1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Tomaiuolo R, Zibetti M, Di Resta C, Banfi G. Challenges of the Effectiveness of Traumatic Brain Injuries Biomarkers in the Sports-Related Context. J Clin Med 2023; 12:jcm12072563. [PMID: 37048647 PMCID: PMC10095236 DOI: 10.3390/jcm12072563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Traumatic brain injury affects 69 million people every year. One of the main limitations in managing TBI patients is the lack of univocal diagnostic criteria, including the absence of standardized assessment methods and guidelines. Computerized axial tomography is the first-choice examination, despite the limited prevalence of positivity; moreover, its performance is undesirable due to the risk of radiological exposure, prolonged stay in emergency departments, inefficient use of resources, high cost, and complexity. Furthermore, immediacy and accuracy in diagnosis and management of TBIs are critically unmet medical needs. Especially in the context of sports-associated TBI, there is a strong need for prognostic indicators to help diagnose and identify at-risk subjects to avoid their returning to play while the brain is still highly vulnerable. Fluid biomarkers may emerge as new prognostic indicators to develop more accurate prediction models, improving risk stratification and clinical decision making. This review describes the current understanding of the cellular sources, temporal profile, and potential utility of leading and emerging blood-based protein biomarkers of TBI; its focus is on biomarkers that could improve the management of mild TBI cases and can be measured readily and directly in the field, as in the case of sports-related contexts.
Collapse
Affiliation(s)
- Rossella Tomaiuolo
- Faculty of Medicine, Università Vita-Salute San Raffaele, 20132 Milan, Italy
| | - Martina Zibetti
- Faculty of Medicine, Università Vita-Salute San Raffaele, 20132 Milan, Italy
| | - Chiara Di Resta
- Faculty of Medicine, Università Vita-Salute San Raffaele, 20132 Milan, Italy
- Correspondence:
| | - Giuseppe Banfi
- Faculty of Medicine, Università Vita-Salute San Raffaele, 20132 Milan, Italy
- IRCCS Galeazzi-Sant’Ambrogio, 20157 Milan, Italy
| |
Collapse
|
3
|
Krausz AD, Korley FK, Burns MA. The Current State of Traumatic Brain Injury Biomarker Measurement Methods. BIOSENSORS 2021; 11:319. [PMID: 34562909 PMCID: PMC8469272 DOI: 10.3390/bios11090319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/16/2022]
Abstract
Traumatic brain injury (TBI) is associated with high rates of morbidity and mortality partially due to the limited tools available for diagnosis and classification. Measuring panels of protein biomarkers released into the bloodstream after injury has been proposed to diagnose TBI, inform treatment decisions, and monitor the progression of the injury. Being able to measure these protein biomarkers at the point-of-care would enable assessment of TBIs from the point-of-injury to the patient's hospital bedside. In this review, we provide a detailed discussion of devices reported in the academic literature and available on the market that have been designed to measure TBI protein biomarkers in various biofluids and contexts. We also assess the challenges associated with TBI biomarker measurement devices and suggest future research directions to encourage translation of these devices to clinical use.
Collapse
Affiliation(s)
- Alyse D. Krausz
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI 48109, USA
| | - Frederick K. Korley
- Emergency Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Mark A. Burns
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI 48109, USA
- Chemical Engineering Department, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
4
|
Integration of logic gates to CRISPR/Cas12a system for rapid and sensitive detection of pathogenic bacterial genes. Anal Chim Acta 2020; 1125:162-168. [DOI: 10.1016/j.aca.2020.05.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022]
|
5
|
Enhancement of Biosensors by Implementing Photoelectrochemical Processes. SENSORS 2020; 20:s20113281. [PMID: 32526947 PMCID: PMC7308923 DOI: 10.3390/s20113281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 12/15/2022]
Abstract
Research on biosensors is growing in relevance, taking benefit from groundbreaking knowledge that allows for new biosensing strategies. Electrochemical biosensors can benefit from research on semiconducting materials for energy applications. This research seeks the optimization of the semiconductor-electrode interfaces including light-harvesting materials, among other improvements. Once that knowledge is acquired, it can be implemented with biological recognition elements, which are able to transfer a chemical signal to the photoelectrochemical system, yielding photo-biosensors. This has been a matter of research as it allows both a superior suppression of background electrochemical signals and the switching ON and OFF upon illumination. Effective electrode-semiconductor interfaces and their coupling with biorecognition units are reviewed in this work.
Collapse
|
6
|
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
| |
Collapse
|
7
|
Llopis-Lorente A, de Luis B, García-Fernández A, Jimenez-Falcao S, Orzáez M, Sancenón F, Villalonga R, Martínez-Máñez R. Hybrid Mesoporous Nanocarriers Act by Processing Logic Tasks: Toward the Design of Nanobots Capable of Reading Information from the Environment. ACS APPLIED MATERIALS & INTERFACES 2018; 10:26494-26500. [PMID: 30016064 DOI: 10.1021/acsami.8b05920] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here, we present the design of smart nanodevices capable of reading molecular information from the environment and acting accordingly by processing Boolean logic tasks. As proof of concept, we prepared Au-mesoporous silica (MS) nanoparticles functionalized with the enzyme glucose dehydrogenase (GDH) on the Au surface and with supramolecular nanovalves as caps on the MS surface, which is loaded with a cargo (dye or drug). The nanodevice acts as an AND logic gate and reads information from the solution (presence of glucose and nicotinamide adenine dinucleotide (NAD+)), which results in cargo release. We show the possibility of coimmobilizing GDH and the enzyme urease on nanoparticles to mimic an INHIBIT logic gate, in which the AND gate is switched off by the presence of urea. We also show that such nanodevices can deliver cytotoxic drugs in cancer cells by recognizing intracellular NAD+ and the presence of glucose.
Collapse
Affiliation(s)
- Antoni Llopis-Lorente
- Instituto de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) , Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia , 46022 València , Spain
- Departamento de Química , Universidad Politécnica de Valencia , Camino de Vera s/n , 46022 Valencia , Spain
- CIBER de Bioingeniería , Biomateriales y Nanomedicina (CIBER-BBN) , Spain
| | - Beatriz de Luis
- Instituto de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) , Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia , 46022 València , Spain
- Departamento de Química , Universidad Politécnica de Valencia , Camino de Vera s/n , 46022 Valencia , Spain
- CIBER de Bioingeniería , Biomateriales y Nanomedicina (CIBER-BBN) , Spain
| | - Alba García-Fernández
- Instituto de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) , Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia , 46022 València , Spain
- CIBER de Bioingeniería , Biomateriales y Nanomedicina (CIBER-BBN) , Spain
- Centro de Investigación Príncipe Felipe , Eduardo Primo Yúfera 3 , 46012 Valencia , Spain
| | - Sandra Jimenez-Falcao
- Nanosensors & Nanomachines Group, Department of Analytical Chemistry, Faculty of Chemistry , Complutense University of Madrid , 28040 Madrid , Spain
| | - Mar Orzáez
- Centro de Investigación Príncipe Felipe , Eduardo Primo Yúfera 3 , 46012 Valencia , Spain
| | - Félix Sancenón
- Instituto de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) , Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia , 46022 València , Spain
- Departamento de Química , Universidad Politécnica de Valencia , Camino de Vera s/n , 46022 Valencia , Spain
- CIBER de Bioingeniería , Biomateriales y Nanomedicina (CIBER-BBN) , Spain
| | - Reynaldo Villalonga
- Nanosensors & Nanomachines Group, Department of Analytical Chemistry, Faculty of Chemistry , Complutense University of Madrid , 28040 Madrid , Spain
| | - Ramón Martínez-Máñez
- Instituto de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) , Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia , 46022 València , Spain
- Departamento de Química , Universidad Politécnica de Valencia , Camino de Vera s/n , 46022 Valencia , Spain
- CIBER de Bioingeniería , Biomateriales y Nanomedicina (CIBER-BBN) , Spain
| |
Collapse
|
8
|
Liang J, Yu X, Yang T, Li M, Shen L, Jin Y, Liu H. A complicated biocomputing system based on multi-responsive P(NIPAM-co-APBA) copolymer film electrodes and electrocatalysis of NADH. Phys Chem Chem Phys 2018; 19:22472-22481. [PMID: 28808714 DOI: 10.1039/c7cp04030j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, poly(N-isopropylacrylamide-co-3-aminophenylboronic acid) (P(NIPAM-co-APBA)) copolymer films were successfully electropolymerized on the Au electrode surface. The electroactive probe ferrocene carboxylic acid (FCA) in solution showed reversible thermal-, glucose- and pH-responsive on-off cyclic voltammetric (CV) behaviors at the film electrodes. The comparative experiments demonstrated that the thermo-responsive property of the film electrode was ascribed to the PNIPAM component of the films, whereas the glucose- and pH-sensitive behaviors came from the PAPBA constituent. The reduced form of nicotinamide adenine dinucleotide (NADH) could be electrocatalytically oxidized by FCA at the film electrodes, which would greatly amplify the multi-responsive CV signal difference between the on and off states. On the basis of these results, a binary 4-input/4-output logic circuit was fabricated with temperature, glucose, pH and NADH as inputs and the CV responses at 4 different levels as outputs. Moreover, a ternary CONSENSUS logic circuit was established on the same platform, which was the first report on the combination of ternary logic gate and bioelectrocatalysis without using enzymes. This work provided a novel idea for constructing complicated biocomputing systems by increasing the number of inputs/outputs with multi-sensitive interfaces and by designing new types of multi-valued logic gates on the basis of bioelectrocatalysis.
Collapse
Affiliation(s)
- Jiying Liang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
| | | | | | | | | | | | | |
Collapse
|
9
|
Lian W, Liang J, Shen L, Jin Y, Liu H. Enzymatic logic calculation systems based on solid-state electrochemiluminescence and molecularly imprinted polymer film electrodes. Biosens Bioelectron 2018; 100:326-332. [DOI: 10.1016/j.bios.2017.09.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/22/2022]
|
10
|
Xu XY, Lian X, Hao JN, Zhang C, Yan B. A Double-Stimuli-Responsive Fluorescent Center for Monitoring of Food Spoilage based on Dye Covalently Modified EuMOFs: From Sensory Hydrogels to Logic Devices. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29. [PMID: 28745439 DOI: 10.1002/adma.201702298] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/01/2017] [Indexed: 05/06/2023]
Abstract
Unsafe food is a huge threat to human health and the economy, and detecting food spoilage early is an ongoing and imperative need. Herein, a simple and effective strategy combining a fluorescence sensor and one-to-two logic operation is designed for monitoring biogenic amines, indicators of food spoilage. Sensors (methyl red@lanthanide metal-organic frameworks (MR@EuMOFs)) are created by covalently modifying MR into NH2 -rich EuMOFs, which have a high quantum yield (48%). A double-stimuli-responsive fluorescence center is produced via energy transfer from the ligands to Eu3+ and MR. Portable sensory hydrogels are obtained by dispersing and solidifying MR@EuMOFs in water-phase sodium salt of carboxy methyl cellulose (CMC-Na). The hydrogels exhibit a color transition upon "smelling" histamine (HI) vapor. This transition and shift in the MR-based emission peak are closely related to the HI concentration. Using the HI concentration as the input signal and the two fluorescence emissions as output signals, an advanced analytical device based on a one-to-two logic gate is constructed. The four output combinations, NOT (0, 1), YES (1, 0), PASS 1 (1, 1), and PASS 0 (0, 0), allow the direct analysis of HI levels, which can be used for real-time food-freshness evaluation. The novel strategy suggested here may be a new application for a molecular logic system in the sensing field.
Collapse
Affiliation(s)
- Xiao-Yu Xu
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
| | - Xiao Lian
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
| | - Ji-Na Hao
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
| | - Chi Zhang
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
| | - Bing Yan
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
| |
Collapse
|
11
|
Gao RR, Yao TM, Lv XY, Zhu YY, Zhang YW, Shi S. Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing. Chem Sci 2017; 8:4211-4222. [PMID: 28626564 PMCID: PMC5469004 DOI: 10.1039/c7sc00361g] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/05/2017] [Indexed: 11/30/2022] Open
Abstract
To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2 : 1 multiplexer, and a 1 : 2 demultiplexer. Moreover, a parity checker which is capable of identifying odd and even numbers from natural numbers is constructed conceptually. Finally, a multi-valued logic gate (ternary inhibit gate) is readily achieved by taking this DNA/Ag NC system as a universal platform. All of the above logic circuits share the same building blocks, indicating the great prospects of the assembly of nanomaterials and DNA for biochemical logic devices. Considering its biocompatibility, the novel prototypes developed here may have potential applications in the fields of biological computers and medical diagnosis and serve as a promising proof of principle in the not-too-distant future.
Collapse
Affiliation(s)
- Ru-Ru Gao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Tian-Ming Yao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Xiao-Yan Lv
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Yan-Yan Zhu
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Yi-Wei Zhang
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Shuo Shi
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| |
Collapse
|
12
|
Domanskyi S, Privman V. Modeling and Modifying Response of Biochemical Processes for Biocomputing and Biosensing Signal Processing. EMERGENCE, COMPLEXITY AND COMPUTATION 2017. [DOI: 10.1007/978-3-319-33921-4_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Fratto BE, Guz N, Fallon TT, Katz E. An Enzyme-based 1:2 Demultiplexer Interfaced with an Electrochemical Actuator. Chemphyschem 2016; 18:1721-1725. [PMID: 27481283 DOI: 10.1002/cphc.201600799] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Indexed: 12/26/2022]
Abstract
An enzyme-based 1:2 demultiplexer is designed in a flow system composed of three cells where each one is modified with a different enzyme: hexokinase, glucose dehydrogenase and glucose-6-phosphate dehydrogenase. The Input signal activating the biocatalytic cascade is represented by glucose, while the Address signal represented by ATP is responsible for directing the Input signal to one of the output channels, depending on the logic value of the Address. The biomolecular 1:2 demultiplexer is extended to include two electrochemical actuators releasing entrapped DNA molecules in the active output channel. The modular design of the system allows for easy exchange and extension of the functional elements. The present demultiplexer can be easily integrated in various biomolecular logic systems, including different logic gates based on the enzyme- or DNA-based reactions, as well as containing different chemical actuators, for example, with a biomolecular release function.
Collapse
Affiliation(s)
- Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Nataliia Guz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Tyler T Fallon
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Liu S, Wang L, Lian W, Liu H, Li CZ. Logic Gate System with Three Outputs and Three Inputs Based on Switchable Electrocatalysis of Glucose by Glucose Oxidase Entrapped in Chitosan Films. Chem Asian J 2014; 10:225-30. [DOI: 10.1002/asia.201402927] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Indexed: 11/11/2022]
|
17
|
Biosensors with built-in biomolecular logic gates for practical applications. BIOSENSORS-BASEL 2014; 4:273-300. [PMID: 25587423 PMCID: PMC4264359 DOI: 10.3390/bios4030273] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 01/20/2023]
Abstract
Molecular logic gates, designs constructed with biological and chemical molecules, have emerged as an alternative computing approach to silicon-based logic operations. These molecular computers are capable of receiving and integrating multiple stimuli of biochemical significance to generate a definitive output, opening a new research avenue to advanced diagnostics and therapeutics which demand handling of complex factors and precise control. In molecularly gated devices, Boolean logic computations can be activated by specific inputs and accurately processed via bio-recognition, bio-catalysis, and selective chemical reactions. In this review, we survey recent advances of the molecular logic approaches to practical applications of biosensors, including designs constructed with proteins, enzymes, nucleic acids, nanomaterials, and organic compounds, as well as the research avenues for future development of digitally operating “sense and act” schemes that logically process biochemical signals through networked circuits to implement intelligent control systems.
Collapse
|
18
|
Yarman A, Schulz C, Sygmund C, Ludwig R, Gorton L, Wollenberger U, Scheller FW. Third Generation ATP Sensor with Enzymatic Analyte Recycling. ELECTROANAL 2014. [DOI: 10.1002/elan.201400231] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
19
|
Huang WT, Luo HQ, Li NB. Boolean Logic Tree of Graphene-Based Chemical System for Molecular Computation and Intelligent Molecular Search Query. Anal Chem 2014; 86:4494-500. [DOI: 10.1021/ac5004008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Wei Tao Huang
- Key Laboratory of Eco-environments
in Three Gorges Reservoir Region (Ministry of Education), School of
Chemistry and Chemical Engineering, Southwest University, Tiansheng
Road, BeiBei District, Chongqing 400715, PR China
| | - Hong Qun Luo
- Key Laboratory of Eco-environments
in Three Gorges Reservoir Region (Ministry of Education), School of
Chemistry and Chemical Engineering, Southwest University, Tiansheng
Road, BeiBei District, Chongqing 400715, PR China
| | - Nian Bing Li
- Key Laboratory of Eco-environments
in Three Gorges Reservoir Region (Ministry of Education), School of
Chemistry and Chemical Engineering, Southwest University, Tiansheng
Road, BeiBei District, Chongqing 400715, PR China
| |
Collapse
|
20
|
Claussen JC, Hildebrandt N, Susumu K, Ancona MG, Medintz IL. Complex logic functions implemented with quantum dot bionanophotonic circuits. ACS APPLIED MATERIALS & INTERFACES 2014; 6:3771-8. [PMID: 24354314 DOI: 10.1021/am404659f] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We combine quantum dots (QDs) with long-lifetime terbium complexes (Tb), a near-IR Alexa Fluor dye (A647), and self-assembling peptides to demonstrate combinatorial and sequential bionanophotonic logic devices that function by time-gated Förster resonance energy transfer (FRET). Upon excitation, the Tb-QD-A647 FRET-complex produces time-dependent photoluminescent signatures from multi-FRET pathways enabled by the capacitor-like behavior of the Tb. The unique photoluminescent signatures are manipulated by ratiometrically varying dye/Tb inputs and collection time. Fluorescent output is converted into Boolean logic states to create complex arithmetic circuits including the half-adder/half-subtractor, 2:1 multiplexer/1:2 demultiplexer, and a 3-digit, 16-combination keypad lock.
Collapse
Affiliation(s)
- Jonathan C Claussen
- Center for Bio/Molecular Science and Engineering, Code 6900; ‡Optical Sciences Division, Code 5600; §Electronics Science and Technology Division, Code 6876; U.S. Naval Research Laboratory , Washington, D.C. 20375, United States
| | | | | | | | | |
Collapse
|
21
|
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.
Collapse
|
22
|
Claussen JC, Algar WR, Hildebrandt N, Susumu K, Ancona MG, Medintz IL. Biophotonic logic devices based on quantum dots and temporally-staggered Förster energy transfer relays. NANOSCALE 2013; 5:12156-12170. [PMID: 24056977 DOI: 10.1039/c3nr03655c] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Integrating photonic inputs/outputs into unimolecular logic devices can provide significantly increased functional complexity and the ability to expand the repertoire of available operations. Here, we build upon a system previously utilized for biosensing to assemble and prototype several increasingly sophisticated biophotonic logic devices that function based upon multistep Förster resonance energy transfer (FRET) relays. The core system combines a central semiconductor quantum dot (QD) nanoplatform with a long-lifetime Tb complex FRET donor and a near-IR organic fluorophore acceptor; the latter acts as two unique inputs for the QD-based device. The Tb complex allows for a form of temporal memory by providing unique access to a time-delayed modality as an alternate output which significantly increases the inherent computing options. Altering the device by controlling the configuration parameters with biologically based self-assembly provides input control while monitoring changes in emission output of all participants, in both a spectral and temporal-dependent manner, gives rise to two input, single output Boolean Logic operations including OR, AND, INHIBIT, XOR, NOR, NAND, along with the possibility of gate transitions. Incorporation of an enzymatic cleavage step provides for a set-reset function that can be implemented repeatedly with the same building blocks and is demonstrated with single input, single output YES and NOT gates. Potential applications for these devices are discussed in the context of their constituent parts and the richness of available signal.
Collapse
|
23
|
Calles B, Lorenzo VD. Expanding the boolean logic of the prokaryotic transcription factor XylR by functionalization of permissive sites with a protease-target sequence. ACS Synth Biol 2013; 2:594-603. [PMID: 23875967 DOI: 10.1021/sb400050k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The σ54-dependent prokaryotic regulator XylR implements a one-input/one-output actuator that transduces the presence of the aromatic effector m-xylene into transcriptional activation of the cognate promoter Pu. Such a signal conversion involves the effector-mediated release of the intramolecular repression of the N-terminal A domain on the central C module of XylR. On this background, we set out to endow this regulator with additional signal-sensing capabilities by inserting a target site of the viral protease NIa in permissive protein locations that once cleaved in vivo could either terminate XylR activity or generate an effector-independent, constitutive transcription factor. To find optimal protein positions to this end, we saturated the xylR gene DNA with a synthetic transposable element designed for randomly delivering in-frame polypeptides throughout the sequence of any given protein. This Tn5-based system supplies the target gene with insertions of a selectable marker that can later be excised, leaving behind the desired (poly) peptides grafted into the protein structure. Implementation of such knock-in-leave-behind (KILB) method to XylR was instrumental to produce a number of variants of this transcription factor (TF) that could compute in vivo two inputs (m-xylene and protease) into a single output following a logic that was dependent on the site of the insertion of the NIa target sequence in the TF. Such NIa-sensitive XylR specimens afforded the design of novel regulatory nodes that entered protease expression as one of the signals recognized in vivo for controlling Pu. This approach is bound to facilitate the functionalization of TFs and other proteins with new traits, especially when their forward engineering is made difficult by, for example, the absence of structural data.
Collapse
Affiliation(s)
- Belen Calles
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco,
28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco,
28049 Madrid, Spain
| |
Collapse
|
24
|
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
| |
Collapse
|
25
|
Liba BD, Kim E, Martin AN, Liu Y, Bentley WE, Payne GF. Biofabricated film with enzymatic and redox-capacitor functionalities to harvest and store electrons. Biofabrication 2013; 5:015008. [DOI: 10.1088/1758-5082/5/1/015008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
26
|
Domanskyi S, Privman V. Design of Digital Response in Enzyme-Based Bioanalytical Systems for Information Processing Applications. J Phys Chem B 2012; 116:13690-5. [DOI: 10.1021/jp309001j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Sergii Domanskyi
- Department of Physics, Clarkson University, Potsdam, New York 13699, United
States
| | - Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, New York 13699, United
States
| |
Collapse
|
27
|
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]
|
28
|
Zavalov O, Bocharova V, Privman V, Katz E. Enzyme-Based Logic: OR Gate with Double-Sigmoid Filter Response. J Phys Chem B 2012; 116:9683-9. [DOI: 10.1021/jp305183d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oleksandr Zavalov
- Department
of Physics, Clarkson University, Potsdam,
New York 13699, United
States
| | - Vera Bocharova
- Department of Chemistry
and
Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6197, United
States
| | - Vladimir Privman
- Department
of Physics, Clarkson University, Potsdam,
New York 13699, United
States
| | - Evgeny Katz
- Department of Chemistry
and
Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States
| |
Collapse
|
29
|
Halámek J, Zavalov O, Halámková L, Korkmaz S, Privman V, Katz E. Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid “Filter” Response. J Phys Chem B 2012; 116:4457-64. [DOI: 10.1021/jp300447w] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jan Halámek
- Department
of Chemistry and Biomolecular Science,
- Department
of Physics, and
- Department
of Biology, Clarkson University, Potsdam, New York 13699, United States
| | - Oleksandr Zavalov
- Department
of Chemistry and Biomolecular Science,
- Department
of Physics, and
- Department
of Biology, Clarkson University, Potsdam, New York 13699, United States
| | - Lenka Halámková
- Department
of Chemistry and Biomolecular Science,
- Department
of Physics, and
- Department
of Biology, Clarkson University, Potsdam, New York 13699, United States
| | - Sevim Korkmaz
- Department
of Chemistry and Biomolecular Science,
- Department
of Physics, and
- Department
of Biology, Clarkson University, Potsdam, New York 13699, United States
| | - Vladimir Privman
- Department
of Chemistry and Biomolecular Science,
- Department
of Physics, and
- Department
of Biology, Clarkson University, Potsdam, New York 13699, United States
| | - Evgeny Katz
- Department
of Chemistry and Biomolecular Science,
- Department
of Physics, and
- Department
of Biology, Clarkson University, Potsdam, New York 13699, United States
| |
Collapse
|
30
|
North SH, Shriver-Lake LC, Taitt CR, Ligler FS. Rapid analytical methods for on-site triage for traumatic brain injury. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2012; 5:35-56. [PMID: 22462400 DOI: 10.1146/annurev-anchem-062011-143105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Traumatic brain injury (TBI) results from an event that causes rapid acceleration and deceleration of the brain or penetration of the skull with an object. Responses to stimuli and questions, loss of consciousness, and altered behavior are symptoms currently used to justify brain imaging for diagnosis and therapeutic guidance. Tests based on such symptoms are susceptible to false-positive and false-negative results due to stress, fatigue, and medications. Biochemical markers of neuronal damage and the physiological response to that damage are being identified. Biosensors capable of rapid measurement of such markers in the circulation offer a solution for on-site triage, as long as three criteria are met: (a) Recognition reagents can be identified that are sufficiently sensitive and specific, (b) the biosensor can provide quantitative assessment of multiple markers rapidly and simultaneously, and (c) both the sensor and reagents are designed for use outside the laboratory.
Collapse
Affiliation(s)
- Stella H North
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375-5348, USA.
| | | | | | | |
Collapse
|
31
|
Perez Rafael S, Vallee-Belisle A, Fabregas E, Plaxco K, Palleschi G, Ricci F. Employing the metabolic "branch point effect" to generate an all-or-none, digital-like response in enzymatic outputs and enzyme-based sensors. Anal Chem 2012; 84:1076-82. [PMID: 22148353 PMCID: PMC3893712 DOI: 10.1021/ac202701c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we demonstrate a strategy to convert the graded Michaelis-Menten response typical of unregulated enzymes into a sharp, effectively all-or-none response. We do so using an approach analogous to the "branch point effect", a mechanism observed in naturally occurring metabolic networks in which two or more enzymes compete for the same substrate. As a model system, we used the enzymatic reaction of glucose oxidase (GOx) and coupled it to a second, nonsignaling reaction catalyzed by the higher affinity enzyme hexokinase (HK) such that, at low substrate concentrations, the second enzyme outcompetes the first, turning off the latter's response. Above an arbitrarily selected "threshold" substrate concentration, the nonsignaling HK enzyme saturates leading to a "sudden" activation of the first signaling GOx enzyme and a far steeper dose-response curve than that observed for simple Michaelis-Menten kinetics. Using the well-known GOx-based amperometric glucose sensor to validate our strategy, we have steepen the normally graded response of this enzymatic sensor into a discrete yes/no output similar to that of a multimeric cooperative enzyme with a Hill coefficient above 13. We have also shown that, by controlling the HK reaction we can precisely tune the threshold target concentration at which we observe the enzyme output. Finally, we demonstrate the utility of this strategy for achieving effective noise attenuation in enzyme logic gates. In addition to supporting the development of biosensors with digital-like output, we envisage that the use of all-or-none enzymatic responses will also improve our ability to engineer efficient enzyme-based catalysis reactions in synthetic biology applications.
Collapse
Affiliation(s)
- Sandra Perez Rafael
- Sensors and Biosensors Group, Department of Chemistry, Autonomous University of Barcelona, 08193 Bellaterra, Catalonia, Spain
| | - Alexis Vallee-Belisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
| | - Esteve Fabregas
- Sensors and Biosensors Group, Department of Chemistry, Autonomous University of Barcelona, 08193 Bellaterra, Catalonia, Spain
| | - Kevin Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Giuseppe Palleschi
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Viale Medaglie d’Oro 305, 00136 Rome, Italy
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Viale Medaglie d’Oro 305, 00136 Rome, Italy
| |
Collapse
|
32
|
Halámek J, Zhou J, Halámková L, Bocharova V, Privman V, Wang J, Katz E. Biomolecular filters for improved separation of output signals in enzyme logic systems applied to biomedical analysis. Anal Chem 2011; 83:8383-6. [PMID: 21981409 DOI: 10.1021/ac202139m] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Biomolecular logic systems processing biochemical input signals and producing "digital" outputs in the form of YES/NO were developed for analysis of physiological conditions characteristic of liver injury, soft tissue injury, and abdominal trauma. Injury biomarkers were used as input signals for activating the logic systems. Their normal physiological concentrations were defined as logic-0 level, while their pathologically elevated concentrations were defined as logic-1 values. Since the input concentrations applied as logic 0 and 1 values were not sufficiently different, the output signals being at low and high values (0, 1 outputs) were separated with a short gap making their discrimination difficult. Coupled enzymatic reactions functioning as a biomolecular signal processing system with a built-in filter property were developed. The filter process involves a partial back-conversion of the optical-output-signal-yielding product, but only at its low concentrations, thus allowing the proper discrimination between 0 and 1 output values.
Collapse
|
33
|
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
| |
Collapse
|
34
|
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.
Collapse
Affiliation(s)
- Binyamin Gil
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | | | |
Collapse
|
35
|
Bocharova V, Halámek J, Zhou J, Strack G, Wang J, Katz E. Alert-type biological dosimeter based on enzyme logic system. Talanta 2011; 85:800-3. [DOI: 10.1016/j.talanta.2011.03.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/12/2011] [Accepted: 03/15/2011] [Indexed: 02/06/2023]
|
36
|
|
37
|
|
38
|
Oztekin Y, Ramanaviciene A, Ramanavicius A. Electrochemical Glutathione Sensor Based on Electrochemically Deposited Poly-m-aminophenol. ELECTROANAL 2011. [DOI: 10.1002/elan.201000584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
39
|
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]
|
40
|
Zhou M, Chen C, Du Y, Li B, Wen D, Dong S, Wang E. An IMP-Reset gate-based reusable and self-powered "smart" logic aptasensor on a microfluidic biofuel cell. LAB ON A CHIP 2010; 10:2932-6. [PMID: 20859581 DOI: 10.1039/c0lc00009d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The development of microfluidic devices has been spurred by the desire to produce low-cost point-of-care diagnostics and environmental monitoring devices. By combining the adaptive behavior of microfluidic biofuel cells (micro-BFCs) self-regulating the power release with aptamer IMP logic, we constructed a novel IMP-Reset gate-based reusable and self-powered on-chip aptasensor, which can be used to logically determine the presence of one specific target in the absence of another target in complex physiological samples (such as human serum) in a single test.
Collapse
Affiliation(s)
- Ming Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | | | | | | | | | | | | |
Collapse
|
41
|
Privman V, Halámek J, Arugula MA, Melnikov D, Bocharova V, Katz E. Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic. J Phys Chem B 2010; 114:14103-9. [DOI: 10.1021/jp108693m] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Vladimir Privman
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Jan Halámek
- 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
| | - Dmitriy Melnikov
- 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
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| |
Collapse
|
42
|
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.
Collapse
Affiliation(s)
- Jan Halámek
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
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
| |
Collapse
|
44
|
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
| |
Collapse
|
45
|
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.
Collapse
Affiliation(s)
- Jan Halámek
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
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.
Collapse
Affiliation(s)
- Mary A Arugula
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory, Clarkson University, Potsdam New York 13699-5810, USA
| | | | | | | | | |
Collapse
|
47
|
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]
|
48
|
|
49
|
Tam T, Pita M, Motornov M, Tokarev I, Minko S, Katz E. Modified Electrodes with Switchable Selectivity for Cationic and Anionic Redox Species. ELECTROANAL 2009. [DOI: 10.1002/elan.200900442] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
50
|
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]
|