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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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2
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Ma T, Chang S, He J, Liang F. Emerging sensing platforms based on Cucurbit[ n]uril functionalized gold nanoparticles and electrodes. Chem Commun (Camb) 2023; 60:150-167. [PMID: 38054368 DOI: 10.1039/d3cc04851a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Cucurbit[n]urils (CB[n]s, n = 5-8, 10, and 14), synthetic macrocycles with unique host-guest properties, have triggered increasing research interest in recent years. Gold nanoparticles (Au NPs) and electrodes stand out as exceptional substrates for sensing due to their remarkable physicochemical characteristics. Coupling the CB[n]s with Au NPs and electrodes has enabled the development of emerging sensing platforms for various promising applications. However, monitoring the behavior of analytes at the single-molecule level is currently one of the most challenging topics in the field of CB[n]-based sensing. Constructing supramolecular junctions in a sensing platform provides an ideal structure for single-molecule analysis, which can provide insights for a fundamental understanding of supramolecular interactions and chemical reactions and guide the design of sensing applications. This feature article outlines the progress in the preparation of the CB[n] functionalized Au NPs and Au electrodes, as well as the construction and application of supramolecular junctions in sensing platforms, based on the methods of recognition tunneling (RT), surface-enhanced Raman spectroscopy (SERS), single-molecule force spectroscopy (SMFS), and electrochemical sensing (ECS). A brief perspective on the future development of and challenges in CB[n] mediated sensing platforms is also covered.
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Affiliation(s)
- Tao Ma
- The State Key Laboratory of Refractories and Metallurgy, Coal Conversion and New Carbon Materials Hubei Key Laboratory, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, Coal Conversion and New Carbon Materials Hubei Key Laboratory, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Jin He
- Department of Physics, Florida International University, Miami, Florida 33199, USA.
| | - Feng Liang
- The State Key Laboratory of Refractories and Metallurgy, Coal Conversion and New Carbon Materials Hubei Key Laboratory, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
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3
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He S, Huang B, Xiao B, Chang S, Podalko M, Nau WM. Stabilization of Guest Molecules inside Cation-Lidded Cucurbiturils Reveals that Hydration of Receptor Sites Can Impede Binding. Angew Chem Int Ed Engl 2023; 62:e202313864. [PMID: 37812692 DOI: 10.1002/anie.202313864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/11/2023]
Abstract
Docking of alkali metal ions to water-soluble macrocyclic receptors generally reduces the affinity of guest molecules due to competitive binding. The idea that solvation water molecules could display a larger steric hindrance towards guest binding than cations has not been considered to date. We show that the docking of large cations to cucurbit[5]uril (CB5) unexpectedly increases (by a factor of 5-8) the binding of hydrophobic guests, methane and ethane. This is due to the removal of water molecules from the carbonyl portals of CB5 during cation binding, which frees up space for hydrophobe encapsulation. In contrast, smaller cations like sodium protrude deeply into the cavity of CB5 and cause the expected decrease in binding, such that the rational selection of alkali cations allows for a variation of up to a factor of 20 in binding of methane and ethane. The statistical analysis of crystallographic data shows that the cavity volume of CB5 can be enlarged by placing large alkali ions (Rb+ and Cs+ ) centro-symmetrically at the portals. The results reveal a hitherto elusive steric hindrance of solvation water molecules near receptor binding sites, which is pertinent for the design of supramolecular catalysts and the understanding of biological receptors.
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Affiliation(s)
- Suhang He
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
- Center of Single-Molecule Sciences, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, China
| | - Bing Huang
- Faculty of Physics, University of Vienna, Kolingasse 14-16, 10905, Vienna, Austria
| | - Bohuai Xiao
- The State Key Laboratory of Refractories and Metallurgy, Faculty of Materials, Wuhan University of Science and Technology, 430081, Wuhan, Hubei, China
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, Faculty of Materials, Wuhan University of Science and Technology, 430081, Wuhan, Hubei, China
| | - Marina Podalko
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
| | - Werner M Nau
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
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4
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Dief EM, Low PJ, Díez-Pérez I, Darwish N. Advances in single-molecule junctions as tools for chemical and biochemical analysis. Nat Chem 2023; 15:600-614. [PMID: 37106094 DOI: 10.1038/s41557-023-01178-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 03/02/2023] [Indexed: 04/29/2023]
Abstract
The development of miniaturized electronics has led to the design and construction of powerful experimental platforms capable of measuring electronic properties to the level of single molecules, along with new theoretical concepts to aid in the interpretation of the data. A new area of activity is now emerging concerned with repurposing the tools of molecular electronics for applications in chemical and biological analysis. Single-molecule junction techniques, such as the scanning tunnelling microscope break junction and related single-molecule circuit approaches have a remarkable capacity to transduce chemical information from individual molecules, sampled in real time, to electrical signals. In this Review, we discuss single-molecule junction approaches as emerging analytical tools for the chemical and biological sciences. We demonstrate how these analytical techniques are being extended to systems capable of probing chemical reaction mechanisms. We also examine how molecular junctions enable the detection of RNA, DNA, and traces of proteins in solution with limits of detection at the zeptomole level.
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Affiliation(s)
- Essam M Dief
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Paul J Low
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Ismael Díez-Pérez
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, London, UK
| | - Nadim Darwish
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
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5
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Chauhan N, Saxena K, Jain U. Single molecule detection; from microscopy to sensors. Int J Biol Macromol 2022; 209:1389-1401. [PMID: 35413320 DOI: 10.1016/j.ijbiomac.2022.04.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 01/31/2023]
Abstract
Single molecule detection is necessary to find out physical, chemical properties and their mechanism involved in the normal functioning of body cells. In this way, they can provide a new direction to the healthcare system. Various techniques have been developed and employed for their successful detection. Herein, we have emphasized various traditional methods as well as biosensing technology which offer single molecule sensitivity. The various methods including plasmonic resonance, nanopores, whispering gallery mode, Simoa assay and recognition tunneling are discussed in the initial part which has been followed by a discussion about biosensor-based detection. Plasmonic, SERS, CRISPR/Cas, and other types of biosensors are focused in this review and found to be highly sensitive for single molecule detection. This review provides an overview of progression in different techniques employed for single molecule detection.
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Affiliation(s)
- Nidhi Chauhan
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India
| | - Kirti Saxena
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India
| | - Utkarsh Jain
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India.
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6
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Brady MM, Meyer AS. Cataloguing the proteome: Current developments in single-molecule protein sequencing. BIOPHYSICS REVIEWS 2022; 3:011304. [PMID: 38505228 PMCID: PMC10903494 DOI: 10.1063/5.0065509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/13/2022] [Indexed: 03/21/2024]
Abstract
The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.
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Affiliation(s)
- Morgan M. Brady
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Anne S. Meyer
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
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Xiao B, Dong J, Wang Z, Wang X, Sun M, Guo J, Qian G, Li Y, Chang S. Conductance modulation of metal-molecule-metal junction via extra acid addition and its mechanism investigation. Chemphyschem 2022; 23:e202100833. [PMID: 35138016 DOI: 10.1002/cphc.202100833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/29/2022] [Indexed: 11/10/2022]
Abstract
The advance of single molecular device fabrication strongly relies on the understanding of the metal-molecule-metal junction that can response to the external stimulus. A model Lewis basic molecule DBP which can react with Lewis acid and protic acid was synthesized, then the molecular conducting behavior of the original molecule and the resulted Lewis acid-base pair were researched. Allowing for their identical physical paths for charge conducting, these results indicated that adjusting the molecular electronic structure, even not directly changing the conductive molecular backbone, could also tune the charge transporting ability by nearly one order of magnitude. Furthermore, the addition of another Lewis base - Triethylamine to Lewis acid-base pair brought the electrical properties back to that of single DBP junction, which establishs a basic understanding in the design and construction of reversible and controllable molecular device based on pyridine derived molecule.
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Affiliation(s)
- Bohuai Xiao
- Wuhan University of Science and Technology, College of Material and Metallurgy, CHINA
| | - Jianqiao Dong
- Wuhan University of Science and Technology, School of Chemistry and Chemical Engineering, 947 Heping Avenue, Qingshan District, Wuhan, CHINA
| | - Zhiye Wang
- Wuhan University of Science and Technology, College of Material and Metallurgy, CHINA
| | - Xu Wang
- Wuhan University of Science and Technology, College of Material and Metallurgy, CHINA
| | - Mingjun Sun
- Wuhan University of Science and Technology, College of Material and Metallurgy, CHINA
| | - Jing Guo
- Wuhan University of Science and Technology, College of Material and Metallurgy, CHINA
| | - Gongming Qian
- Wuhan University of Science and Technology, College of Resources and Environment, CHINA
| | - Yunchuan Li
- Wuhan University of Science and Technology, College of Material and Metallurgy, 947 Heping Avenue, Qingshan District, 430081, Wuhan, CHINA
| | - Shuai Chang
- Wuhan University of Science and Technology, College of Material and Metallurgy, CHINA
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8
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Wang Y, Sadar J, Tsao CW, Mukherjee S, Qing Q. Nanopore chip with self-aligned transverse tunneling junction for DNA detection. Biosens Bioelectron 2021; 193:113552. [PMID: 34416434 DOI: 10.1016/j.bios.2021.113552] [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: 04/04/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
To achieve better signal quality and resolution in nanopore sequencing, there has been strong interest in quantum tunneling based detection which requires integration of tunneling junctions in nanopores. However, there has been very limited success due to precision and reproducibility issues. Here we report a new strategy based on feedback-controlled electrochemical processes in a confined nanoscale space to construct nanopore devices with self-aligned transverse tunneling junctions, all embedded on a nanofluidic chip. We demonstrate high-yield (>93%) correlated detection of translocating DNAs from both the ionic channel and the tunneling junction with enriched event rate. We also observed events attributed to non-translocating DNA making contact with the transverse electrodes. Existing challenges for precise sequencing are discussed, including fast translocation speed, and interference from transient electrostatic signals from fast-moving DNAs. Our work can serve as a first step to provide an accessible, and reproducible platform enabling further optimizations for tunneling-based DNA detection, and potentially sequencing.
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Affiliation(s)
- Yuan Wang
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Joshua Sadar
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Ching-Wei Tsao
- School for Engineering of Matter, Transport & Energy, And Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, United States
| | - Sanjana Mukherjee
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Quan Qing
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States; Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, United States.
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9
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Huang M, Yu L, Zhang M, Wang Z, Xiao B, Liu Y, He J, Chang S. Developing Longer-Lived Single Molecule Junctions with a Functional Flexible Electrode. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101911. [PMID: 34292668 DOI: 10.1002/smll.202101911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/30/2021] [Indexed: 06/13/2023]
Abstract
Creating single-molecule junctions with a long-lived lifetime at room temperature is an open challenge. Finding simple and efficient approaches to increase the durability of single-molecule junction is also of practical value in molecular electronics. Here it is shown that a flexible gold-coated nanopipette electrode can be utilized in scanning tunneling microscope (STM) break-junction measurements to efficiently enhance the stability of molecular junctions by comparing with the measurements using conventional solid gold probes. The stabilizing effect of the flexible electrode displays anchor group dependence, which increases with the binding energy between the anchor group and gold. An empirical model is proposed and shows that the flexible electrode could promote stable binding geometries at the gold-molecule interface and slow down the junction breakage caused by the external perturbations, thereby extending the junction lifetime. Finally, it is demonstrated for the first time that the internal conduit of the flexible STM tip can be utilized for the controlled molecule delivery and molecular junction formation.
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Affiliation(s)
- Mingzhu Huang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
- Department of Physics, Biomolecular Science Institute, Florida International University, Miami, FL, 33199, USA
| | - Lei Yu
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Mingyang Zhang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Zhe Wang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Bohuai Xiao
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Yichong Liu
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Jin He
- Department of Physics, Biomolecular Science Institute, Florida International University, Miami, FL, 33199, USA
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
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10
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Yan S, Zhang J, Wang Y, Guo W, Zhang S, Liu Y, Cao J, Wang Y, Wang L, Ma F, Zhang P, Chen HY, Huang S. Single Molecule Ratcheting Motion of Peptides in a Mycobacterium smegmatis Porin A (MspA) Nanopore. NANO LETTERS 2021; 21:6703-6710. [PMID: 34319744 DOI: 10.1021/acs.nanolett.1c02371] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Diverse functions of proteins, including synthesis, catalysis, and signaling, result from their highly variable amino acid sequences. The technology allowing for direct analysis of protein sequences, however, is still unsatisfactory. Recent developments of nanopore sequencing of DNA or RNA have motivated attempts to realize nanopore sequencing of peptides in a similar manner. The core challenge has been to achieve a controlled ratcheting motion of the target peptide, which is currently restricted to a limited choice of compatible enzymes. By constructing peptide-oligonucleotide conjugates (POCs) and measurements with nanopore-induced phase-shift sequencing (NIPSS), direct observation of the ratcheting motion of peptides has been successfully achieved. The generated events show a clear sequence dependence on the peptide that is being tested. The method is compatible with peptides with either a conjugated N- or C-terminus. The demonstrated results suggest a proof of concept of nanopore sequencing of peptide and can be useful for peptide fingerprinting.
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Affiliation(s)
- Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yu Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Weiming Guo
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jiao Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Fubo Ma
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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11
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Wasfi A, Awwad F, Ayesh AI. Detection of DNA Bases via Field Effect Transistor of Graphene Nanoribbon with a Nanopore: Semi-empirical Modeling. IEEE Trans Nanobioscience 2021; 21:347-357. [PMID: 33945483 DOI: 10.1109/tnb.2021.3077364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
DNA sequencing techniques are critical in order to investigate genes' functions. Obtaining fast, accurate, and affordable DNA bases detection makes it possible to acquire personalized medicine. In this article, a semi-empirical technique is used to calculate the electron transport characteristics of the developed z-shaped graphene device to detect the DNA bases. The z-shaped transistor consists of a pair of zigzag graphene nanoribbon (ZGNR) connected through an armchair graphene nanoribbon (AGNR) channel with a nanopore where the DNA nucleobases are positioned. Non-equilibrium Green's function (NEGF) integrated with semi-empirical methodologies are employed to analyze the different electronic transport characteristics. The semi-empirical approach applied is an extension of the extended Hückel (EH) method integrated with self-consistent (SC) Hartree potential. By employing the NEGF+SC-EH, it is proved that each one of the four DNA nucleobases positioned within the nanopore, with the hydrogen passivated edge carbon atoms, results in a unique electrical signature. Both electrical current signal and transmission spectrum measurements of DNA nucleobases inside the device's pore are studied for the different bases with modification of their orientation and lateral translation. Moreover, the electronic noise effect of various factors is studied. The sensor sensitivity is improved by using nitrogen instead of hydrogen to passivate the nanopore and by adding a dual gate to surround the central semiconducting channel of the z-shaped graphene nanoribbon.
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12
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Application of Solid-State Nanopore in Protein Detection. Int J Mol Sci 2020; 21:ijms21082808. [PMID: 32316558 PMCID: PMC7215903 DOI: 10.3390/ijms21082808] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.
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13
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Abstract
Chirality is a fundamental property of a molecule, and the significant progress in chirality detection and quantification of a molecule has inspired major advances in various fields ranging from chemistry, biology, to biotechnology and pharmacology. Chiral molecules have identical molecular formulas, atom-to-atom linkages, and bonding distances, and as such they are difficult to distinguish both sensitively and selectively. Today, most new drugs and those under development are chiral, which requires technological developments in the separation and detection of chiral molecules. Therefore, rapid and facile methods to detect and discriminate chiral compounds are necessary to accelerate advances in many research fields. The challenges in analysis stem from the obvious fact that chiral molecules have the same physical properties. Although significant progress on the detection of enantiomeric composition has been achieved in the past decade, in order to fully realize the capacity of chiral molecular interrogation, highly sensitive and selective, portable, and easy-to-use detection remains challenging because of the limitation of conventional techniques.Soft nanoarchitectonics is a new concept for the fabrication of functional soft material systems through harmonization of various actions including atomic/molecular-level manipulation, chemical reactions, self-assembly and self-organization, and their modulation by external fields/stimuli. Soft nanoarchitectonics has been widely used as a key enabling technology for integrating predefined molecular functionalities including electrochemical, optical, catalytic, or biological properties into biosensing devices, which provides exciting opportunities to design, assemble, and fabricate tailored nanosystems to enable new sensing strategies for chiral molecules.In this Account, we aim to concisely discuss how these molecule-inspired soft nanoarchitectonics work for enantioselective sensing. We will first outline the basic principle and mechanistic insights of the soft nanoarchitectonics approach for enantioselective sensing, and then we will describe the new breakthroughs and trends in the area that have been most recently reported by our groups and others. There will also be a discussion on the merits of soft nanoarchitectonics based sensing in comparison to conventional analytical methods. Finally, with this Account, we hope to spark new chiral molecule sensing strategies by fundamentally understanding chiral recognition and engineering soft nanoarchitectonics with programmable structures and predictable sensing properties.
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Affiliation(s)
- Jing Liu
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia
| | - Hong Zhou
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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14
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Graf M, Lihter M, Altus D, Marion S, Radenovic A. Transverse Detection of DNA Using a MoS 2 Nanopore. NANO LETTERS 2019; 19:9075-9083. [PMID: 31710497 DOI: 10.1021/acs.nanolett.9b04180] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Classical nanopore sensing relies on the measurement of the ion current passing through a nanopore. Whenever a molecule electrophoretically translocates through the narrow constriction, it modulates the ion current. Although this approach allows one to measure single molecules, the access resistance limits the spatial resolution. This physical limitation could potentially be overcome by an alternative sensing scheme taking advantage of the current across the membrane material itself. Such an electronic readout would also allow better temporal resolution than the ionic current. In this work, we present the fabrication of an electrically contacted molybdenum disulfide (MoS2) nanoribbon integrated with a nanopore. DNA molecules are sensed by correlated signals from the ionic current through the nanopore and the transverse current through the nanoribbon. The resulting signal suggests a field-effect sensing scheme where the charge of the molecule is directly sensed by the nanoribbon. We discuss different sensing schemes such as local potential sensing and direct charge sensing. Furthermore, we show that the fabrication of freestanding MoS2 ribbons with metal contacts is reliable and discuss the challenges that arise in the fabrication and usage of these devices.
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Affiliation(s)
- Michael Graf
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
| | - Martina Lihter
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
| | - Damir Altus
- Institute of Physics , HR-10000 Zagreb , Croatia
| | - Sanjin Marion
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
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15
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Callahan N, Tullman J, Kelman Z, Marino J. Strategies for Development of a Next-Generation Protein Sequencing Platform. Trends Biochem Sci 2019; 45:76-89. [PMID: 31676211 DOI: 10.1016/j.tibs.2019.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 02/08/2023]
Abstract
Proteomic analysis can be a critical bottleneck in cellular characterization. The current paradigm relies primarily on mass spectrometry of peptides and affinity reagents (i.e., antibodies), both of which require a priori knowledge of the sample. An unbiased protein sequencing method, with a dynamic range that covers the full range of protein concentrations in proteomes, would revolutionize the field of proteomics, allowing a more facile characterization of novel gene products and subcellular complexes. To this end, several new platforms based on single-molecule protein-sequencing approaches have been proposed. This review summarizes four of these approaches, highlighting advantages, limitations, and challenges for each method towards advancing as a core technology for next-generation protein sequencing.
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Affiliation(s)
- Nicholas Callahan
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA.
| | - Jennifer Tullman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
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16
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Can One Define the Conductance of Amino Acids? Biomolecules 2019; 9:biom9100580. [PMID: 31591358 PMCID: PMC6843363 DOI: 10.3390/biom9100580] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/16/2019] [Accepted: 09/26/2019] [Indexed: 01/23/2023] Open
Abstract
We studied the electron-transport properties of ten different amino acids and one dimer (di-methionine) using the mechanically controlled break-junction (MCBJ) technique. For methionine and cysteine, additional measurements were performed with the scanning tunneling microscope break-junction (STM-BJ) technique. By means of a statistical clustering technique, we identified several conductance groups for each of the molecules considered. Ab initio calculations revealed that the observed broad conductance distribution stems from the possibility of various binding geometries which can be formed during stretching combined with a multitude of possible conformational changes. The results suggest that it would be helpful to explore different experimental techniques such as recognition tunneling and conditions to help identify the nature of amino-acid-based junctions even further, for example, with the goal to establish a firm platform for their unambiguous recognition by tunneling break-junction experiments.
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17
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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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18
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Direct Analysis of Incorporation of an Anticancer Drug into DNA at Single-Molecule Resolution. Sci Rep 2019; 9:3886. [PMID: 30846775 PMCID: PMC6405915 DOI: 10.1038/s41598-019-40504-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/18/2019] [Indexed: 01/10/2023] Open
Abstract
Identifying positions at which anticancer drug molecules incorporate into DNA is essential to define mechanisms underlying their activity, but current methodologies cannot yet achieve this. The thymidine fluorine substitution product trifluridine (FTD) is a DNA-damaging anticancer agent thought to incorporate into thymine positions in DNA. This mechanism, however, has not been directly confirmed. Here, we report a means to detect FTD in a single-stranded oligonucleotide using a method to distinguish single molecules by differences in electrical conductance. Entire sequences of 21-base single-stranded DNAs with and without incorporated drug were determined based on single-molecule conductances of the drug and four deoxynucleosides, the first direct observation of its kind. This methodology may foster rapid development of more effective anticancer drugs.
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19
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Ma T, Guo J, Chang S, Wang X, Zhou J, Liang F, He J. Modulating and probing the dynamic intermolecular interactions in plasmonic molecule-pair junctions. Phys Chem Chem Phys 2019; 21:15940-15948. [DOI: 10.1039/c9cp02030f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The intermolecular interactions, including hydrogen bonds, are electromechanically modulated and probed in metal–molecule pair–metal junctions.
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Affiliation(s)
- Tao Ma
- The State Key Laboratory of Refractories and Metallurgy
- School of Chemistry and Chemical Engineering
- School of Materials and Metallurgy
- Wuhan University of Science and Technology
- Wuhan
| | - Jing Guo
- Department of Physics
- Florida International University
- Miami
- USA
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy
- School of Chemistry and Chemical Engineering
- School of Materials and Metallurgy
- Wuhan University of Science and Technology
- Wuhan
| | - Xuewen Wang
- Department of Physics
- Florida International University
- Miami
- USA
| | - Jianghao Zhou
- The State Key Laboratory of Refractories and Metallurgy
- School of Chemistry and Chemical Engineering
- School of Materials and Metallurgy
- Wuhan University of Science and Technology
- Wuhan
| | - Feng Liang
- The State Key Laboratory of Refractories and Metallurgy
- School of Chemistry and Chemical Engineering
- School of Materials and Metallurgy
- Wuhan University of Science and Technology
- Wuhan
| | - Jin He
- Department of Physics
- Florida International University
- Miami
- USA
- Biomolecular Science Institute
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20
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Taniguchi M, Ohshiro T. Nanopore Device for Single-Molecule Sensing Method and Its Application. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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21
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Xiao B, Liang F, Liu S, Im J, Li Y, Liu J, Zhang B, Zhou J, He J, Chang S. Cucurbituril mediated single molecule detection and identification via recognition tunneling. NANOTECHNOLOGY 2018; 29:365501. [PMID: 29882746 DOI: 10.1088/1361-6528/aacb63] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Recognition tunneling (RT) is an emerging technique for investigating single molecules in a tunnel junction. We have previously demonstrated its capability of single molecule detection and identification, as well as probing the dynamics of intermolecular bonding at the single molecule level. Here by introducing cucurbituril as a new class of recognition molecule, we demonstrate a powerful platform for electronically investigating the host-guest chemistry at single molecule level. In this report, we first investigated the single molecule electrical properties of cucurbituril in a tunnel junction. Then we studied two model guest molecules, aminoferrocene and amantadine, which were encapsulated by cucurbituril. Small differences in conductance and lifetime can be recognized between the host-guest complexes with the inclusion of different guest molecules. By using a machine learning algorithm to classify the RT signals in a hyper dimensional space, the accuracy of guest molecule recognition can be significantly improved, suggesting the possibility of using cucurbituril molecule for single molecule identification. This work enables a new class of recognition molecule for RT technique and opens the door for detecting a vast variety of small molecules by electrical measurements.
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Affiliation(s)
- Bohuai Xiao
- The State Key laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan 430081, People's Republic of China
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22
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Restrepo-Pérez L, Joo C, Dekker C. Paving the way to single-molecule protein sequencing. NATURE NANOTECHNOLOGY 2018; 13:786-796. [PMID: 30190617 DOI: 10.1038/s41565-018-0236-6] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/16/2018] [Indexed: 05/22/2023]
Abstract
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example, requiring a sizable amount of sample. Single-molecule techniques would revolutionize proteomics research, providing ultimate sensitivity for the detection of low-abundance proteins and the realization of single-cell proteomics. In recent years, novel single-molecule protein sequencing schemes that use fluorescence, tunnelling currents and nanopores have been proposed. Here, we present a review of these approaches, together with the first experimental efforts towards their realization. We discuss their advantages and drawbacks, and present our perspective on the development of single-molecule protein sequencing techniques.
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Affiliation(s)
- Laura Restrepo-Pérez
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Chirlmin Joo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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23
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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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24
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Korshoj LE, Afsari S, Chatterjee A, Nagpal P. Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition. J Am Chem Soc 2017; 139:15420-15428. [PMID: 29017006 DOI: 10.1021/jacs.7b08246] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.
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Affiliation(s)
- Lee E Korshoj
- Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute (RASEI), §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Sepideh Afsari
- Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute (RASEI), §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute (RASEI), §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Prashant Nagpal
- Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute (RASEI), §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States
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25
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Carey R, Chen L, Gu B, Franco I. When can time-dependent currents be reproduced by the Landauer steady-state approximation? J Chem Phys 2017; 146:174101. [DOI: 10.1063/1.4981915] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Pirrotta A, De Vico L, Solomon GC, Franco I. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes. J Chem Phys 2017. [DOI: 10.1063/1.4976626] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alessandro Pirrotta
- Nano-Science Center and Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Luca De Vico
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Gemma C. Solomon
- Nano-Science Center and Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Ignacio Franco
- Departments of Chemistry and Physics, University of Rochester, Rochester, New York 14627-0216, USA
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27
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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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28
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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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29
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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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30
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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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31
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Wimmer M, Palma JL, Tarakeshwar P, Mujica V. Single-Molecule Conductance through Hydrogen Bonds: The Role of Resonances. J Phys Chem Lett 2016; 7:2977-2980. [PMID: 27424944 DOI: 10.1021/acs.jpclett.6b01318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The single-molecule conductance of hydrogen-bonded and alkane systems are compared in this theoretical investigation. The results indicate that for short chains, the H-bonded molecules exhibit larger conductance than the alkanes. Although earlier experimental investigations attributed this observation to a large density of states (DOS) corresponding to an occupied molecular orbital below the Fermi energy, the current work indicates the presence of a Fano resonance in the transmission function in the vicinity of the Fermi energy. The inclusion of this observation is essential in understanding the behavior of these systems. We also address the characteristics of the H-bond for transport and provide an explanation for the presence of a turnover regime wherein the conductance of the alkanes becomes larger than the H-bonded systems. Incidentally, this feature cannot be explained using a simple DOS argument.
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Affiliation(s)
- Micah Wimmer
- Arizona State University School of Molecular Sciences Physical Sciences Center PSD-D102, Tempe, Arizona 85287, United States
| | - Julio L Palma
- Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Pilarisetty Tarakeshwar
- Arizona State University School of Molecular Sciences Physical Sciences Center PSD-D102, Tempe, Arizona 85287, United States
| | - Vladimiro Mujica
- Arizona State University School of Molecular Sciences Physical Sciences Center PSD-D102, Tempe, Arizona 85287, United States
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea, 4, 20018 Donostia, Gipuzkoa, Spain
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32
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Yanagi I, Oura T, Haga T, Ando M, Yamamoto J, Mine T, Ishida T, Hatano T, Akahori R, Yokoi T, Anazawa T. Side-gated ultrathin-channel nanopore FET sensors. NANOTECHNOLOGY 2016; 27:115501. [PMID: 26876025 DOI: 10.1088/0957-4484/27/11/115501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A side-gated, ultrathin-channel nanopore FET (SGNAFET) is proposed for fast and label-free DNA sequencing. The concept of the SGNAFET comprises the detection of changes in the channel current during DNA translocation through a nanopore and identifying the four types of nucleotides as a result of these changes. To achieve this goal, both p- and n-type SGNAFETs with a channel thicknesses of 2 or 4 nm were fabricated, and the stable transistor operation of both SGNAFETs in air, water, and a KCl buffer solution were confirmed. In addition, synchronized current changes were observed between the ionic current through the nanopore and the SGNAFET's drain current during DNA translocation through the nanopore.
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Affiliation(s)
- Itaru Yanagi
- Hitachi Ltd, Research & Development Group, Center for Technology Innovation-Healthcare, 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8603, Japan
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33
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Heerema SJ, Dekker C. Graphene nanodevices for DNA sequencing. NATURE NANOTECHNOLOGY 2016; 11:127-36. [PMID: 26839258 DOI: 10.1038/nnano.2015.307] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 11/23/2015] [Indexed: 05/24/2023]
Abstract
Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.
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Affiliation(s)
- Stephanie J Heerema
- Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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34
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Rosenstein JK, Lemay SG, Shepard KL. Single-molecule bioelectronics. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2015; 7:475-93. [PMID: 25529538 PMCID: PMC4476964 DOI: 10.1002/wnan.1323] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 08/04/2014] [Accepted: 10/29/2014] [Indexed: 01/08/2023]
Abstract
Experimental techniques that interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. In this study, we review several technologies that can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms.
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Affiliation(s)
| | - Serge G Lemay
- MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
| | - Kenneth L Shepard
- Departments of Electrical and Biomedical Engineering, Columbia University, New York, NY, USA
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35
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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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36
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37
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Abstract
The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.
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Affiliation(s)
- Yue Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Qiuping Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Zhimin Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
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38
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Affiliation(s)
- Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University , 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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39
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Huang S. Nanopore-based sensing devices and applications to genome sequencing: a brief history and the missing pieces. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0641-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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40
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Artés JM, López-Martínez M, Díez-Pérez I, Sanz F, Gorostiza P. Nanoscale charge transfer in redox proteins and DNA: Towards biomolecular electronics. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2014.05.089] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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41
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Zhao Y, Ashcroft B, Zhang P, Liu H, Sen S, Song W, Im J, Gyarfas B, Manna S, Biswas S, Borges C, Lindsay S. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling. NATURE NANOTECHNOLOGY 2014; 9:466-73. [PMID: 24705512 PMCID: PMC4047173 DOI: 10.1038/nnano.2014.54] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 02/18/2014] [Indexed: 05/18/2023]
Abstract
The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic 'fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore.
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Affiliation(s)
- Yanan Zhao
- 1] Department of Physics, Arizona State University, PO Box 871504 Tempe, Arizona 85287, USA [2] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [3]
| | - Brian Ashcroft
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2]
| | - Peiming Zhang
- Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA
| | - Hao Liu
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Suman Sen
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Weisi Song
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - JongOne Im
- 1] Department of Physics, Arizona State University, PO Box 871504 Tempe, Arizona 85287, USA [2] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA
| | - Brett Gyarfas
- Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA
| | - Saikat Manna
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Sovan Biswas
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Chad Borges
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- 1] Department of Physics, Arizona State University, PO Box 871504 Tempe, Arizona 85287, USA [2] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [3] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
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42
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Ivanov AP, Freedman KJ, Kim MJ, Albrecht T, Edel JB. High precision fabrication and positioning of nanoelectrodes in a nanopore. ACS NANO 2014; 8:1940-1948. [PMID: 24446951 DOI: 10.1021/nn406586m] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A simple and versatile method for the direct fabrication of tunneling electrodes with controllable gap distance by using electron-beam-induced deposition (EBID) is presented. We show that tunneling nanogaps smaller than the minimum feature size realizable by conventional EBID can be achieved with a standard scanning electron microscope. These gaps can easily be embedded in nanopores with high accuracy. The controllability of this fabrication method and the nanogap geometry was verified by SEM and TEM imaging. Furthermore, tunneling spectroscopy in a group of solvents with different barrier heights was used to determine the nanogap functionality. Ultimately, the presented fabrication method can be further applied for the fabrication of arrays of nanogap/nanopores or nanogap electrodes with tunable electrode materials. Additionally, this method can also offer direct fabrication of nanoscale electrode systems with tunable spacing for redox cycling and plasmonic applications, which represents an important step in the development of tunneling nanopore structures and in enhancing the capabilities of nanopore sensors.
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Affiliation(s)
- Aleksandar P Ivanov
- Department of Chemistry, Imperial College London , Exhibition Road, London SW7 2AZ, United Kingdom
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43
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Krishnakumar P, Gyarfas B, Song W, Sen S, Zhang P, Krstić P, Lindsay S. Slowing DNA translocation through a nanopore using a functionalized electrode. ACS NANO 2013; 7:10319-26. [PMID: 24161197 PMCID: PMC3875158 DOI: 10.1021/nn404743f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanopores were fabricated with an integrated microscale Pd electrode coated with either a hydrogen-bonding or hydrophobic monolayer. Bare pores, or those coated with octanethiol, translocated single-stranded DNA with times of a few microseconds per base. Pores functionalized with 4(5)-(2-mercaptoethyl)-1H-imidazole-2-carboxamide slowed average translocation times, calculated as the duration of the event divided by the number of bases translocated, to about 100 μs per base at biases in the range of 50 to 80 mV.
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Affiliation(s)
- Padmini Krishnakumar
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Brett Gyarfas
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Weisi Song
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Suman Sen
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
| | - Peiming Zhang
- Department of Physics, Arizona State University, Tempe, AZ 85287
| | - Predrag Krstić
- Joint Institute of Computational Science, University of Tennessee, Oak Ridge, TN 37831
- TheoretiK, Knoxville, TN 37921, USA
| | - Stuart Lindsay
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
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44
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Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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45
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Miles BN, Ivanov AP, Wilson KA, Doğan F, Japrung D, Edel JB. Single molecule sensing with solid-state nanopores: novel materials, methods, and applications. Chem Soc Rev 2013; 42:15-28. [DOI: 10.1039/c2cs35286a] [Citation(s) in RCA: 362] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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46
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Chang S, Sen S, Zhang P, Gyarfas B, Ashcroft B, Lefkowitz S, Peng H, Lindsay S. Palladium electrodes for molecular tunnel junctions. NANOTECHNOLOGY 2012; 23:425202. [PMID: 23037952 PMCID: PMC3501205 DOI: 10.1088/0957-4484/23/42/425202] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gold has been the metal of choice for research on molecular tunneling junctions, but it is incompatible with complementary metal-oxide-semiconductor fabrication because it forms deep level traps in silicon. Palladium electrodes do not contaminate silicon, and also give higher tunnel current signals in the molecular tunnel junctions that we have studied. The result is cleaner signals in a recognition-tunneling junction that recognizes the four natural DNA bases as well as 5-methyl cytosine, with no spurious background signals. More than 75% of all the recorded signal peaks indicate the base correctly.
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Affiliation(s)
- Shuai Chang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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47
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Chang S, Huang S, Liu H, Zhang P, Liang F, Akahori R, Li S, Gyarfas B, Shumway J, Ashcroft B, He J, Lindsay S. Chemical recognition and binding kinetics in a functionalized tunnel junction. NANOTECHNOLOGY 2012; 23:235101. [PMID: 22609769 PMCID: PMC3392519 DOI: 10.1088/0957-4484/23/23/235101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
4(5)-(2-mercaptoethyl)-1H-imidazole-2-carboxamide is a molecule that has multiple hydrogen bonding sites and a short flexible linker. When tethered to a pair of electrodes, it traps target molecules in a tunnel junction. Surprisingly large recognition-tunneling signals are generated for all naturally occurring DNA bases A, C, G, T and 5-methyl-cytosine. Tunnel current spikes are stochastic and broadly distributed, but characteristic enough so that individual bases can be identified as a tunneling probe is scanned over DNA oligomers. Each base yields a recognizable burst of signal, the duration of which is controlled entirely by the probe speed, down to speeds of 1 nm s -1, implying a maximum off-rate of 3 s -1 for the recognition complex. The same measurements yield a lower bound on the on-rate of 1 M -1 s -1. Despite the stochastic nature of the signals, an optimized multiparameter fit allows base calling from a single signal peak with an accuracy that can exceed 80% when a single type of nucleotide is present in the junction, meaning that recognition-tunneling is capable of true single-molecule analysis. The accuracy increases to 95% when multiple spikes in a signal cluster are analyzed.
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Affiliation(s)
- Shuai Chang
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shuo Huang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Liu
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Peiming Zhang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Feng Liang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Rena Akahori
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shengqin Li
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Brett Gyarfas
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - John Shumway
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Brian Ashcroft
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jin He
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Stuart Lindsay
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
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48
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Abstract
The quantum-mechanical tunnelling effect allows charge transport across nanometre-scale gaps between conducting electrodes. Application of a voltage between these electrodes leads to a measurable tunnelling current, which is highly sensitive to the gap size, the voltage applied and the medium in the gap. Applied to liquid environments, this offers interesting prospects of using tunnelling currents as a sensitive tool to study fundamental interfacial processes, to probe chemical reactions at the single-molecule level and to analyse the composition of biopolymers such as DNA, RNA or proteins. This offers the possibility of a new class of sensor devices with unique capabilities.
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Affiliation(s)
- T Albrecht
- Imperial College London, Department of Chemistry, Exhibition Road, London SW7 2AZ, UK.
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49
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Lindsay S. Biochemistry and semiconductor electronics--the next big hit for silicon? JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:164201. [PMID: 22465874 PMCID: PMC3489000 DOI: 10.1088/0953-8984/24/16/164201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two recent developments portend a new era for silicon electronics in biomedical applications. Firstly, highly specific chemical recognition and massively parallel sample preparation techniques are being combined with VLSI to make new kinds of analytical chips. Secondly, critical dimensions are beginning to approach the size of biomolecules, opening new pathways for physical interactions between molecules and semiconductor structures. Future generations of hybrid chemical-CMOS devices could revolutionize diagnosis and make personalized medicine cheap enough to become widespread.
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Affiliation(s)
- Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
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50
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Pobelov IV, Mészáros G, Yoshida K, Mishchenko A, Gulcur M, Bryce MR, Wandlowski T. An approach to measure electromechanical properties of atomic and molecular junctions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:164210. [PMID: 22466399 DOI: 10.1088/0953-8984/24/16/164210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We describe a new setup for simultaneous measurements of force and current in conductive nanocontacts in a liquid environment with a high sampling rate and resolution. A lab-built current-to-voltage converter allows measurements of the current over seven orders of magnitude. As examples, we studied conductances and mechanical forces upon formation and breaking of gold atomic contacts and of two molecular junctions containing 1,2-di(4-pyridyl)ethyne (M1) and 1,4-di(4-pyridyl)buta-1,3-diyne (M2). We found that the forces required to deform or break gold atomic contacts depend critically on the surrounding medium. Further, they show non-linear behaviour in dependence of the number N of gold atoms detached. The electromechanical properties of the two types of molecular junctions upon stretching were analysed by correlating breaking forces with simultaneously measured junction conductances. A rather complex behaviour in a wide range of forces was discovered. Comparison of the current-probe atomic force microscopy experiments on the rupture of molecular junctions with STM-based break junction experiments enables the assignment of breaking forces of molecular junctions to the corresponding junction conductances.
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Affiliation(s)
- Ilya V Pobelov
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.
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