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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. [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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2
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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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3
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Sun R, Lv J, Xue X, Yu S, Tan Z. Chemical Sensors using Single-Molecule Electrical Measurements. Chem Asian J 2023; 18:e202300181. [PMID: 37080926 DOI: 10.1002/asia.202300181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023]
Abstract
Driven by the digitization and informatization of contemporary society, electrical sensors are developing toward minimal structure, intelligent function, and high detection resolution. Single-molecule electrical measurement techniques have been proven to be capable of label-free molecular recognition and detection, which opens a new strategy for the design of efficient single-molecule detection sensors. In this review, we outline the main advances and potentials of single-molecule electronics for qualitative identification and recognition assays at the single-molecule level. Strategies for single-molecule electro-sensing and its main applications are reviewed, mainly in the detection of ions, small molecules, oligomers, genetic materials, and proteins. This review summarizes the remaining challenges in the current development of single-molecule electrical sensing and presents some potential perspectives for this field.
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Affiliation(s)
- Ruiqin Sun
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Jieyao Lv
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Xinyi Xue
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Shiyong Yu
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Zhibing Tan
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
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4
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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: 12] [Impact Index Per Article: 12.0] [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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5
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Jena MK, Pathak B. Development of an Artificially Intelligent Nanopore for High-Throughput DNA Sequencing with a Machine-Learning-Aided Quantum-Tunneling Approach. NANO LETTERS 2023; 23:2511-2521. [PMID: 36799480 DOI: 10.1021/acs.nanolett.2c04062] [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: 06/18/2023]
Abstract
Solid-state nanopore-based single-molecule DNA sequencing with quantum tunneling technology poses formidable challenges to achieve long-read sequencing and high-throughput analysis. Here, we propose a method for developing an artificially intelligent (AI) nanopore that does not require extraction of the signature transmission function for each nucleotide of the whole DNA strand by integrating supervised machine learning (ML) and transverse quantum transport technology with a graphene nanopore. The optimized ML model can predict the transmission function of all other nucleotides after training with data sets of all the orientations of any nucleotide inside the nanopore with a root-mean-square error (RMSE) of as low as 0.062. Further, up to 96.01% accuracy is achieved in classifying the unlabeled nucleotides with their transmission readouts. We envision that an AI nanopore can alleviate the experimental challenges of the quantum-tunneling method and pave the way for rapid and high-precision DNA sequencing by predicting their signature transmission functions.
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Affiliation(s)
- Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh 453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh 453552, India
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6
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Fyta M. Functionalized electrodes embedded in nanopores: read-out enhancement? Chem Asian J 2023; 18:e202200916. [PMID: 36372991 PMCID: PMC10107472 DOI: 10.1002/asia.202200916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
In this review, functionalized nanogaps embedded in nanopores are discussed in view of their high biosensitivity in detecting biomolecules, their length, type, and sequence. Specific focus is given on nanoelectrodes functionalized with tiny nanometer-sized diamond-like particles offering vast functionalization possibilities for gold junction electrodes. This choice of the functionalization, in turn, offers nucleotide-specific binding possibilities improving the detection signals arising from such functionalized electrodes potentially embedded in a nanopore. The review sheds light onto the use and enhancement of the tunnelling recognition in functionalized nanogaps towards sensing DNA nucleotides and mutation detection, providing important input for a practical realization.
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Affiliation(s)
- Maria Fyta
- Computational Biotechnology, RWTH-Aachen University, Worringerweg 3, 52072, Aachen, Germany
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7
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Zou H, Wen S, Wu X, Wong KW, Yam C. DNA sequencing based on electronic tunneling in a gold nanogap: a first-principles study. Phys Chem Chem Phys 2022; 24:5748-5754. [PMID: 35191434 DOI: 10.1039/d1cp04910k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deoxyribonucleic acid (DNA) sequencing has found wide applications in medicine including treatment of diseases, diagnosis and genetics studies. Rapid and cost-effective DNA sequencing has been achieved by measuring the transverse electronic conductance as a single-stranded DNA is driven through a nanojunction. With the aim of improving the accuracy and sensitivity of DNA sequencing, we investigate the electron transport properties of DNA nucleobases within gold nanogaps based on first-principles quantum transport simulations. Considering the fact that the DNA bases can rotate within the nanogap during measurements, different nucleobase orientations and their corresponding residence time within the nanogap are explicitly taken into account based on their energetics. This allows us to obtain an average current that can be compared directly to experimental measurements. Our results indicate that bare gold electrodes show low distinguishability among the four DNA nucleobases while the distinguishability can be substantially enhanced with sulfur atom decorated electrodes. We further optimized the size of the nanogap by maximizing the residence time of the desired orientation.
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Affiliation(s)
- Hao Zou
- Beijing Computational Science Research Center, Haidian District, Beijing 100193, China.
| | - Shizheng Wen
- Beijing Computational Science Research Center, Haidian District, Beijing 100193, China. .,Jiangsu Province Key Laboratory of Modern Measurement Technology and Intelligent Systems, School of Physics and Electronic Electrical Engineering, Huaiyin Normal University, Huaian 223300, China
| | - Xiaoyan Wu
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen 518109, China
| | - Ka-Wai Wong
- Genvida Technology Company Limited, Hong Kong, China.
| | - ChiYung Yam
- Beijing Computational Science Research Center, Haidian District, Beijing 100193, China. .,Shenzhen JL Computational Science and Applied Research Institute, Shenzhen 518109, China
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8
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Fried JP, Swett JL, Nadappuram BP, Mol JA, Edel JB, Ivanov AP, Yates JR. In situ solid-state nanopore fabrication. Chem Soc Rev 2021; 50:4974-4992. [PMID: 33623941 DOI: 10.1039/d0cs00924e] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.
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Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS, UK
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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9
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Tang L, Nadappuram BP, Cadinu P, Zhao Z, Xue L, Yi L, Ren R, Wang J, Ivanov AP, Edel JB. Combined quantum tunnelling and dielectrophoretic trapping for molecular analysis at ultra-low analyte concentrations. Nat Commun 2021; 12:913. [PMID: 33568635 PMCID: PMC7876030 DOI: 10.1038/s41467-021-21101-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/06/2021] [Indexed: 01/04/2023] Open
Abstract
Quantum tunnelling offers a unique opportunity to study nanoscale objects with atomic resolution using electrical readout. However, practical implementation is impeded by the lack of simple, stable probes, that are required for successful operation. Existing platforms offer low throughput and operate in a limited range of analyte concentrations, as there is no active control to transport molecules to the sensor. We report on a standalone tunnelling probe based on double-barrelled capillary nanoelectrodes that do not require a conductive substrate to operate unlike other techniques, such as scanning tunnelling microscopy. These probes can be used to efficiently operate in solution environments and detect single molecules, including mononucleotides, oligonucleotides, and proteins. The probes are simple to fabricate, exhibit remarkable stability, and can be combined with dielectrophoretic trapping, enabling active analyte transport to the tunnelling sensor. The latter allows for up to 5-orders of magnitude increase in event detection rates and sub-femtomolar sensitivity. Probes that effectively utilize quantum tunneling are sought after for high-resolution study of nanoscale objects. Here the authors present an easily fabricated probe of two nanoelectrodes that enables highly sensitive quantum-tunneling-based sensing of single molecules.
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Affiliation(s)
- Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering; International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China. .,Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK. .,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China.
| | | | - Paolo Cadinu
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Zhiyu Zhao
- Center of Electron Microscopy and State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, China
| | - Liang Xue
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Long Yi
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Ren Ren
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Jiangwei Wang
- Center of Electron Microscopy and State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, China
| | - Aleksandar P Ivanov
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
| | - Joshua B Edel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
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10
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Zhang B, Deng H, Mukherjee S, Song W, Wang X, Lindsay S. Engineering an Enzyme for Direct Electrical Monitoring of Activity. ACS NANO 2020; 14:1360-1368. [PMID: 31594304 PMCID: PMC7047563 DOI: 10.1021/acsnano.9b06875] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteins have been shown to be electrically conductive if tethered to an electrode by means of a specific binding agent, allowing single molecules to be wired into an electrical sensing circuit. Such circuits allow enzymes to be used as sensors, detectors, and sequencing devices. We have engineered contact points into a Φ29 polymerase by introducing biotinylatable peptide sequences. The modified enzyme was bound to electrodes functionalized with streptavidin. Φ29 connected by one biotinylated contact, and a second nonspecific contact showed rapid small fluctuations in current when activated. Signals were greatly enhanced with two specific contacts. Features in the distributions of DC conductance increased by a factor 2 or more over the open to closed conformational transition of the polymerase. Polymerase activity is manifested by a rapid (millisecond) large (25% of background) current fluctuations imposed on the DC conductance.
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Affiliation(s)
- Bintian Zhang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Hanqing Deng
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Sohini Mukherjee
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Weisi Song
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
- Department of Physics, Arizona State University, Tempe, AZ 85287
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11
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Lahiri H, Banerjee S, Mukhopadhyay R. Free-Energy-Based Gene Mutation Detection Using LNA Probes. ACS Sens 2019; 4:2688-2696. [PMID: 31549503 DOI: 10.1021/acssensors.9b01115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We have developed a label-free approach for direct detection of gene mutations using free-energy values that are derived from single-molecule force spectroscopy (SMFS)-based nucleic acid unbinding experiments. From the duplex unbinding force values acquired by SMFS, the force-loading-rate-independent Gibbs free-energy values were derived using Jarzinsky's equality treatment. Because it provides molecule-by-molecule information, this approach is a major shift compared to the earlier reports on label-free detection of DNA sequences, which are mostly based on ensemble level data. We tested our approach in the disease model framework of multiple drug-resistant tuberculosis using the nuclease-resistant and conformationally rigid locked nucleic acid probes that are a robust and efficient alternative to the DNA probes. All of the major mutations in Mycobacterium tuberculosis (MTB), as relevant to MTB's resistance to the first-line anti-TB drugs rifampicin and isoniazid, could be identified, and the wild type could be discriminated from the most prevalent mutation and the most prevalent mutation from the less occurring ones. Our approach could also identify DNA sequences (45 mer), having overhang stretches at different positions with respect to the complementary stretch. Probably for the first time, the findings show that free-energy-based detection of gene mutations is possible at molecular resolution.
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Affiliation(s)
- Hiya Lahiri
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Siddhartha Banerjee
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
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12
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Liu X, Zhang Y, Nagel R, Reisner W, Dunbar WB. Controlling DNA Tug-of-War in a Dual Nanopore Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901704. [PMID: 31192541 DOI: 10.1002/smll.201901704] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. A method is created for reducing and controlling the speed of DNA that uses two independently controllable nanopores operated with an active control logic. The pores are positioned sufficiently close to permit cocapture of a single DNA by both pores. Once cocapture occurs, control logic turns on constant competing voltages at the pores leading to a "tug-of-war" whereby opposing forces are applied to regions of the molecules threading through the pores. These forces exert both conformational and speed control over the cocaptured molecule, removing folds and reducing the translocation rate. When the voltages are tuned so that the electrophoretic force applied to both pores comes into balance, the life time of the tug-of-war state is limited purely by diffusive sliding of the DNA between the pores. A tug-of-war state is produced on 76.8% of molecules that are captured with a maximum two-order of magnitude increase in average pore translocation time relative to the average time for single-pore translocation. Moreover, the translocation slow-down is quantified as a function of voltage tuning and it is shown that the slow-down is well described by a first passage analysis for a 1D subdiffusive process. The ionic current of each nanopore provides an independent sensor that synchronously measures a different region of the same molecule, enabling sequential detection of physical labels, such as monostreptavidin tags. With advances in devices and control logic, future dual-pore applications include genome mapping and enzyme-free sequencing.
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Affiliation(s)
- Xu Liu
- Ontera, Inc., Santa Cruz, CA, 95060, USA
| | - Yuning Zhang
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | | | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
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13
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Furuhata T, Ohshiro T, Akimoto G, Ueki R, Taniguchi M, Sando S. Highly Conductive Nucleotide Analogue Facilitates Base-Calling in Quantum-Tunneling-Based DNA Sequencing. ACS NANO 2019; 13:5028-5035. [PMID: 30888791 DOI: 10.1021/acsnano.9b01250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Quantum-tunneling-based DNA sequencing is a single molecular technology that has great potential for achieving facile and high-throughput DNA sequencing. In principle, the sequence of DNA could be read out by the time trace of the tunnel current that can be changed according to molecular conductance of nucleobases passing through nanosized gap electrodes. However, efficient base-calling of four genetic alphabets has been seriously impeded due to the similarity of molecular conductance among canonical nucleotides. In this article, we demonstrate that replacement of canonical 2'-deoxyadenosine (dA) with a highly conductive dA analogue, 7-deaza dA, could expand the difference of molecular conductance between four genetic alphabets. Additionally, systematic evaluation of molecular conductance using a series of dA and dG analogues revealed that molecular conductance of the nucleotide is highly dependent on the HOMO level. Thus, the present study demonstrating that signal characteristics of the nucleotide can be modulated based on the HOMO level provides a widely applicable chemical approach and insight for facilitation of single molecular sensing as well as DNA sequencing based on quantum tunneling.
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Affiliation(s)
- Takafumi Furuhata
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Takahito Ohshiro
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Gaku Akimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
- Department of Bioengineering, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
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14
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Im J, Sen S, Lindsay S, Zhang P. Recognition Tunneling of Canonical and Modified RNA Nucleotides for Their Identification with the Aid of Machine Learning. ACS NANO 2018; 12:7067-7075. [PMID: 29932668 DOI: 10.1021/acsnano.8b02819] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In the present study, we demonstrate a tunneling nanogap technique to identify individual RNA nucleotides, which can be used as a mechanism to read the nucleobases for direct sequencing of RNA in a solid-state nanopore. The tunneling nanogap is composed of two electrodes separated by a distance of <3 nm and functionalized with a recognition molecule. When a chemical entity is captured in the gap, it generates electron tunneling currents, a process we call recognition tunneling (RT). Using RT nanogaps created in a scanning tunneling microscope (STM), we acquired the electron tunneling signals for the canonical and two modified RNA nucleotides. To call the individual RNA nucleotides from the RT data, we adopted a machine learning algorithm, support vector machine (SVM), for the data analysis. Through the SVM, we were able to identify the individual RNA nucleotides and distinguish them from their DNA counterparts with reasonably high accuracy. Since each RNA nucleoside contains a hydroxyl group at the 2'-position of its sugar ring in an RNA strand, it allows for the formation of a tunneling junction at a larger nanogap compared to the DNA nucleoside in a DNA strand, which lacks the 2' hydroxyl group. It also proves advantageous for the manufacture of RT devices. This study is a proof-of-principle demonstration for the development of an RT nanopore device for directly sequencing single RNA molecules, including those bearing modifications.
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15
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Zhao Z, Liu R, Mayer D, Coppola M, Sun L, Kim Y, Wang C, Ni L, Chen X, Wang M, Li Z, Lee T, Xiang D. Shaping the Atomic-Scale Geometries of Electrodes to Control Optical and Electrical Performance of Molecular Devices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703815. [PMID: 29542239 DOI: 10.1002/smll.201703815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/16/2018] [Indexed: 05/27/2023]
Abstract
A straightforward method to generate both atomic-scale sharp and atomic-scale planar electrodes is reported. The atomic-scale sharp electrodes are generated by precisely stretching a suspended nanowire, while the atomic-scale planar electrodes are obtained via mechanically controllable interelectrodes compression followed by a thermal-driven atom migration process. Notably, the gap size between the electrodes can be precisely controlled at subangstrom accuracy with this method. These two types of electrodes are subsequently employed to investigate the properties of single molecular junctions. It is found, for the first time, that the conductance of the amine-linked molecular junctions can be enhanced ≈50% as the atomic-scale sharp electrodes are used. However, the atomic-scale planar electrodes show great advantages to enhance the sensitivity of Raman scattering upon the variation of nanogap size. The underlying mechanisms for these two interesting observations are clarified with the help of density functional theory calculation and finite-element method simulation. These findings not only provide a strategy to control the electron transport through the molecule junction, but also pave a way to modulate the optical response as well as to improve the stability of single molecular devices via the rational design of electrodes geometries.
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Affiliation(s)
- Zhikai Zhao
- Key Laboratory of Optical Information Science and Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Nankai, 300071, China
| | - Ran Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Dirk Mayer
- Peter-Grünberg-Institute PGI-8, Bioelectronic Research Center Jülich GmbH and JARA, Fundamentals of Future Information Technology, Jülich, 52425, Germany
| | - Maristella Coppola
- Peter-Grünberg-Institute PGI-8, Bioelectronic Research Center Jülich GmbH and JARA, Fundamentals of Future Information Technology, Jülich, 52425, Germany
| | - Lu Sun
- Key Laboratory of Optical Information Science and Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Nankai, 300071, China
| | - Youngsang Kim
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chuankui Wang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Lifa Ni
- Key Laboratory of Optical Information Science and Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Nankai, 300071, China
| | - Xing Chen
- Penn State Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA, 16802, USA
| | - Maoning Wang
- Key Laboratory of Optical Information Science and Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Nankai, 300071, China
| | - Zongliang Li
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Takhee Lee
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea
| | - Dong Xiang
- Key Laboratory of Optical Information Science and Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Nankai, 300071, China
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16
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Detecting Single-Nucleotides by Tunneling Current Measurements at Sub-MHz Temporal Resolution. SENSORS 2017; 17:s17040885. [PMID: 28420199 PMCID: PMC5424762 DOI: 10.3390/s17040885] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 04/11/2017] [Accepted: 04/14/2017] [Indexed: 01/22/2023]
Abstract
Label-free detection of single-nucleotides was performed by fast tunneling current measurements in a polar solvent at 1 MHz sampling rate using SiO2-protected Au nanoprobes. Short current spikes were observed, suggestive of trapping/detrapping of individual nucleotides between the nanoelectrodes. The fall and rise features of the electrical signatures indicated signal retardation by capacitance effects with a time constant of about 10 microseconds. The high temporal resolution revealed current fluctuations, reflecting the molecular conformation degrees of freedom in the electrode gap. The method presented in this work may enable direct characterizations of dynamic changes in single-molecule conformations in an electrode gap in liquid.
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17
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Morikawa T, Yokota K, Tsutsui M, Taniguchi M. Fast and low-noise tunnelling current measurements for single-molecule detection in an electrolyte solution using insulator-protected nanoelectrodes. NANOSCALE 2017; 9:4076-4081. [PMID: 28116385 DOI: 10.1039/c6nr09278k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Reliable ways of DNA sequencing by tunnelling current require low-noise and high-speed measurements of tunnelling current in aqueous environments. Here we report a use of insulator-protected nanoprobes for achieving 7.6 pA rms noise at 50 kHz sampling rates in an electrolyte solution. We utilized dielectric-covered mechanically-controllable break junctions to create a pair of nano-exposed insulator/Au coaxial electrodes closely separated by 1 nm. We observed insulator layer thickness dependent noise levels, which was attributed to decreased capacitance through replacing capacitive electric double layers by the low-k dielectrics. We also demonstrated the detection of sharpened features in tunnelling current signatures that reflect dynamic motions of single-nucleotides in the electrode gaps by virtue of suppressed smearing effects in the low-capacitance nanoelectrode system.
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Affiliation(s)
- Takanori Morikawa
- The Institute of Scientific and Industrial Research, Osaka University, Japan.
| | - Kazumichi Yokota
- The Institute of Scientific and Industrial Research, Osaka University, Japan.
| | - Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Japan.
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Japan.
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18
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Carlsen AT, Briggs K, Hall AR, Tabard-Cossa V. Solid-state nanopore localization by controlled breakdown of selectively thinned membranes. NANOTECHNOLOGY 2017; 28:085304-85304. [PMID: 28045003 PMCID: PMC5408306 DOI: 10.1088/1361-6528/aa564d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We demonstrate precise positioning of nanopores fabricated by controlled breakdown (CBD) on solid-state membranes by spatially varying the electric field strength with localized membrane thinning. We show 100 × 100 nm2 precision in standard SiN x membranes (30-100 nm thick) after selective thinning by as little as 25% with a helium ion beam. Control over nanopore position is achieved through the strong dependence of the electric field-driven CBD mechanism on membrane thickness. Confinement of pore formation to the thinned region of the membrane is confirmed by TEM imaging and by analysis of DNA translocations. These results enhance the functionality of CBD as a fabrication approach and enable the production of advanced nanopore devices for single-molecule sensing applications.
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Affiliation(s)
- Autumn T. Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Adam R. Hall
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest University School of Medicine, Winston Salem, North Carolina 27101, United States
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19
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Wang C, Nam SW, Cotte JM, Jahnes CV, Colgan EG, Bruce RL, Brink M, Lofaro MF, Patel JV, Gignac LM, Joseph EA, Rao SP, Stolovitzky G, Polonsky S, Lin Q. Wafer-scale integration of sacrificial nanofluidic chips for detecting and manipulating single DNA molecules. Nat Commun 2017; 8:14243. [PMID: 28112157 PMCID: PMC5264239 DOI: 10.1038/ncomms14243] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 12/12/2016] [Indexed: 12/18/2022] Open
Abstract
Wafer-scale fabrication of complex nanofluidic systems with integrated electronics is essential to realizing ubiquitous, compact, reliable, high-sensitivity and low-cost biomolecular sensors. Here we report a scalable fabrication strategy capable of producing nanofluidic chips with complex designs and down to single-digit nanometre dimensions over 200 mm wafer scale. Compatible with semiconductor industry standard complementary metal-oxide semiconductor logic circuit fabrication processes, this strategy extracts a patterned sacrificial silicon layer through hundreds of millions of nanoscale vent holes on each chip by gas-phase Xenon difluoride etching. Using single-molecule fluorescence imaging, we demonstrate these sacrificial nanofluidic chips can function to controllably and completely stretch lambda DNA in a two-dimensional nanofluidic network comprising channels and pillars. The flexible nanofluidic structure design, wafer-scale fabrication, single-digit nanometre channels, reliable fluidic sealing and low thermal budget make our strategy a potentially universal approach to integrating functional planar nanofluidic systems with logic circuits for lab-on-a-chip applications. The wide use of microfluidics for biological analysis demands scalable preparation methods, yet in practice it is very challenging. Here, Wang et al. show a wafer-scale fabrication of nanofluidic chips with single-digit nanometre dimension, which is compatible with standard semiconductor processing.
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Affiliation(s)
- Chao Wang
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA.,School of Electrical, Computer and Energy Engineering, and Biodesign Center for Molecular Design &Biomimetics, Arizona State University, Tempe, Arizona 85287, USA
| | - Sung-Wook Nam
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - John M Cotte
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Christopher V Jahnes
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Evan G Colgan
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Robert L Bruce
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Markus Brink
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Michael F Lofaro
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Jyotica V Patel
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Lynne M Gignac
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Eric A Joseph
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Satyavolu Papa Rao
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Gustavo Stolovitzky
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA.,Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Stanislav Polonsky
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Qinghuang Lin
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
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20
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Pedersen JN, Boynton P, Ventra MD, Jauho AP, Flyvbjerg H. Classification of DNA nucleotides with transverse tunneling currents. NANOTECHNOLOGY 2017; 28:015502. [PMID: 27897144 PMCID: PMC5227067 DOI: 10.1088/0957-4484/28/1/015502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
It has been theoretically suggested and experimentally demonstrated that fast and low-cost sequencing of DNA, RNA, and peptide molecules might be achieved by passing such molecules between electrodes embedded in a nanochannel. The experimental realization of this scheme faces major challenges, however. In realistic liquid environments, typical currents in tunneling devices are of the order of picoamps. This corresponds to only six electrons per microsecond, and this number affects the integration time required to do current measurements in real experiments. This limits the speed of sequencing, though current fluctuations due to Brownian motion of the molecule average out during the required integration time. Moreover, data acquisition equipment introduces noise, and electronic filters create correlations in time-series data. We discuss how these effects must be included in the analysis of, e.g., the assignment of specific nucleobases to current signals. As the signals from different molecules overlap, unambiguous classification is impossible with a single measurement. We argue that the assignment of molecules to a signal is a standard pattern classification problem and calculation of the error rates is straightforward. The ideas presented here can be extended to other sequencing approaches of current interest.
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Affiliation(s)
- Jonas Nyvold Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. Center for Nanostructured Graphene (CNG), DTU Nanotech, Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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21
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Singh P, Singh AK. Palladium(ii) complexes of N,N-diphenylacetamide based thio/selenoethers and flower shaped Pd16S7and prismatic Pd17Se15nano-particles tailored as catalysts for C–C and C–O coupling. Dalton Trans 2017; 46:10037-10049. [DOI: 10.1039/c7dt01279a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Pd16S7/Pd17Se15NPs of shapes unknown hitherto and their Pd precursors (0.0001 mol%) are efficient/reusable catalysts for Suzuki–Miyaura/C–O coupling.
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Affiliation(s)
- Poornima Singh
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi–110016
- India
| | - Ajai K. Singh
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi–110016
- India
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22
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Zhang B, Song W, Pang P, Zhao Y, Zhang P, Csabai I, Vattay G, Lindsay S. Observation of Giant Conductance Fluctuations in a Protein. NANO FUTURES 2017; 1:035002. [PMID: 29552645 PMCID: PMC5851656 DOI: 10.1088/2399-1984/aa8f91] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Proteins are insulating molecular solids, yet even those containing easily reduced or oxidized centers can have single-molecule electronic conductances that are too large to account for with conventional transport theories. Here, we report the observation of remarkably high electronic conductance states in an electrochemically-inactive protein, the ~200 kD αVβ3 extracelluar domain of human integrin. Large current pulses (up to nA) were observed for long durations (many ms, corresponding to many pC of charge transfer) at large gap (>5nm) distances in an STM when the protein was bound specifically by a small peptide ligand attached to the electrodes. The effect is greatly reduced when a homologous, weakly-binding protein (α4β1) is used as a control. In order to overcome the limitations of the STM, the time- and voltage-dependence of the conductance were further explored using a fixed-gap (5 nm) tunneling junction device that was small enough to trap a single protein molecule at any one time. Transitions to a high conductance (~ nS) state were observed, the protein being "on" for times from ms to tenths of a second. The high-conductance states only occur above ~ 100mV applied bias, and thus are not an equilibrium property of the protein. Nanoamp two-level signals indicate the specific capture of a single molecule in an electrode gap functionalized with the ligand. This offers a new approach to label-free electronic detection of single protein molecules. Electronic structure calculations yield a distribution of energy level spacings that is consistent with a recently proposed quantum-critical state for proteins, in which small fluctuations can drive transitions between localized and band-like electronic states.
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Affiliation(s)
- Bintian Zhang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Weisi Song
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Pei Pang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Yanan Zhao
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Peiming Zhang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117 Budapest, Pázmány P. s. 1/A, Hungary
| | - Gábor Vattay
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117 Budapest, Pázmány P. s. 1/A, Hungary
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- To whom correspondence should be addressed:
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23
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Biswas S, Sen S, Im J, Biswas S, Krstic P, Ashcroft B, Borges C, Zhao Y, Lindsay S, Zhang P. Universal Readers Based on Hydrogen Bonding or π-π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions. ACS NANO 2016; 10:11304-11316. [PMID: 28024337 DOI: 10.1021/acsnano.6b06466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A reader molecule, which recognizes all the naturally occurring nucleobases in an electron tunnel junction, is required for sequencing DNA by a recognition tunneling (RT) technique, referred to as a universal reader. In the present study, we have designed a series of heterocyclic carboxamides based on hydrogen bonding and a large-sized pyrene ring based on a π-π stacking interaction as universal reader candidates. Each of these compounds was synthesized to bear a thiolated linker for attachment to metal electrodes and examined for their interactions with naturally occurring DNA nucleosides and nucleotides by 1H NMR, ESI-MS, computational calculations, and surface plasmon resonance. RT measurements were carried out in a scanning tunnel microscope. All of these molecules generated electrical signals with DNA nucleotides in tunneling junctions under physiological conditions (phosphate buffered aqueous solution, pH 7.4). Using a support vector machine as a tool for data analysis, we found that these candidates distinguished among naturally occurring DNA nucleotides with the accuracy of pyrene (by π-π stacking interactions) > azole carboxamides (by hydrogen-bonding interactions). In addition, the pyrene reader operated efficiently in a larger tunnel junction. However, the azole carboxamide could read abasic (AP) monophosphate, a product from spontaneous base hydrolysis or an intermediate of base excision repair. Thus, we envision that sequencing DNA using both π-π stacking and hydrogen-bonding-based universal readers in parallel should generate more comprehensive genome sequences than sequencing based on either reader molecule alone.
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Affiliation(s)
| | | | | | | | - Predrag Krstic
- Institute for Advanced Computational Science, Stony Brook University , Stony Brook, New York 11794-5250, United States
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24
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Im J, Biswas S, Liu H, Zhao Y, Sen S, Biswas S, Ashcroft B, Borges C, Wang X, Lindsay S, Zhang P. Electronic single-molecule identification of carbohydrate isomers by recognition tunnelling. Nat Commun 2016; 7:13868. [PMID: 28000682 PMCID: PMC5187581 DOI: 10.1038/ncomms13868] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022] Open
Abstract
Carbohydrates are one of the four main building blocks of life, and are categorized as monosaccharides (sugars), oligosaccharides and polysaccharides. Each sugar can exist in two alternative anomers (in which a hydroxy group at C-1 takes different orientations) and each pair of sugars can form different epimers (isomers around the stereocentres connecting the sugars). This leads to a vast combinatorial complexity, intractable to mass spectrometry and requiring large amounts of sample for NMR characterization. Combining measurements of collision cross section with mass spectrometry (IM–MS) helps, but many isomers are still difficult to separate. Here, we show that recognition tunnelling (RT) can classify many anomers and epimers via the current fluctuations they produce when captured in a tunnel junction functionalized with recognition molecules. Most importantly, RT is a nanoscale technique utilizing sub-picomole quantities of analyte. If integrated into a nanopore, RT would provide a unique approach to sequencing linear polysaccharides.
Carbohydrates are common biological molecules, but display huge stereochemical complexity that often cannot be elucidated by mass spectrometry. Here the authors show that recognition tunnelling can distinguish individual stereoisomers, utilizing picomole quantities of analytes.
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Affiliation(s)
- JongOne Im
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,Department of Physics, Arizonan State University, Tempe, Arizona 85287, USA
| | - Sovan Biswas
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Hao Liu
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Yanan Zhao
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA
| | - Suman Sen
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Sudipta Biswas
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Brian Ashcroft
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA
| | - Chad Borges
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Xu Wang
- School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA.,Department of Physics, Arizonan State University, Tempe, Arizona 85287, USA
| | - Peiming Zhang
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA
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25
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Tanimoto S, Tsutsui M, Yokota K, Taniguchi M. Dipole effects on the formation of molecular junctions. NANOSCALE HORIZONS 2016; 1:399-406. [PMID: 32260630 DOI: 10.1039/c6nh00088f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Measuring the tunnelling current is a promising way of identifying individual molecules in a liquid, wherein molecular conformations in an electrode gap play a crucial role in the electron transport properties. Here we report that molecular dipole interactions with the electric field effectively restrict the configurational degrees of freedom in metal-molecule-metal systems. We utilized a mechanically tunable Au nanoelectrode gap to electrically detect diaminobenzene isomers. We found suppression of a variation in the single-molecule conductance of 1,2-benzenediamines (BDAs) in water suggesting a significant influence of the huge electric field created between the nanoprobes to align the molecular dipole along the potential gradient and concomitant formation of well-defined junction structures for the molecules through-space coupled to one side of the electrodes. On the other hand, the field effect was absent in 1,3- and 1,4-BDAs, which is attributed to their smaller dipole moments and the more rigid chemical connections to the electrodes via Au-amine bonds.
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Affiliation(s)
- Sachie Tanimoto
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, Japan.
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26
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Tanaka S, Tsutsui M, Theodore H, Yuhui H, Arima A, Tsuji T, Doi K, Kawano S, Taniguchi M, Kawai T. Tailoring particle translocation via dielectrophoresis in pore channels. Sci Rep 2016; 6:31670. [PMID: 27527126 PMCID: PMC4985646 DOI: 10.1038/srep31670] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/21/2016] [Indexed: 11/25/2022] Open
Abstract
Understanding and controlling electrophoretic motions of nanoscopic objects in fluidic channels are a central challenge in developing nanopore technology for molecular analyses. Although progress has been made in slowing the translocation velocity to meet the requirement for electrical detections of analytes via picoampere current measurements, there exists no method useful for regulating particle flows in the transverse directions. Here, we report the use of dielectrophoresis to manipulate the single-particle passage through a solid-state pore. We created a trap field by applying AC voltage between electrodes embedded in a low-aspect-ratio micropore. We demonstrated a traffic control of particles to go through center or near side surface via the voltage frequency. We also found enhanced capture efficiency along with faster escaping speed of particles by virtue of the AC-mediated electroosmosis. This method is compatible with nanopore sensing and would be widely applied for reducing off-axis effects to achieve single-molecule identification.
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Affiliation(s)
- Shoji Tanaka
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Hu Theodore
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Luo Yu Road, Wuhan 430074, China
| | - He Yuhui
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Luo Yu Road, Wuhan 430074, China
| | - Akihide Arima
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Tsuji
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kentaro Doi
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Satoyuki Kawano
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
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27
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Xiang D, Wang X, Jia C, Lee T, Guo X. Molecular-Scale Electronics: From Concept to Function. Chem Rev 2016; 116:4318-440. [DOI: 10.1021/acs.chemrev.5b00680] [Citation(s) in RCA: 816] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Dong Xiang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Key
Laboratory of Optical Information Science and Technology, Institute
of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chuancheng Jia
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Takhee Lee
- Department
of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea
| | - Xuefeng Guo
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Department
of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, China
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28
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Affiliation(s)
- Stuart Lindsay
- Biodesign Institute, Department of Physics and Department of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
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29
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Belkin M, Chao SH, Jonsson MP, Dekker C, Aksimentiev A. Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA. ACS NANO 2015; 9:10598-611. [PMID: 26401685 PMCID: PMC4660389 DOI: 10.1021/acsnano.5b04173] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/24/2015] [Indexed: 05/20/2023]
Abstract
With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.
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Affiliation(s)
- Maxim Belkin
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Shu-Han Chao
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Magnus P. Jonsson
- Organic Electronics, Department of Science and Technology (ITN), Linköping University, SE-58183 Linköping, Sweden
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, The Netherlands
- Address correspondence to , ,
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, The Netherlands
- Address correspondence to , ,
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
- Address correspondence to , ,
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30
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Biswas S, Song W, Borges C, Lindsay S, Zhang P. Click Addition of a DNA Thread to the N-Termini of Peptides for Their Translocation through Solid-State Nanopores. ACS NANO 2015; 9:9652-64. [PMID: 26364915 PMCID: PMC5648329 DOI: 10.1021/acsnano.5b04984] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Foremost among the challenges facing single molecule sequencing of proteins by nanopores is the lack of a universal method for driving proteins or peptides into nanopores. In contrast to nucleic acids, the backbones of which are uniformly negatively charged nucleotides, proteins carry positive, negative and neutral side chains that are randomly distributed. Recombinant proteins carrying a negatively charged oligonucleotide or polypeptide at the C-termini can be translocated through a α-hemolysin (α-HL) nanopore, but the required genetic engineering limits the generality of these approaches. In this present study, we have developed a chemical approach for addition of a charged oligomer to peptides so that they can be translocated through nanopores. As an example, an oligonucleotide PolyT20 was tethered to peptides through first selectively functionalizing their N-termini with azide followed by a click reaction. The data show that the peptide-PolyT20 conjugates translocated through nanopores, whereas the unmodified peptides did not. Surprisingly, the conjugates with their peptides tethered at the 5'-end of PolyT20 passed the nanopores more rapidly than the PolyT20 alone. The PolyT20 also yielded a wider distribution of blockade currents. The same broad distribution was found for a conjugate with its peptide tethered at the 3'-end of PolyT20, suggesting that the larger blockades (and longer translocation times) are associated with events in which the 5'-end of the PolyT20 enters the pore first.
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Affiliation(s)
- Sudipta Biswas
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Weisi Song
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Chad Borges
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Corresponding Author: The author(s) to whom correspondence should be addressed: ;
| | - Peiming Zhang
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
- Corresponding Author: The author(s) to whom correspondence should be addressed: ;
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31
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Harrer S, Kim SC, Schieber C, Kannam S, Gunn N, Moore S, Scott D, Bathgate R, Skafidas S, Wagner JM. Label-free screening of single biomolecules through resistive pulse sensing technology for precision medicine applications. NANOTECHNOLOGY 2015; 26:182502. [PMID: 25875197 DOI: 10.1088/0957-4484/26/18/182502] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Employing integrated nano- and microfluidic circuits for detecting and characterizing biological compounds through resistive pulse sensing technology is a vibrant area of research at the interface of biotechnology and nanotechnology. Resistive pulse sensing platforms can be customized to study virtually any particle of choice which can be threaded through a fluidic channel and enable label-free single-particle interrogation with the primary read-out signal being an electric current fingerprint. The ability to perform label-free molecular screening with single-molecule and even single binding site resolution makes resistive pulse sensing technology a powerful tool for analyzing the smallest units of biological systems and how they interact with each other on a molecular level. This task is at the core of experimental systems biology and in particular 'omics research which in combination with next-generation DNA-sequencing and next-generation drug discovery and design forms the foundation of a novel disruptive medical paradigm commonly referred to as personalized medicine or precision medicine. DNA-sequencing has approached the 1000-Dollar-Genome milestone allowing for decoding a complete human genome with unmatched speed and at low cost. Increased sequencing efficiency yields massive amounts of genomic data. Analyzing this data in combination with medical and biometric health data eventually enables understanding the pathways from individual genes to physiological functions. Access to this information triggers fundamental questions for doctors and patients alike: what are the chances of an outbreak for a specific disease? Can individual risks be managed and if so how? Which drugs are available and how should they be applied? Could a new drug be tailored to an individual's genetic predisposition fast and in an affordable way? In order to provide answers and real-life value to patients, the rapid evolvement of novel computing approaches for analyzing big data in systems genomics has to be accompanied by an equally strong effort to develop next-generation DNA-sequencing and next-generation drug screening and design platforms. In that context lab-on-a-chip devices utilizing nanopore- and nanochannel based resistive pulse-sensing technology for DNA-sequencing and protein screening applications occupy a key role. This paper describes the status quo of resistive pulse sensing technology for these two application areas with a special focus on current technology trends and challenges ahead.
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Affiliation(s)
- S Harrer
- IBM Research-Australia, 204 Lygon Street, 3053 Carlton, VIC, Australia. University of Melbourne, 3010 Parkville, VIC, Australia
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32
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Feng Y, Zhang Y, Ying C, Wang D, Du C. Nanopore-based fourth-generation DNA sequencing technology. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:4-16. [PMID: 25743089 PMCID: PMC4411503 DOI: 10.1016/j.gpb.2015.01.009] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/14/2015] [Accepted: 01/23/2015] [Indexed: 12/24/2022]
Abstract
Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein. Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale. In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.
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Affiliation(s)
- Yanxiao Feng
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuechuan Zhang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Cuifeng Ying
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; MOE Key Laboratory of Weak-light Nonlinear Photonics, School of Physics, Nankai University, Tianjin 300071, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chunlei Du
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Abstract
Recognition tunneling (RT) identifies target molecules trapped between tunneling electrodes functionalized with recognition molecules that serve as specific chemical linkages between the metal electrodes and the trapped target molecule. Possible applications include single molecule DNA and protein sequencing. This paper addresses several fundamental aspects of RT by multiscale theory, applying both all-atom and coarse-grained DNA models: (1) we show that the magnitude of the observed currents are consistent with the results of non-equilibrium Green's function calculations carried out on a solvated all-atom model. (2) Brownian fluctuations in hydrogen bond-lengths lead to current spikes that are similar to what is observed experimentally. (3) The frequency characteristics of these fluctuations can be used to identify the trapped molecules with a machine-learning algorithm, giving a theoretical underpinning to this new method of identifying single molecule signals.
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Affiliation(s)
- Predrag Krstić
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, NY 11794-5250, USA
| | - Brian Ashcroft
- Biodesign Institute, PO Box 5601, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- Biodesign Institute, PO Box 5601, Tempe, Arizona 85287, USA
- Department of Physics, PO Box 5601, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry Arizona State University, PO Box 5601, Tempe, Arizona 85287, USA
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