1
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Dias T, Figueiras R, Vagueiro S, Domingues R, Hung YH, Sethi J, Persia E, Arsène P. An electro-optical platform for the ultrasensitive detection of small extracellular vesicle sub-types and their protein epitope counts. iScience 2024; 27:109866. [PMID: 38840839 PMCID: PMC11152657 DOI: 10.1016/j.isci.2024.109866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/12/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Methods for detecting proteins in small extracellular vesicles (sEVs) lack sensitivity and quantitative accuracy, missing clues about health and disease. Our study introduces the Nano-Extracellular Omics Sensing (NEXOS) platform, merging electrical (E-NEXOS) and optical detection (O-NEXOS). E-NEXOS determines the concentration of target sEV sub-types, and O-NEXOS quantifies the concentration of target protein epitopes (TEPs) on those TEVs. In this work, both technologies were compared to several sEV detection tools, showing superior detection limits for CD9+CD81+ and CD9+HER2+ sEVs. Furthermore, the additional information on TEVs and TEPs from bulk sEV samples, provided new phenotyping capabilities. We determined the average number of CD81 and HER2 proteins on CD9+ sEVs, a number which was later validated on spiked human plasma. These results highlight the compatibility of NEXOS with complex biofluids and, as importantly, hint at its many potential applications, ranging from basic research to the anticipated clinical translation of sEVs.
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2
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Guo J, Chen PK, Chang S. Molecular-Scale Electronics: From Individual Molecule Detection to the Application of Recognition Sensing. Anal Chem 2024; 96:9303-9316. [PMID: 38809941 DOI: 10.1021/acs.analchem.3c04656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
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3
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Demir B, Akin Gultakti C, Koker Z, Anantram MP, Oren EE. Electronic Properties of DNA Origami Nanostructures Revealed by In Silico Calculations. J Phys Chem B 2024; 128:4646-4654. [PMID: 38712954 PMCID: PMC11103695 DOI: 10.1021/acs.jpcb.4c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/18/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
Abstract
DNA origami is a pioneering approach for producing complex 2- or 3-D shapes for use in molecular electronics due to its inherent self-assembly and programmability properties. The electronic properties of DNA origami structures are not yet fully understood, limiting the potential applications. Here, we conduct a theoretical study with a combination of molecular dynamics, first-principles, and charge transmission calculations. We use four separate single strand DNAs, each having 8 bases (4 × G4C4 and 4 × A4T4), to form two different DNA nanostructures, each having two helices bundled together with one crossover. We also generated double-stranded DNAs to compare electronic properties to decipher the effects of crossovers and bundle formations. We demonstrate that density of states and band gap of DNA origami depend on its sequence and structure. The crossover regions could reduce the conductance due to a lack of available states near the HOMO level. Furthermore, we reveal that, despite having the same sequence, the two helices in the DNA origami structure could exhibit different electronic properties, and electrode position can affect the resulting conductance values. Our study provides better understanding of the electronic properties of DNA origamis and enables us to tune these properties for electronic applications such as nanowires, switches, and logic gates.
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Affiliation(s)
- Busra Demir
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Department
of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Caglanaz Akin Gultakti
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
| | - Zeynep Koker
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
| | - M. P. Anantram
- Department
of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Ersin Emre Oren
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
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4
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Lee Y, Buchheim J, Hellenkamp B, Lynall D, Yang K, Young EF, Penkov B, Sia S, Stojanovic MN, Shepard KL. Carbon-nanotube field-effect transistors for resolving single-molecule aptamer-ligand binding kinetics. NATURE NANOTECHNOLOGY 2024; 19:660-667. [PMID: 38233588 DOI: 10.1038/s41565-023-01591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Small molecules such as neurotransmitters are critical for biochemical functions in living systems. While conventional ultraviolet-visible spectroscopy and mass spectrometry lack portability and are unsuitable for time-resolved measurements in situ, techniques such as amperometry and traditional field-effect detection require a large ensemble of molecules to reach detectable signal levels. Here we demonstrate the potential of carbon-nanotube-based single-molecule field-effect transistors (smFETs), which can detect the charge on a single molecule, as a new platform for recognizing and assaying small molecules. smFETs are formed by the covalent attachment of a probe molecule, in our case a DNA aptamer, to a carbon nanotube. Conformation changes on binding are manifest as discrete changes in the nanotube electrical conductance. By monitoring the kinetics of conformational changes in a binding aptamer, we show that smFETs can detect and quantify serotonin at the single-molecule level, providing unique insights into the dynamics of the aptamer-ligand system. In particular, we show the involvement of G-quadruplex formation and the disruption of the native hairpin structure in the conformational changes of the serotonin-aptamer complex. The smFET is a label-free approach to analysing molecular interactions at the single-molecule level with high temporal resolution, providing additional insights into complex biological processes.
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Affiliation(s)
- Yoonhee Lee
- Department of Electrical Engineering, Columbia University, New York, NY, USA
- Division of Electronics & Information System, ICT Research Institute, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Jakob Buchheim
- Department of Electrical Engineering, Columbia University, New York, NY, USA
- Deutsches Zentrum für Luft- und Raumfahrt e.V. (DLR), Institute of Quantum Technologies, Ulm, Germany
| | - Björn Hellenkamp
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - David Lynall
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Kyungae Yang
- Department of Medicine, Columbia University, New York, NY, USA
| | - Erik F Young
- Quicksilver Biosciences, Inc., New York, NY, USA
| | - Boyan Penkov
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Samuel Sia
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA.
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
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5
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Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401877. [PMID: 38639403 DOI: 10.1002/advs.202401877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
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Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Li Cheng
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Mengmeng Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Suhang He
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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6
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Bouwens T, Bakker TMA, Zhu K, Huijser A, Mathew S, Reek JNH. Rotaxane-Functionalized Dyes for Charge-Rectification in p-Type Photoelectrochemical Devices. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306032. [PMID: 38110821 PMCID: PMC10916627 DOI: 10.1002/advs.202306032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Indexed: 12/20/2023]
Abstract
A supramolecular photovoltaic strategy is applied to enhance power conversion efficiencies (PCE) of photoelectrochemical devices by suppressing electron-hole recombination after photoinduced electron transfer (PET). Here, the author exploit supramolecular localization of the redox mediator-in close proximity to the dye-through a rotaxane topology, reducing electron-hole recombination in p-type dye-sensitized solar cells (p-DSSCs). Dye PRotaxane features 1,5-dioxynaphthalene recognition sites (DNP-arms) with a mechanically-interlocked macrocyclic redox mediator naphthalene diimide macrocycle (3-NDI-ring), stoppering synthetically via click chemistry. The control molecule PStopper has stoppered DNP-arms, preventing rotaxane formation with the 3-NDI-ring. Transient absorption and time-resolved fluorescence spectroscopy studies show ultrafast (211 ± 7 fs and 2.92 ± 0.05 ps) PET from the dye-moiety of PRotaxane to its mechanically interlocked 3-NDI-ring-acceptor, slowing down the electron-hole recombination on NiO surfaces compared to the analogue . p-DSSCs employing PRotaxane (PCE = 0.07%) demonstrate a 30% PCE increase compared to PStopper (PCE = 0.05%) devices, combining enhancements in both open-circuit voltages (VOC = 0.43 vs 0.36 V) and short-circuit photocurrent density (JSC = -0.39 vs -0.34 mA cm-2 ). Electrochemical impedance spectroscopy shows that PRotaxane devices exhibit hole lifetimes (τh ) approaching 1 s, a 16-fold improvement compared to traditional I- /I3 - -based systems (τh = 50 ms), demonstrating the benefits obtained upon nanoengineering of interfacial dye-regeneration at the photocathode.
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Affiliation(s)
- Tessel Bouwens
- van ’t Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 904Amsterdam1098 XHThe Netherlands
| | - Tijmen M. A. Bakker
- van ’t Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 904Amsterdam1098 XHThe Netherlands
| | - Kaijian Zhu
- PhotoCatalytic Synthesis GroupMESA+ Institute for NanotechnologyUniversity of TwenteP.O. Box 217Enschede7500 AEThe Netherlands
| | - Annemarie Huijser
- PhotoCatalytic Synthesis GroupMESA+ Institute for NanotechnologyUniversity of TwenteP.O. Box 217Enschede7500 AEThe Netherlands
| | - Simon Mathew
- van ’t Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 904Amsterdam1098 XHThe Netherlands
| | - Joost N. H. Reek
- van ’t Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 904Amsterdam1098 XHThe Netherlands
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7
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Liu B, Demir B, Gultakti CA, Marrs J, Gong Y, Li R, Oren EE, Hihath J. Self-Aligning Nanojunctions for Integrated Single-Molecule Circuits. ACS NANO 2024; 18:4972-4980. [PMID: 38214957 DOI: 10.1021/acsnano.3c10844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Robust, high-yield integration of nanoscale components such as graphene nanoribbons, nanoparticles, or single-molecules with conventional electronic circuits has proven to be challenging. This difficulty arises because the contacts to these nanoscale devices must be precisely fabricated with angstrom-level resolution to make reliable connections, and at manufacturing scales this cannot be achieved with even the highest-resolution lithographic tools. Here we introduce an approach that circumvents this issue by precisely creating nanometer-scale gaps between metallic carbon electrodes by using a self-aligning, solution-phase process, which allows facile integration with conventional electronic systems with yields approaching 50%. The electrode separation is controlled by covalently binding metallic single-walled carbon nanotube (mCNT) electrodes to individual DNA duplexes to create mCNT-DNA-mCNT nanojunctions, where the gap is precisely matched to the DNA length. These junctions are then integrated with top-down lithographic techniques to create single-molecule circuits that have electronic properties dominated by the DNA in the junction, have reproducible conductance values with low dispersion, and are stable and robust enough to be utilized as active, high-specificity electronic biosensors for dynamic single-molecule detection of specific oligonucleotides, such as those related to the SARS-CoV-2 genome. This scalable approach for high-yield integration of nanometer-scale devices will enable opportunities for manufacturing of hybrid electronic systems for a wide range of applications.
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Affiliation(s)
- Bo Liu
- Biodesign Center for Bioelectronics and Biosensors at Arizona State University, Tempe, Arizona 85287, United States
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Tureky
| | - Caglanaz Akin Gultakti
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Tureky
| | - Jonathan Marrs
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California 95616, United States
| | - Yichen Gong
- Biodesign Center for Bioelectronics and Biosensors at Arizona State University, Tempe, Arizona 85287, United States
| | - Ruihao Li
- Biodesign Center for Bioelectronics and Biosensors at Arizona State University, Tempe, Arizona 85287, United States
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Tureky
| | - Joshua Hihath
- Biodesign Center for Bioelectronics and Biosensors at Arizona State University, Tempe, Arizona 85287, United States
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California 95616, United States
- School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, Arizona 85287, United States
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8
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Escorihuela E, Del Barrio J, Davidson RJ, Beeby A, Low PJ, Prez-Murano F, Cea P, Martin S. Large area arrays of discrete single-molecule junctions derived from host-guest complexes. NANOSCALE 2024; 16:1238-1246. [PMID: 38116590 DOI: 10.1039/d3nr05122f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The desire to continually reduce the lower limits of semiconductor integrated circuit (IC) fabrication methods continues to inspire interest in unimolecular electronics as a platform technology for the realization of future (opto)electronic devices. However, despite successes in developing methods for the construction and measurement of single-molecule and large-area molecular junctions, exercising control over the precise junction geometry remains a significant challenge. Here, host-guest complexes of the wire-like viologen derivative 1,1'-bis(4-(methylthio)-phenyl)-[4,4'-bipyridine]-1,1'-diium chloride ([1][Cl]2) and cucurbit[7]uril (CB[7]) have been self-assembled in a regular pattern over a gold substrate. Subsequently, ligandless gold nanoparticles (AuNPs) synthesized in situ are deposited over the host-guest array. The agreement between the conductance of individual mono-molecular junctions, appropriately chosen as a function of the AuNP diameter, within this array determined by conductive probe atomic force microscope (c-AFM) and true single-molecule measurements for a closely similar host-guest complex within a scanning tunneling microscope break-junction (STM-BJ) indicates the formation of molecular junctions derived from these host-guest complexes without deleterious intermolecular coupling effects.
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Affiliation(s)
- Enrique Escorihuela
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009, Zaragoza, Spain.
- Departamento de Química Física, Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Jesús Del Barrio
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009, Zaragoza, Spain.
- Departamento de Química Orgánica, Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Ross J Davidson
- Department of Chemistry, Durham University, South Rd, Durham, DH1 3LE, UK
| | - Andrew Beeby
- Department of Chemistry, Durham University, South Rd, Durham, DH1 3LE, UK
| | - Paul J Low
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Francesc Prez-Murano
- Institute of Microelectronics of Barcelona (IMB-CNM, CSIC), 08193, Bellaterra, Spain
| | - Pilar Cea
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009, Zaragoza, Spain.
- Departamento de Química Física, Universidad de Zaragoza, 50009, Zaragoza, Spain
- Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, 50018, Zaragoza, Spain
| | - Santiago Martin
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009, Zaragoza, Spain.
- Departamento de Química Física, Universidad de Zaragoza, 50009, Zaragoza, Spain
- Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, 50018, Zaragoza, Spain
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9
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Amamizu N, Nishida M, Sasaki K, Kishi R, Kitagawa Y. Theoretical Study on the Open-Shell Electronic Structure and Electron Conductivity of [18]Annulene as a Molecular Parallel Circuit Model. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 14:98. [PMID: 38202553 PMCID: PMC10781064 DOI: 10.3390/nano14010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Herein, the electron conductivities of [18]annulene and its derivatives are theoretically examined as a molecular parallel circuit model consisting of two linear polyenes. Their electron conductivities are estimated by elastic scattering Green's function (ESGF) theory and density functional theory (DFT) methods. The calculated conductivity of the [18]annulene does not follow the classical conductivity, i.e., Ohm's law, suggesting the importance of a quantum interference effect in single molecules. By introducing electron-withdrawing groups into the annulene framework, on the other hand, a spin-polarized electronic structure appears, and the quantum interference effect is significantly suppressed. In addition, the total current is affected by the spin polarization because of the asymmetry in the coupling constant between the molecule and electrodes. From these results, it is suggested that the electron conductivity as well as the quantum interference effect of π-conjugated molecular systems can be designed using their open-shell nature, which is chemically controlled by the substituents.
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Affiliation(s)
- Naoka Amamizu
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan; (M.N.); (K.S.); (R.K.)
| | - Mitsuhiro Nishida
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan; (M.N.); (K.S.); (R.K.)
| | - Keisuke Sasaki
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan; (M.N.); (K.S.); (R.K.)
| | - Ryohei Kishi
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan; (M.N.); (K.S.); (R.K.)
- Center for Quantum Information and Quantum Biology (QIQB), International Advanced Research Institute (IARI), Osaka University, Toyonaka, Osaka 560-0043, Japan
- Research Center for Solar Energy Chemistry (RCSEC), Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI), Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasutaka Kitagawa
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan; (M.N.); (K.S.); (R.K.)
- Center for Quantum Information and Quantum Biology (QIQB), International Advanced Research Institute (IARI), Osaka University, Toyonaka, Osaka 560-0043, Japan
- Research Center for Solar Energy Chemistry (RCSEC), Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI), Osaka University, Suita, Osaka 565-0871, Japan
- Spintronics Research Network Division, Institute for Open and Transdisciplinary Research Initiatives (SRN-OTRI), Osaka University, Toyonaka, Osaka 560-8531, Japan
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10
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Sullivan RP, Morningstar JT, Castellanos-Trejo E, Welker ME, Jurchescu OD. The Stark Effect: A Tool for the Design of High-Performance Molecular Rectifiers. NANO LETTERS 2023. [PMID: 37974048 DOI: 10.1021/acs.nanolett.3c03068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Molecular electronic devices offer a path to the miniaturization of electronic circuits and could potentially facilitate novel functionalities that can be embedded into the molecular structure. Given their nanoscale dimensions, device properties are strongly influenced by quantum effects, yet many of these phenomena have been largely overlooked. We investigated the mechanism responsible for current rectification in molecular diodes and found that efficient rectification is achieved by enhancing the Stark effect strength and enabling a large number of molecules to participate in transport. These findings provided insights into the operation of molecular rectifiers and guided the development of high-performance devices via the design of molecules containing polarizable aromatic rings. Our results are consistent for different molecular structures and are expected to have broad applicability to all molecular devices by answering key questions related to charge transport mechanisms in such systems.
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Affiliation(s)
- Ryan P Sullivan
- Department of Physics and Center for Functional Materials, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - John T Morningstar
- Department of Chemistry and Center for Functional Materials, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Eduardo Castellanos-Trejo
- Department of Physics and Center for Functional Materials, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Mark E Welker
- Department of Chemistry and Center for Functional Materials, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Oana D Jurchescu
- Department of Physics and Center for Functional Materials, Wake Forest University, Winston-Salem, North Carolina 27109, United States
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11
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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12
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Jiang T, Zeng BF, Zhang B, Tang L. Single-molecular protein-based bioelectronics via electronic transport: fundamentals, devices and applications. Chem Soc Rev 2023; 52:5968-6002. [PMID: 37498342 DOI: 10.1039/d2cs00519k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Biomolecular electronics is a rapidly growing multidisciplinary field that combines biology, nanoscience, and engineering to bridge the two important fields of life sciences and molecular electronics. Proteins are remarkable for their ability to recognize molecules and transport electrons, making the integration of proteins into electronic devices a long sought-after goal and leading to the emergence of the field of protein-based bioelectronics, also known as proteotronics. This field seeks to design and create new biomolecular electronic platforms that allow for the understanding and manipulation of protein-mediated electronic charge transport and related functional applications. In recent decades, there have been numerous reports on protein-based bioelectronics using a variety of nano-gapped electrical devices and techniques at the single molecular level, which are not achievable with conventional ensemble approaches. This review focuses on recent advances in physical electron transport mechanisms, device fabrication methodologies, and various applications in protein-based bioelectronics. We discuss the most recent progress of the single or few protein-bridged electrical junction fabrication strategies, summarise the work on fundamental and functional applications of protein bioelectronics that enable high and dynamic electron transport, and highlight future perspectives and challenges that still need to be addressed. We believe that this specific review will stimulate the interdisciplinary research of topics related to protein-related bioelectronics, and open up new possibilities for single-molecule biophysics and biomedicine.
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Affiliation(s)
- Tao Jiang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China.
| | - Biao-Feng Zeng
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China.
| | - Bintian Zhang
- Shenzhen Key Laboratory of Precision Measurement and Early Warning Technology for Urban Environmental Health Risks, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China.
- Institute of Quantum Sensing, Interdisciplinary Centre for Quantum Information, Zhejiang University, Hangzhou 310027, China
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13
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Abstract
Bio/chemical sensors possess a plethora of advantageous features that have proven to be invaluable tools in detecting and monitoring biomolecules, facilitating advancements in healthcare, environmental monitoring, food safety, and more. However, when it comes to their routine use in continuous fluid flow conditions, an intricate web of solid-liquid interfacial phenomena emerges, which requires a deep understanding of the sensor surface and fluid interations. These interfacial phenomena encompass a broad spectrum of physical, chemical, and biological processes, other than the actual detection, that influence the sensor's response. In this context, perhaps exploring a new theme "active solid"-"moving liquid" interface will unleash the full potential of bio/chemical sensors in any flow-based application.
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Affiliation(s)
- Nikhil Bhalla
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, 2-24 York Street, Belfast, Northern Ireland BT15 1AP, United Kingdom
- Healthcare Technology Hub, Ulster University, 2-24 York Street, Belfast, Northern Ireland BT15 1AP, United Kingdom
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14
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Balasubramanian PS, Lal A. GHz ultrasonic sensor for ionic content with high sensitivity and localization. iScience 2023; 26:106907. [PMID: 37305695 PMCID: PMC10250832 DOI: 10.1016/j.isci.2023.106907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/02/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Sensing the ionic content of a solution at high spatial and temporal resolution and sensitivity is a challenge in nanosensing. This paper describes a comprehensive investigation of the possibility of GHz ultrasound acoustic impedance sensors to sense the content of an ionic aqueous medium. At the 1.55 GHz ultrasonic frequency used in this study, the micron-scale wavelength and the decay lengths in liquid result in a highly localized sense volume with the added potential for high temporal resolution and sensitivity. The amplitude of the back reflected pulse is related to the acoustic impedance of the medium and a function of ionic species concentration of the KCl, NaCl, and CaCl2 solutions used in this study. A concentration sensitivity as high as 1 mM and concentration detection range of 0 to 3 M was achieved. These bulk acoustic wave pulse-echo acoustic impedance sensors can also be used to record dynamic ionic flux.
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Affiliation(s)
| | - Amit Lal
- School of Electrical and Computer Engineering, Cornell University, Ithaca, NY 14853, USA
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15
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Li T, Bandari VK, Schmidt OG. Molecular Electronics: Creating and Bridging Molecular Junctions and Promoting Its Commercialization. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2209088. [PMID: 36512432 DOI: 10.1002/adma.202209088] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/28/2022] [Indexed: 06/02/2023]
Abstract
Molecular electronics is driven by the dream of expanding Moore's law to the molecular level for next-generation electronics through incorporating individual or ensemble molecules into electronic circuits. For nearly 50 years, numerous efforts have been made to explore the intrinsic properties of molecules and develop diverse fascinating molecular electronic devices with the desired functionalities. The flourishing of molecular electronics is inseparable from the development of various elegant methodologies for creating nanogap electrodes and bridging the nanogap with molecules. This review first focuses on the techniques for making lateral and vertical nanogap electrodes by breaking, narrowing, and fixed modes, and highlights their capabilities, applications, merits, and shortcomings. After summarizing the approaches of growing single molecules or molecular layers on the electrodes, the methods of constructing a complete molecular circuit are comprehensively grouped into three categories: 1) directly bridging one-molecule-electrode component with another electrode, 2) physically bridging two-molecule-electrode components, and 3) chemically bridging two-molecule-electrode components. Finally, the current state of molecular circuit integration and commercialization is discussed and perspectives are provided, hoping to encourage the community to accelerate the realization of fully scalable molecular electronics for a new era of integrated microsystems and applications.
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Affiliation(s)
- Tianming Li
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09111, Chemnitz, Germany
| | - Vineeth Kumar Bandari
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09111, Chemnitz, Germany
| | - Oliver G Schmidt
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09111, Chemnitz, Germany
- Nanophysics, Dresden University of Technology, 01069, Dresden, Germany
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16
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Iyer V, Issadore DA, Aflatouni F. The next generation of hybrid microfluidic/integrated circuit chips: recent and upcoming advances in high-speed, high-throughput, and multifunctional lab-on-IC systems. LAB ON A CHIP 2023; 23:2553-2576. [PMID: 37114950 DOI: 10.1039/d2lc01163h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Since the field's inception, pioneers in microfluidics have made significant progress towards realizing complete lab-on-chip systems capable of sophisticated sample analysis and processing. One avenue towards this goal has been to join forces with the related field of microelectronics, using integrated circuits (ICs) to perform on-chip actuation and sensing. While early demonstrations focused on using microfluidic-IC hybrid chips to miniaturize benchtop instruments, steady advancements in the field have enabled a new generation of devices that expand past miniaturization into high-performance applications that would not be possible without IC hybrid integration. In this review, we identify recent examples of labs-on-chip that use high-resolution, high-speed, and multifunctional electronic and photonic chips to expand the capabilities of conventional sample analysis. We focus on three particularly active areas: a) high-throughput integrated flow cytometers; b) large-scale microelectrode arrays for stimulation and multimodal sensing of cells over a wide field of view; c) high-speed biosensors for studying molecules with high temporal resolution. We also discuss recent advancements in IC technology, including on-chip data processing techniques and lens-free optics based on integrated photonics, that are poised to further advance microfluidic-IC hybrid chips.
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Affiliation(s)
- Vasant Iyer
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - David A Issadore
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Firooz Aflatouni
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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17
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Atkinson JT, Chavez MS, Niman CM, El-Naggar MY. Living electronics: A catalogue of engineered living electronic components. Microb Biotechnol 2023; 16:507-533. [PMID: 36519191 PMCID: PMC9948233 DOI: 10.1111/1751-7915.14171] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.
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Affiliation(s)
- Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.,Department of Chemistry, University of Southern California, Los Angeles, California, USA
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18
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Mo F, Spano CE, Ardesi Y, Ruo Roch M, Piccinini G, Graziano M. Design of Pyrrole-Based Gate-Controlled Molecular Junctions Optimized for Single-Molecule Aflatoxin B1 Detection. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23031687. [PMID: 36772727 PMCID: PMC9919708 DOI: 10.3390/s23031687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 05/27/2023]
Abstract
Food contamination by aflatoxins is an urgent global issue due to its high level of toxicity and the difficulties in limiting the diffusion. Unfortunately, current detection techniques, which mainly use biosensing, prevent the pervasive monitoring of aflatoxins throughout the agri-food chain. In this work, we investigate, through ab initio atomistic calculations, a pyrrole-based Molecular Field Effect Transistor (MolFET) as a single-molecule sensor for the amperometric detection of aflatoxins. In particular, we theoretically explain the gate-tuned current modulation from a chemical-physical perspective, and we support our insights through simulations. In addition, this work demonstrates that, for the case under consideration, the use of a suitable gate voltage permits a considerable enhancement in the sensor performance. The gating effect raises the current modulation due to aflatoxin from 100% to more than 103÷104%. In particular, the current is diminished by two orders of magnitude from the μA range to the nA range due to the presence of aflatoxin B1. Our work motivates future research efforts in miniaturized FET electrical detection for future pervasive electrical measurement of aflatoxins.
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Affiliation(s)
- Fabrizio Mo
- Department of Electronics and Telecommunication, Politecnico di Torino, 10129 Torino, Italy
| | - Chiara Elfi Spano
- Department of Electronics and Telecommunication, Politecnico di Torino, 10129 Torino, Italy
| | - Yuri Ardesi
- Department of Electronics and Telecommunication, Politecnico di Torino, 10129 Torino, Italy
| | - Massimo Ruo Roch
- Department of Electronics and Telecommunication, Politecnico di Torino, 10129 Torino, Italy
| | - Gianluca Piccinini
- Department of Electronics and Telecommunication, Politecnico di Torino, 10129 Torino, Italy
| | - Mariagrazia Graziano
- Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
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19
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Martin HG, Radivojevic T, Zucker J, Bouchard K, Sustarich J, Peisert S, Arnold D, Hillson N, Babnigg G, Marti JM, Mungall CJ, Beckham GT, Waldburger L, Carothers J, Sundaram S, Agarwal D, Simmons BA, Backman T, Banerjee D, Tanjore D, Ramakrishnan L, Singh A. Perspectives for self-driving labs in synthetic biology. Curr Opin Biotechnol 2023; 79:102881. [PMID: 36603501 DOI: 10.1016/j.copbio.2022.102881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 01/04/2023]
Abstract
Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, interpreted, and explained by machines for human benefit. While there are functioning SDLs in the fields of chemistry and materials science, we contend that synthetic biology provides a unique opportunity since the genome provides a single target for affecting the incredibly wide repertoire of biological cell behavior. However, the level of investment required for the creation of biological SDLs is only warranted if directed toward solving difficult and enabling biological questions. Here, we discuss challenges and opportunities in creating SDLs for synthetic biology.
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Affiliation(s)
- Hector G Martin
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States; BCAM, Basque Center for Applied Mathematics, Bilbao, Spain.
| | - Tijana Radivojevic
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Jeremy Zucker
- Earth and Biological Sciences Division, Pacific Northwest National Laboratories, Richland, WA, United States
| | - Kristofer Bouchard
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States; Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience, Berkeley, CA, United States
| | - Jess Sustarich
- Joint BioEnergy Institute, Emeryville, CA, United States; Biomaterials and Biomanufacturing Division, Sandia National Laboratories, Livermore, CA, United States
| | - Sean Peisert
- Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States; University of California, Davis, Department of Computer Science, Davis, CA, United States
| | - Dan Arnold
- Lawrence Berkeley National Laboratory, Energy Storage and Distributed Resources Division, Berkeley, CA, United States
| | - Nathan Hillson
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Gyorgy Babnigg
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | - Jose M Marti
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States; Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Christopher J Mungall
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States
| | - Gregg T Beckham
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Lucas Waldburger
- Department of Bioengineering, University of California, Berkeley, CA, United States
| | - James Carothers
- Department of Chemical Engineering, Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA, United States
| | - ShivShankar Sundaram
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States; Center for Bioengineering, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Deb Agarwal
- Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States
| | - Blake A Simmons
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Tyler Backman
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepanwita Banerjee
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepti Tanjore
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lavanya Ramakrishnan
- Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States
| | - Anup Singh
- Joint BioEnergy Institute, Emeryville, CA, United States; Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
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20
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Mou J, Ding J, Qin W. Deep Learning-Enhanced Potentiometric Aptasensing with Magneto-Controlled Sensors. Angew Chem Int Ed Engl 2023; 62:e202210513. [PMID: 36404278 DOI: 10.1002/anie.202210513] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/20/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]
Abstract
Bioelectronic sensors that report charge changes of a biomolecule upon target binding enable direct and sensitive analyte detection but remain a major challenge for potentiometric measurement, mainly due to Debye Length limitations and the need for molecular-level platforms. Here, we report on a magneto-controlled potentiometric method to directly and sensitively measure the target-binding induced charge change of DNA aptamers assembled on magnetic beads using a polymeric membrane potentiometric ion sensor. The potentiometric responses of the negatively charged aptamer, serving as a receptor and reporter, were dynamically controlled and modulated by applying a magnetic field. Based on a potentiometric array, this non-equilibrium measurement technique combined with deep learning algorithms allows for rapidly and reliably classifying and quantifying diverse small molecules using antibiotics as models. This potentiometric strategy opens new modalities for sensing applications.
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Affiliation(s)
- Junsong Mou
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai, 264003, Shandong, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jiawang Ding
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai, 264003, Shandong, P. R. China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, Shandong (P. R., China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, Shandong, P. R. China
| | - Wei Qin
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai, 264003, Shandong, P. R. China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, Shandong (P. R., China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, Shandong, P. R. China
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21
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Sullivan RP, Castellanos-Trejo E, Ma R, Welker ME, Jurchescu OD. Humidity sensors based on molecular rectifiers. NANOSCALE 2022; 15:171-176. [PMID: 36484707 DOI: 10.1039/d2nr04498f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ambient humidity plays a key role in the health and well-being of us and our surroundings, making it necessary to carefully monitor and control it. To achieve this goal, several types of instruments based on various materials and operating principles have been developed. Reducing the production costs for such systems without affecting their sensitivity and reliability would allow for broader use and greater efficiency. Organic materials are prime candidates for incorporation in humidity sensors given their extraordinary chemical diversity, low cost, and ease of processing. Here, we designed, assembled and tested humidity sensors based on molecular rectifiers that can electrically transduce the changes in the ambient humidity to offer accurate quantitative information in the range of 0 to 70% relative humidity. Their operation relies on the changes occurring in the electric field experienced by the molecular layer upon absorption of the polar water molecules, resulting in modifications in the height and shape of the tunneling barrier. The response is reversible and reproducible upon multiple cycles and, coupled with the simplicity of the device architecture and manufacturing, makes these nanoscale sensors attractive for incorporation in various applications.
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Affiliation(s)
- Ryan P Sullivan
- Department of Physics, Center for Functional Materials, Wake Forest University, Winston-Salem, NC, 27109, USA.
| | - Eduardo Castellanos-Trejo
- Department of Physics, Center for Functional Materials, Wake Forest University, Winston-Salem, NC, 27109, USA.
| | - Renate Ma
- Department of Chemistry, Center for Functional Materials, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Mark E Welker
- Department of Chemistry, Center for Functional Materials, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Oana D Jurchescu
- Department of Physics, Center for Functional Materials, Wake Forest University, Winston-Salem, NC, 27109, USA.
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22
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Hall DA, Ananthapadmanabhan N, Choi C, Zheng L, Pan PP, Von Jutrzenka C, Nguyen T, Rizo J, Weinstein M, Lobaton R, Sinha P, Sauerbrey T, Sigala C, Bailey K, Mudondo PJ, Chaudhuri AR, Severi S, Fuller CW, Tour JM, Jin S, Mola PW, Merriman B. A Scalable CMOS Molecular Electronics Chip for Single-Molecule Biosensing. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2022; 16:1030-1043. [PMID: 36191107 DOI: 10.1109/tbcas.2022.3211420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This work reports the first CMOS molecular electronics chip. It is configured as a biosensor, where the primary sensing element is a single molecule "molecular wire" consisting of a ∼100 GΩ, 25 nm long alpha-helical peptide integrated into a current monitoring circuit. The engineered peptide contains a central conjugation site for attachment of various probe molecules, such as DNA, proteins, enzymes, or antibodies, which program the biosensor to detect interactions with a specific target molecule. The current through the molecular wire under a dc applied voltage is monitored with millisecond temporal resolution. The detected signals are millisecond-scale, picoampere current pulses generated by each transient probe-target molecular interaction. Implemented in a 0.18 μm CMOS technology, 16k sensors are arrayed with a 20 μm pitch and read out at a 1 kHz frame rate. The resulting biosensor chip provides direct, real-time observation of the single-molecule interaction kinetics, unlike classical biosensors that measure ensemble averages of such events. This molecular electronics chip provides a platform for putting molecular biosensing "on-chip" to bring the power of semiconductor chips to diverse applications in biological research, diagnostics, sequencing, proteomics, drug discovery, and environmental monitoring.
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23
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Cervantes-Salguero K, Freeley M, Gwyther REA, Jones DD, Chávez JL, Palma M. Single molecule DNA origami nanoarrays with controlled protein orientation. BIOPHYSICS REVIEWS 2022; 3:031401. [PMID: 38505279 PMCID: PMC10903486 DOI: 10.1063/5.0099294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/20/2022] [Indexed: 03/21/2024]
Abstract
The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.
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Affiliation(s)
- K. Cervantes-Salguero
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - M. Freeley
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - R. E. A. Gwyther
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - D. D. Jones
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - J. L. Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright Patterson Air Force Base, Dayton, Ohio 45433-7901, USA
| | - M. Palma
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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24
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Sullivan RP, Morningstar JT, Castellanos-Trejo E, Bradford RW, Hofstetter YJ, Vaynzof Y, Welker ME, Jurchescu OD. Intermolecular charge transfer enhances the performance of molecular rectifiers. SCIENCE ADVANCES 2022; 8:eabq7224. [PMID: 35930649 PMCID: PMC9355360 DOI: 10.1126/sciadv.abq7224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Molecular-scale diodes made from self-assembled monolayers (SAMs) could complement silicon-based technologies with smaller, cheaper, and more versatile devices. However, advancement of this emerging technology is limited by insufficient electronic performance exhibited by the molecular current rectifiers. We overcome this barrier by exploiting the charge-transfer state that results from co-assembling SAMs of molecules with strong electron donor and acceptor termini. We obtain a substantial enhancement in current rectification, which correlates with the degree of charge transfer, as confirmed by several complementary techniques. These findings provide a previously enexplored method for manipulating the properties of molecular electronic devices by exploiting donor/acceptor interactions. They also serve as a model test platform for the study of doping mechanisms in organic systems. Our devices have the potential for fast widespread adoption due to their low-cost processing and self-assembly onto silicon substrates, which could allow seamless integration with current technologies.
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Affiliation(s)
- Ryan P. Sullivan
- Deparment of Physics and Center for Functional Materials, Wake Forest University, Winston-Salem, NC 27109, USA
| | - John T. Morningstar
- Deparment of Chemistry and Center for Functional Materials, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Eduardo Castellanos-Trejo
- Deparment of Physics and Center for Functional Materials, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Robert W. Bradford
- Deparment of Physics and Center for Functional Materials, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Yvonne J. Hofstetter
- Integrated Centre for Applied Physics and Photonic Materials, Technische Universität Dresden, Nöthnitzer Str. 61, 01187 Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01089 Dresden, Germany
| | - Yana Vaynzof
- Integrated Centre for Applied Physics and Photonic Materials, Technische Universität Dresden, Nöthnitzer Str. 61, 01187 Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01089 Dresden, Germany
| | - Mark E. Welker
- Deparment of Chemistry and Center for Functional Materials, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Oana D. Jurchescu
- Deparment of Physics and Center for Functional Materials, Wake Forest University, Winston-Salem, NC 27109, USA
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