signals linearly and pass them through a nonlinear activation function and represent specific bactoneurons, were built by designing and creating small synthetic genetic networks inside E. coli. The weights of each of the inputs and biases of individual bactoneurons in the bacterial ANN were adjusted by optimizing the synthetic genetic networks. When arranging the five bactoneurons through an ANN-type architecture, the system generated a double Feynman gate function at the population level. To our knowledge, this is the first reversible double Feynman gate realization with living cells. This work may have significance in development of biocomputer technology, reversible computation, ANN wetware, and synthetic biology.
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Affiliation(s)
- Rajkamal Srivastava
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Block A/F, Sector-I, Bidhannagar, Kolkata700064, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai400094, India
| | - Sangram Bagh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Block A/F, Sector-I, Bidhannagar, Kolkata700064, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai400094, India
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2
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Cellular Computational Logic Using Toehold Switches. Int J Mol Sci 2022; 23:ijms23084265. [PMID: 35457085 PMCID: PMC9033136 DOI: 10.3390/ijms23084265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/16/2022] Open
Abstract
The development of computational logic that carries programmable and predictable features is one of the key requirements for next-generation synthetic biological devices. Despite considerable progress, the construction of synthetic biological arithmetic logic units presents numerous challenges. In this paper, utilizing the unique advantages of RNA molecules in building complex logic circuits in the cellular environment, we demonstrate the RNA-only bitwise logical operation of XOR gates and basic arithmetic operations, including a half adder, a half subtractor, and a Feynman gate, in Escherichia coli. Specifically, de-novo-designed riboregulators, known as toehold switches, were concatenated to enhance the functionality of an OR gate, and a previously utilized antisense RNA strategy was further optimized to construct orthogonal NIMPLY gates. These optimized synthetic logic gates were able to be seamlessly integrated to achieve final arithmetic operations on small molecule inputs in cells. Toehold-switch-based ribocomputing devices may provide a fundamental basis for synthetic RNA-based arithmetic logic units or higher-order systems in cells.
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3
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Zhong P, Hong M, He H, Zhang J, Chen Y, Wang Z, Chen P, Ouyang J. Diagnosis of Acute Leukemia by Multiparameter Flow Cytometry with the Assistance of Artificial Intelligence. Diagnostics (Basel) 2022; 12:diagnostics12040827. [PMID: 35453875 PMCID: PMC9029950 DOI: 10.3390/diagnostics12040827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 11/28/2022] Open
Abstract
We developed an artificial intelligence (AI) model that evaluates the feasibility of AI-assisted multiparameter flow cytometry (MFC) diagnosis of acute leukemia. Two hundred acute leukemia patients and 94 patients with cytopenia(s) or hematocytosis were selected to study the AI application in MFC diagnosis of acute leukemia. The kappa test analyzed the consistency of the diagnostic results and the immunophenotype of acute leukemia. Bland–Altman and Pearson analyses evaluated the consistency and correlation of the abnormal cell proportion between the AI and manual methods. The AI analysis time for each case (83.72 ± 23.90 s, mean ± SD) was significantly shorter than the average time for manual analysis (15.64 ± 7.16 min, mean ± SD). The total consistency of diagnostic results was 0.976 (kappa (κ) = 0.963). The Bland–Altman evaluation of the abnormal cell proportion between the AI analysis and manual analysis showed that the bias ± SD was 0.752 ± 6.646, and the 95% limit of agreement was from −12.775 to 13.779 (p = 0.1225). The total consistency of the AI immunophenotypic diagnosis and the manual results was 0.889 (kappa, 0.775). The consistency and speedup of the AI-assisted workflow indicate its promising clinical application.
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Affiliation(s)
- Pengqiang Zhong
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; (P.Z.); (M.H.); (J.Z.); (Y.C.)
| | - Mengzhi Hong
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; (P.Z.); (M.H.); (J.Z.); (Y.C.)
| | - Huanyu He
- Deepcyto LLC, 2304 Falcon Drive, West Linn, OR 97068, USA; (H.H.); (Z.W.)
| | - Jiang Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; (P.Z.); (M.H.); (J.Z.); (Y.C.)
| | - Yaoming Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; (P.Z.); (M.H.); (J.Z.); (Y.C.)
| | - Zhigang Wang
- Deepcyto LLC, 2304 Falcon Drive, West Linn, OR 97068, USA; (H.H.); (Z.W.)
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; (P.Z.); (M.H.); (J.Z.); (Y.C.)
- Correspondence: (P.C.); (J.O.)
| | - Juan Ouyang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; (P.Z.); (M.H.); (J.Z.); (Y.C.)
- Correspondence: (P.C.); (J.O.)
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Srivastava R, Sarkar K, Bonnerjee D, Bagh S. Synthetic Genetic Reversible Feynman Gate in a Single E. coli Cell and Its Application in Bacterial to Mammalian Cell Information Transfer. ACS Synth Biol 2022; 11:1040-1048. [PMID: 35179369 DOI: 10.1021/acssynbio.1c00392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reversible computing is a nonconventional form of computing where the inputs and outputs are mapped in a unique one-to-one fashion. Reversible logic gates in single living cells have not been demonstrated. Here, we constructed a synthetic genetic reversible Feynman gate in single E. coli cells, and the input-output relations were measured in a clonal population. The inputs were extracellular chemicals, isopropyl β-d-1-thiogalactopyranoside (IPTG), and anhydrotetracycline (aTc), and the outputs were two fluorescence proteins. We developed a simple mathematical model and simulation to capture the essential features of the circuit and experimentally demonstrated that the behavior of the circuit was ultrasensitive and predictive. We showed an application by creating an intercellular Feynman gate, where input information from bacteria was computed and transferred to HeLa cells through shRNAs delivery and the output signals were observed as silencing of native AKT1 and CTNNB1 genes. The introduction of reversible logics in synthetic biology is new, and given that one-to-one input-output mapping, such reversible genetic systems might have applications in sensing, diagnostics, cellular computing, and synthetic biology.
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Affiliation(s)
- Rajkamal Srivastava
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Block A/F, Sector-I, Bidhannagar, Kolkata 700064, India
| | - Kathakali Sarkar
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Block A/F, Sector-I, Bidhannagar, Kolkata 700064, India
| | - Deepro Bonnerjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Block A/F, Sector-I, Bidhannagar, Kolkata 700064, India
| | - Sangram Bagh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Block A/F, Sector-I, Bidhannagar, Kolkata 700064, India
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Massana Roquero D, McCorduck B, Bollella P, Smutok O, Melman A, Katz E. Biomolecule Release from Alginate Composite Hydrogels Triggered by Logically Processed Signals. Chemphyschem 2021; 22:1967-1975. [PMID: 34309163 DOI: 10.1002/cphc.202100458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Indexed: 12/31/2022]
Abstract
Alginate composite hydrogels that exhibit highly sensitive stimuli-responsive behavior were used for signal-stimulated release of pre-loaded insulin. The alginate pores, particularly located at the periphery, were blocked by interpenetration of polyvinyl alcohol (PVA) cross-linked with 1,3-benzenediboronic acid (IPN), thus, significantly reducing uncontrolled leakage of the entrapped biomolecules. The beads were loaded with insulin and various enzymes mimicking different Boolean logic gates (AND, OR, NOR, IMP, INHIB). The enzymes were activated with biologically relevant input signals applied in four logic combinations: 0,0; 1,0; 0,1; 1,1, having the production of H2 O2 as the result of the biocatalytic reactions. The "successful" combination of the input signals leading to the H2 O2 production was different for different logic gates, following the corresponding truth tables of the logic gates. When H2 O2 was produced, boronate ester bonds were oxidized and the IPN was irreversibly degraded, thus re-opening the original pores of the hydrogel. This process allowed release of insulin from the alginate beads. The smart soft material that we have developed tackled well-known limitations of these systems and it may prove valuable in future medical diagnostics or treatments.
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Affiliation(s)
- Daniel Massana Roquero
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Brandon McCorduck
- 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.,Department of Chemistry, University of Bari A. Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Artem Melman
- 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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6
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Wei W, Li J, Yao H, Shi K, Liu H. A versatile molecular logic system based on Eu(III) coordination polymer film electrodes combined with multiple properties of NADH. Phys Chem Chem Phys 2020; 22:22746-22757. [PMID: 33020777 DOI: 10.1039/d0cp03020a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herein, a new type of lanthanide coordination polymer film made up of europium (Eu(iii)) and poly(N-methacryloylglycine) (Eu(iii)-PMAG) was prepared on an ITO electrode surface driven by the coordination between N-methacryloylglycine (MAG) and Eu(iii) through a single-step polymerization process. The fluorescence signal of Eu(iii)-PMAG films at 617 nm originating from Eu(iii) could be well retained in the buffer solution but was regulated by the concentration of Cu(ii) and the complexing agent EDTA. The switching of fluorescence by Cu(ii) was attributed to the inhibition of the "antenna effect" between Eu(iii) and the MAG ligand in the films. The coexistence of reduced β-nicotinamide adenine dinucleotide (NADH) in the solution can apparently quench the fluorescence of Eu(iii)-PMAG films through the internal filtration effect of UV absorbance overlapping the excitation wavelength, but itself exhibiting a fluorescence emission at 468 nm. In addition, the electrocatalytic oxidation of NADH with the help of the ferrocenedicarboxylic acid (FcDA) probe demonstrated a cyclic voltammetry (CV) signal at 0.45 V (vs. SCE). Based on various reversible stimulus-responsive behaviours, a 4-input/10-output logic network was built using Cu(ii), EDTA, NADH and FcDA as inputs and the signals of fluorescence from Eu(iii)-PMAG (617 nm) and NADH (468 nm), the CV response from FcDA and the UV-vis absorbance from the Cu(ii)-EDTA complex as outputs. Meanwhile, 6 different functional logic devices were constructed based on the same versatile platform, including a 2-to-1 encoder, a 1-to-2 decoder, a 1-to-2 demultiplexer, a parity checker, a transfer gate and a reprogrammable 3-input/2-output keypad lock. Combined with the new type of lanthanide coordination polymer film, NADH played central roles in designing sophisticated computing systems with its fluorescence, UV and electrocatalytic properties. This work might provide a novel avenue to develop intelligent multi-analyte sensing and information processing at the molecular level based on one single platform.
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Affiliation(s)
- Wenting Wei
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China.
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7
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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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Masi M, Bollella P, Katz E. DNA Release from a Modified Electrode Triggered by a Bioelectrocatalytic Process. ACS APPLIED MATERIALS & INTERFACES 2019; 11:47625-47634. [PMID: 31794177 DOI: 10.1021/acsami.9b18427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA release from an electrode surface was stimulated by application of a mild electrical potential (0 V vs Ag/AgCl). The release process was activated by interfacial pH increase originating from H+ consumption during O2 reduction bio-electrocatalyzed by bilirubin oxidase immobilized at the electrode surface. The pH increase resulted in a change of the electrical charge from positive to negative at the surface of SiO2 nanoparticles (200 nm) associated with the electrode surface and functionalized with trigonelline and boronic acid. While the negatively charged DNA molecules were electrostatically bound to the positively charged surface, the negative charge produced upon O2 reduction resulted in the DNA repulsion and release from the modified interface. The small electrical potential for O2 reduction resulting in the interface recharge was allowed due to the bio-electrocatalysis using bilirubin oxidase enzyme. While, in the first set of experiments, the potential was applied on the modified electrode from an electrochemical instrument, later it was generated in situ by biocatalytic or photo-biocatalytic processes at a connected electrode. A multistep biocatalytic cascade generating NADH or photosynthetic process in thylakoid membranes was used to produce in situ a small potential to stimulate the DNA release catalyzed by bilirubin oxidase. The designed system can be used for different release processes triggered by various signals (electrical, biomolecular, and light signals, etc.), thus representing a general interfacial platform for the controlled release of different biomolecules and nanosize species.
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Affiliation(s)
- Madeline Masi
- Department of Chemistry and Biomolecular Science , Clarkson University , Potsdam , New York 13699-5810 , United States
| | - Paolo Bollella
- Department of Chemistry and Biomolecular Science , Clarkson University , Potsdam , New York 13699-5810 , United States
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science , Clarkson University , Potsdam , New York 13699-5810 , United States
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9
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Bollella P, Bellare M, Kadambar VK, Guo Z, Alexandrov K, Melman A, Katz E. Boolean Logic Networks Mimicked with Chimeric Enzymes Activated/Inhibited by Several Input Signals. Chemphyschem 2019; 21:589-593. [DOI: 10.1002/cphc.201901050] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699-5810 USA
| | - Madhura Bellare
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699-5810 USA
| | | | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance Centre for Tropical Crops and Biocommodities Queensland University of Technology Brisbane 4001, QLD Australia
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance Centre for Tropical Crops and Biocommodities Queensland University of Technology Brisbane 4001, QLD Australia
| | - Artem Melman
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699-5810 USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699-5810 USA
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10
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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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11
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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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12
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Deng J, Tao Z, Liu Y, Lin X, Qian P, Lyu Y, Li Y, Fu K, Wang S. A target-induced logically reversible logic gate for intelligent and rapid detection of pathogenic bacterial genes. Chem Commun (Camb) 2018. [DOI: 10.1039/c8cc00178b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A target-induced Feynman gate acts as an intelligent biosensor to distinguish all information of the targets from the output signal patterns.
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Affiliation(s)
- Jiankang Deng
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Zhanhui Tao
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Yaqing Liu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Xiaodong Lin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Pengcheng Qian
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Yanlong Lyu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Yunfei Li
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Kejing Fu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- 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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14
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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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15
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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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16
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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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Gamella M, Zakharchenko A, Guz N, Masi M, Minko S, Kolpashchikov DM, Iken H, Poghossian A, Schöning MJ, Katz E. DNA Computing Systems Activated by Electrochemically-triggered DNA Release from a Polymer-brush-modified Electrode Array. ELECTROANAL 2017; 29:398-408. [PMID: 29379265 PMCID: PMC5786385 DOI: 10.1002/elan.201600389] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 06/23/2016] [Indexed: 12/23/2022]
Abstract
An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA-based Identity, AND and XOR logic gates. Single-stranded DNA molecules were loaded on the mixed poly(N,N-di-methylaminoethyl methacrylate) (PDMAEMA)/poly-(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAE-MA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at -1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals.
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Affiliation(s)
- Maria Gamella
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA, http://people.clarkson.edu/~ekatz/
| | - Andrey Zakharchenko
- Nanostructured Materials Lab, The University of Georgia, Athens, GA 30602, USA
| | - Nataliia Guz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA, http://people.clarkson.edu/~ekatz/
| | - Madeline Masi
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA, http://people.clarkson.edu/~ekatz/
| | - Sergiy Minko
- Nanostructured Materials Lab, The University of Georgia, Athens, GA 30602, USA
| | - Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
| | - Heiko Iken
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Muβmann-Str. 1, D-52428 Jülich, Germany
| | - Arshak Poghossian
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Muβmann-Str. 1, D-52428 Jülich, Germany
- Institute of Bio- and Nanosystems, Research Centre Jülich, GmbH, D-52425 Jülich Germany
| | - Michael J. Schöning
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Muβmann-Str. 1, D-52428 Jülich, Germany
- Institute of Bio- and Nanosystems, Research Centre Jülich, GmbH, D-52425 Jülich Germany
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA, http://people.clarkson.edu/~ekatz/
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18
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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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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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20
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Guz N, Fedotova TA, Fratto BE, Schlesinger O, Alfonta L, Kolpashchikov DM, Katz E. Bioelectronic Interface Connecting Reversible Logic Gates Based on Enzyme and DNA Reactions. Chemphyschem 2016; 17:2247-55. [PMID: 27145731 DOI: 10.1002/cphc.201600129] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 12/17/2022]
Abstract
It is believed that connecting biomolecular computation elements in complex networks of communicating molecules may eventually lead to a biocomputer that can be used for diagnostics and/or the cure of physiological and genetic disorders. Here, a bioelectronic interface based on biomolecule-modified electrodes has been designed to bridge reversible enzymatic logic gates with reversible DNA-based logic gates. The enzyme-based Fredkin gate with three input and three output signals was connected to the DNA-based Feynman gate with two input and two output signals-both representing logically reversible computing elements. In the reversible Fredkin gate, the routing of two data signals between two output channels was controlled by the control signal (third channel). The two data output signals generated by the Fredkin gate were directed toward two electrochemical flow cells, responding to the output signals by releasing DNA molecules that serve as the input signals for the next Feynman logic gate based on the DNA reacting cascade, producing, in turn, two final output signals. The Feynman gate operated as the controlled NOT gate (CNOT), where one of the input channels controlled a NOT operation on another channel. Both logic gates represented a highly sophisticated combination of input-controlled signal-routing logic operations, resulting in redirecting chemical signals in different channels and performing orchestrated computing processes. The biomolecular reaction cascade responsible for the signal processing was realized by moving the solution from one reacting cell to another, including the reacting flow cells and electrochemical flow cells, which were organized in a specific network mimicking electronic computing circuitries. The designed system represents the first example of high complexity biocomputing processes integrating enzyme and DNA reactions and performing logically reversible signal processing.
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Affiliation(s)
- Nataliia Guz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA
| | - Tatiana A Fedotova
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA
| | - Orr Schlesinger
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Lital Alfonta
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA.
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21
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Fratto BE, Lewer JM, Katz E. An Enzyme-Based Half-Adder and Half-Subtractor with a Modular Design. Chemphyschem 2016; 17:2210-7. [PMID: 27037520 DOI: 10.1002/cphc.201600173] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 01/01/2023]
Abstract
A half-adder and a half-subtractor have been realized using enzymatic reaction cascades performed in a flow cell device. The individual cells were modified with different enzymes and assembled in complex networks to perform logic operations and arithmetic functions. The modular design of the logic devices allowed for easy re-configuration, enabling them to perform various functions. The final output signals, represented by redox species [Fe(CN)6 ](3-/4-) or NADH/NAD(+) , were analyzed optically to derive the calculation results. These output signals might be applicable in the future for actuation processes, for example, substance release activated by logically processed signals.
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Affiliation(s)
- Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Jessica M Lewer
- 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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Zhou C, Wang K, Fan D, Wu C, Liu D, Liu Y, Wang E. An enzyme-free and DNA-based Feynman gate for logically reversible operation. Chem Commun (Camb) 2016; 51:10284-6. [PMID: 26028329 DOI: 10.1039/c5cc02865e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A logically reversible Feynman gate was successfully realized under enzyme-free conditions by integrating graphene oxide and DNA for the first time. The gate has a one-to-one mapping function to identify inputs from the corresponding outputs. This type of reversible logic gate may have great potential applications in information processing and biosensing systems.
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Affiliation(s)
- Chunyang Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.
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Controlled Logic Gates—Switch Gate and Fredkin Gate Based on Enzyme‐Biocatalyzed Reactions Realized in Flow Cells. Chemphyschem 2016; 17:1046-53. [DOI: 10.1002/cphc.201501095] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Indexed: 12/27/2022]
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