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Guo J, Chen PK, Chang S. Molecular-Scale Electronics: From Individual Molecule Detection to the Application of Recognition Sensing. Anal Chem 2024. [PMID: 38809941 DOI: 10.1021/acs.analchem.3c04656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
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2
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Li F, Luo Y, Xi G, Fu J, Tu J. Single-Molecule Analysis of DNA structures using nanopore sensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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3
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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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4
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Huang M, Zhou Q, Liang F, Yu L, Xiao B, Li Y, Zhang M, Chen Y, He J, Xiao S, Chang S. Detecting Individual Bond Switching within Amides in a Tunneling Junction. NANO LETTERS 2021; 21:5409-5414. [PMID: 34124909 DOI: 10.1021/acs.nanolett.1c01882] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Amides are essential in the chemistry of life. Detecting the chemical bond states within amides could unravel the nature of amide stabilization and planarity, which is critical to the structure and reactivity of such molecules. Yet, so far, no work has been reported to detect or measure the bond changes at the single-molecule level within amides. Here, we show that a transition between single and double bonds between N and C atoms in an amide can be monitored in real time in a nanogap between gold electrodes via the generation of distinctive conductance features. Density functional theory simulations show that the switching between amide isomers proceeds via a proton transfer process facilitated by a water molecule bridge, and the resulting molecular junctions display bimodal conductance states with a difference as much as nine times.
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Affiliation(s)
- Mingzhu Huang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
- Department of Physics, Biomolecular Science Institute, Florida International University, Miami, Florida 33199, United States
| | - Qinghai Zhou
- The Education Ministry Key Lab of Resource Chemistry, Joint International Research Laboratory of Resource Chemistry, Ministry of Education, Shanghai Key Laboratory of Rare Earth Functional Materials, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Feng Liang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Lei Yu
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, 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, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Yunchuan Li
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, 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, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Yan Chen
- The Education Ministry Key Lab of Resource Chemistry, Joint International Research Laboratory of Resource Chemistry, Ministry of Education, Shanghai Key Laboratory of Rare Earth Functional Materials, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Jin He
- Department of Physics, Biomolecular Science Institute, Florida International University, Miami, Florida 33199, United States
| | - Shengxiong Xiao
- The Education Ministry Key Lab of Resource Chemistry, Joint International Research Laboratory of Resource Chemistry, Ministry of Education, Shanghai Key Laboratory of Rare Earth Functional Materials, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
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5
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Yuan S, Gao T, Cao W, Pan Z, Liu J, Shi J, Hong W. The Characterization of Electronic Noise in the Charge Transport through Single-Molecule Junctions. SMALL METHODS 2021; 5:e2001064. [PMID: 34927823 DOI: 10.1002/smtd.202001064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/09/2020] [Indexed: 06/14/2023]
Abstract
With the goal of creating single-molecule devices and integrating them into circuits, the emergence of single-molecule electronics provides various techniques for the fabrication of single-molecule junctions and the investigation of charge transport through such junctions. Among the techniques for characterization of charge transport through molecular junctions, electronic noise characterization is an effective strategy with which issues from molecule-electrode interfaces, mechanisms of charge transport, and changes in junction configurations are studied. Electronic noise analysis in single-molecule junctions can be used to identify molecular conformations and even monitor reaction kinetics. This review summarizes the various types of electronic noise that have been characterized during single-molecule electrical detection, including the functions of random telegraph signal (RTS) noise, flicker noise, shot noise, and their corresponding applications, which provide some guidelines for the future application of these techniques to problems of charge transport through single-molecule junctions.
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Affiliation(s)
- Saisai Yuan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering iChEM, Xiamen University, Xiamen, 361005, China
| | - Tengyang Gao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering iChEM, Xiamen University, Xiamen, 361005, China
| | - Wenqiang Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering iChEM, Xiamen University, Xiamen, 361005, China
| | - Zhichao Pan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering iChEM, Xiamen University, Xiamen, 361005, China
| | - Junyang Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering iChEM, Xiamen University, Xiamen, 361005, China
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering iChEM, Xiamen University, Xiamen, 361005, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering iChEM, Xiamen University, Xiamen, 361005, China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
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6
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Abstract
The measured electronic properties of proteins are known to depend critically on contacts, although little is known at the single-molecule level. Here, we have measured the conductance of single-protein molecules in their natural aqueous environment, but in conditions where no ion current flows, finding large conductances (nanosiemens) over long paths (many nanometers) when the protein is tethered by chemical contacts formed by binding-specific ligands. This provides a method for forming reliable contacts to proteins, and for the specific detection of single molecules. Thus, single antibodies, such as anti-Ebola IgG, can be detected electrically when they bind a peptide epitope tethered to electrodes, with no background signal from molecules that do not bind specifically. Proteins are widely regarded as insulators, despite reports of electrical conductivity. Here we use measurements of single proteins between electrodes, in their natural aqueous environment to show that the factor controlling measured conductance is the nature of the electrical contact to the protein, and that specific ligands make highly selective electrical contacts. Using six proteins that lack known electrochemical activity, and measuring in a potential region where no ion current flows, we find characteristic peaks in the distributions of measured single-molecule conductances. These peaks depend on the contact chemistry, and hence, on the current path through the protein. In consequence, the measured conductance distribution is sensitive to changes in this path caused by ligand binding, as shown with streptavidin–biotin complexes. Measured conductances are on the order of nanosiemens over distances of many nanometers, orders of magnitude more than could be accounted for by electron tunneling. The current is dominated by contact resistance, so the conductance for a given path is independent of the distance between electrodes, as long as the contact points on the protein can span the gap between electrodes. While there is no currently known biological role for high electronic conductance, its dependence on specific contacts has important technological implications, because no current is observed at all without at least one strongly bonded contact, so direct electrical detection is a highly selective and label-free single-molecule detection method. We demonstrate single-molecule, highly specific, label- and background free-electronic detection of IgG antibodies to HIV and Ebola viruses.
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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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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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9
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Carlsen AT, Briggs K, Hall AR, Tabard-Cossa V. Solid-state nanopore localization by controlled breakdown of selectively thinned membranes. NANOTECHNOLOGY 2017; 28:085304-85304. [PMID: 28045003 PMCID: PMC5408306 DOI: 10.1088/1361-6528/aa564d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We demonstrate precise positioning of nanopores fabricated by controlled breakdown (CBD) on solid-state membranes by spatially varying the electric field strength with localized membrane thinning. We show 100 × 100 nm2 precision in standard SiN x membranes (30-100 nm thick) after selective thinning by as little as 25% with a helium ion beam. Control over nanopore position is achieved through the strong dependence of the electric field-driven CBD mechanism on membrane thickness. Confinement of pore formation to the thinned region of the membrane is confirmed by TEM imaging and by analysis of DNA translocations. These results enhance the functionality of CBD as a fabrication approach and enable the production of advanced nanopore devices for single-molecule sensing applications.
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Affiliation(s)
- Autumn T. Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Adam R. Hall
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest University School of Medicine, Winston Salem, North Carolina 27101, United States
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10
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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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11
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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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12
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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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Lemmer M, Inkpen MS, Kornysheva K, Long NJ, Albrecht T. Unsupervised vector-based classification of single-molecule charge transport data. Nat Commun 2016; 7:12922. [PMID: 27694904 PMCID: PMC5063956 DOI: 10.1038/ncomms12922] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/16/2016] [Indexed: 01/04/2023] Open
Abstract
The stochastic nature of single-molecule charge transport measurements requires collection of large data sets to capture the full complexity of a molecular system. Data analysis is then guided by certain expectations, for example, a plateau feature in the tunnelling current distance trace, and the molecular conductance extracted from suitable histogram analysis. However, differences in molecular conformation or electrode contact geometry, the number of molecules in the junction or dynamic effects may lead to very different molecular signatures. Since their manifestation is a priori unknown, an unsupervised classification algorithm, making no prior assumptions regarding the data is clearly desirable. Here we present such an approach based on multivariate pattern analysis and apply it to simulated and experimental single-molecule charge transport data. We demonstrate how different event shapes are clearly separated using this algorithm and how statistics about different event classes can be extracted, when conventional methods of analysis fail.
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Affiliation(s)
- Mario Lemmer
- Department of Chemistry, Imperial College London, Imperial College Road, London SW7 2AZ, UK
| | - Michael S. Inkpen
- Department of Chemistry, Imperial College London, Imperial College Road, London SW7 2AZ, UK
| | - Katja Kornysheva
- Institute for Cognitive Neuroscience, University College London, Alexandra House, 17-19 Queen Square, London WC1N 3AR, UK
| | - Nicholas J. Long
- Department of Chemistry, Imperial College London, Imperial College Road, London SW7 2AZ, UK
| | - Tim Albrecht
- Department of Chemistry, Imperial College London, Imperial College Road, London SW7 2AZ, UK
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14
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Affiliation(s)
- Stuart Lindsay
- Biodesign Institute, Department of Physics and Department of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
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15
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Henley RY, Ashcroft BA, Farrell I, Cooperman BS, Lindsay SM, Wanunu M. Electrophoretic Deformation of Individual Transfer RNA Molecules Reveals Their Identity. NANO LETTERS 2016; 16:138-44. [PMID: 26609994 PMCID: PMC4890568 DOI: 10.1021/acs.nanolett.5b03331] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
It has been hypothesized that the ribosome gains additional fidelity during protein translation by probing structural differences in tRNA species. We measure the translocation kinetics of different tRNA species through ∼3 nm diameter synthetic nanopores. Each tRNA species varies in the time scale with which it is deformed from equilibrium, as in the translocation step of protein translation. Using machine-learning algorithms, we can differentiate among five tRNA species, analyze the ratios of tRNA binary mixtures, and distinguish tRNA isoacceptors.
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Affiliation(s)
- Robert Y. Henley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Brian Alan Ashcroft
- Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Ian Farrell
- Anima Cell Metrology, Inc., Bernardsville, New Jersey 07924, United States
| | - Barry S. Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Stuart M. Lindsay
- Department of Physics, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85281, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Corresponding Author. . Fax: (617) 373 2943
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16
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Krstic P. Response of a DNA Hydrogen Bond to a Force in Liquid. ADVANCES IN QUANTUM CHEMISTRY 2016. [DOI: 10.1016/bs.aiq.2015.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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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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Pang P, Ashcroft BA, Song W, Zhang P, Biswas S, Qing Q, Yang J, Nemanich RJ, Bai J, Smith JT, Reuter K, Balagurusamy VSK, Astier Y, Stolovitzky G, Lindsay S. Fixed-gap tunnel junction for reading DNA nucleotides. ACS NANO 2014; 8:11994-2003. [PMID: 25380505 PMCID: PMC4278685 DOI: 10.1021/nn505356g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 11/07/2014] [Indexed: 05/21/2023]
Abstract
Previous measurements of the electronic conductance of DNA nucleotides or amino acids have used tunnel junctions in which the gap is mechanically adjusted, such as scanning tunneling microscopes or mechanically controllable break junctions. Fixed-junction devices have, at best, detected the passage of whole DNA molecules without yielding chemical information. Here, we report on a layered tunnel junction in which the tunnel gap is defined by a dielectric layer, deposited by atomic layer deposition. Reactive ion etching is used to drill a hole through the layers so that the tunnel junction can be exposed to molecules in solution. When the metal electrodes are functionalized with recognition molecules that capture DNA nucleotides via hydrogen bonds, the identities of the individual nucleotides are revealed by characteristic features of the fluctuating tunnel current associated with single-molecule binding events.
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Affiliation(s)
- Pei Pang
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Brian Alan Ashcroft
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Weisi Song
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Peiming Zhang
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sovan Biswas
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Quan Qing
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Jialing Yang
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Robert J. Nemanich
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Jingwei Bai
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Joshua T. Smith
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Kathleen Reuter
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
| | | | - Yann Astier
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
- Address correspondence to ,
| | - Gustavo Stolovitzky
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Stuart Lindsay
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
- Address correspondence to ,
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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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20
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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: 21] [Impact Index Per Article: 1.9] [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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21
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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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22
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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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