101
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Nishino T, Shiigi H, Kiguchi M, Nagaoka T. Specific single-molecule detection of glucose in a supramolecularly designed tunnel junction. Chem Commun (Camb) 2018; 53:5212-5215. [PMID: 28443849 DOI: 10.1039/c6cc09932g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Scanning tunneling microscopy tips were functionalized with a boronic acid derivative. In combination with a similarly modified substrate, the molecular tip forms a supramolecular complex selectively with a glucose molecule. The conductance of the resulting single complex allows one to achieve the specific single-molecule detection of glucose.
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Affiliation(s)
- Tomoaki Nishino
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
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102
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Cao Z, Zhu Y, Liu Y, Dong S, Chen X, Bai F, Song S, Fu J. Dielectrophoresis-Based Protein Enrichment for a Highly Sensitive Immunoassay Using Ag/SiO 2 Nanorod Arrays. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703265. [PMID: 29377602 DOI: 10.1002/smll.201703265] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/06/2017] [Indexed: 06/07/2023]
Abstract
A nanoscale insulator-based dielectrophoresis (iDEP) technique is developed for rapid enrichment of proteins and highly sensitive immunoassays. Dense arrays of nanorods (NDs) by oblique angle deposition create a super high electric field gradient of 2.6 × 1024 V2 m-3 and the concomitant strong dielectrophoresis force successfully traps small proteins at a bias as low as 5 V. 1800-fold enrichment of bovine serum albumin protein at a remarkable rate of up to 180-fold s-1 is achieved using oxide coated Ag nanorod arrays with pre-patterned sawtooth electrodes. Based on this system, an ultrasensitive immunoassay of mouse immunoglobulin G is demonstrated with a reduction in the limit of detection from 5.8 ng mL-1 (37.6 pM) down to 275.3 fg mL-1 (1.8 f M), compared with identical assays performed on glass plates. This methodology is also applied to detect a cancer biomarker prostate-specific antigen spiked in human serum with a detection limit of 2.6 ng mL-1 . This high sensitivity results from rapid biomarker enrichment and metal enhanced fluorescence through the integration of nanostructures. The concentrated proteins also accelerate binding kinetics and enable signal saturation within 1 min. Given the easy fabrication process, this nanoscale iDEP system provides a highly sensitive detection platform for point-of-care diagnostics.
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Affiliation(s)
- Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Yu Zhu
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Yang Liu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Xin Chen
- Department of Physics, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Fan Bai
- Department of Physics, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Shengxin Song
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Junxue Fu
- Department of Physics, Hong Kong Baptist University, Kowloon Tong, Hong Kong
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103
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Direct observation of single-molecule hydrogen-bond dynamics with single-bond resolution. Nat Commun 2018; 9:807. [PMID: 29476061 PMCID: PMC5825177 DOI: 10.1038/s41467-018-03203-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/26/2018] [Indexed: 12/18/2022] Open
Abstract
The hydrogen bond represents a fundamental interaction widely existing in nature, which plays a key role in chemical, physical and biochemical processes. However, hydrogen bond dynamics at the molecular level are extremely difficult to directly investigate. Here, in this work we address direct electrical measurements of hydrogen bond dynamics at the single-molecule and single-event level on the basis of the platform of molecular nanocircuits, where a quadrupolar hydrogen bonding system is covalently incorporated into graphene point contacts to build stable supramolecule-assembled single-molecule junctions. The dynamics of individual hydrogen bonds in different solvents at different temperatures are studied in combination with density functional theory. Both experimental and theoretical results consistently show a multimodal distribution, stemming from the stochastic rearrangement of the hydrogen bond structure mainly through intermolecular proton transfer and lactam-lactim tautomerism. This work demonstrates an approach of probing hydrogen bond dynamics with single-bond resolution, making an important contribution to broad fields beyond supramolecular chemistry.
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104
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Guan J, Jia C, Li Y, Liu Z, Wang J, Yang Z, Gu C, Su D, Houk KN, Zhang D, Guo X. Direct single-molecule dynamic detection of chemical reactions. SCIENCE ADVANCES 2018; 4:eaar2177. [PMID: 29487914 PMCID: PMC5817934 DOI: 10.1126/sciadv.aar2177] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/16/2018] [Indexed: 05/03/2023]
Abstract
Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.
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Affiliation(s)
- Jianxin Guan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Chuancheng Jia
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yanwei Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
| | - Zitong Liu
- Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Jinying Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Chunhui Gu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Dingkai Su
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Deqing Zhang
- Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, P. R. China
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105
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Fu K, Bohn PW. Nanopore Electrochemistry: A Nexus for Molecular Control of Electron Transfer Reactions. ACS CENTRAL SCIENCE 2018; 4:20-29. [PMID: 29392173 PMCID: PMC5785767 DOI: 10.1021/acscentsci.7b00576] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Indexed: 05/12/2023]
Abstract
Pore-based structures occur widely in living organisms. Ion channels embedded in cell membranes, for example, provide pathways, where electron and proton transfer are coupled to the exchange of vital molecules. Learning from mother nature, a recent surge in activity has focused on artificial nanopore architectures to effect electrochemical transformations not accessible in larger structures. Here, we highlight these exciting advances. Starting with a brief overview of nanopore electrodes, including the early history and development of nanopore sensing based on nanopore-confined electrochemistry, we address the core concepts and special characteristics of nanopores in electron transfer. We describe nanopore-based electrochemical sensing and processing, discuss performance limits and challenges, and conclude with an outlook for next-generation nanopore electrode sensing platforms and the opportunities they present.
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Affiliation(s)
- Kaiyu Fu
- Department
of Chemistry and Biochemistry and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W. Bohn
- Department
of Chemistry and Biochemistry and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- E-mail: . Tel: +1 574 631 1849. Fax: +1 574 631 8366
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106
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Asandei A, Rossini AE, Chinappi M, Park Y, Luchian T. Protein Nanopore-Based Discrimination between Selected Neutral Amino Acids from Polypeptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14451-14459. [PMID: 29178796 DOI: 10.1021/acs.langmuir.7b03163] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nanopore probing of biological polymers has the potential to achieve single-molecule sequencing at low cost, high throughput, portability, and minimal sample preparation and apparatus. In this article, we explore the possibility of discrimination between neutral amino acid residues from the primary structure of 30 amino acids long, engineered peptides, through the analysis of single-molecule ionic current fluctuations accompanying their slowed-down translocation across the wild type α-hemolysin (α-HL) nanopore, and molecular dynamics simulations. We found that the transient presence inside the α-HL of alanine or tryptophan residues from the primary sequence of engineered peptides results in distinct features of the ionic current fluctuation pattern associated with the peptide reversibly blocking the nanopore. We propose that α-HL sensitivity to the molecular exclusion at the most constricted region mediates ionic current blockade events correlated with the volumes that are occluded by at least three alanine or tryptophan residues, and provides the specificity needed to discriminate between groups of neutral amino acids. Further, we find that the pattern of current fluctuations depends on the orientation of the threaded amino acid residues, suggestive of a conformational anisotropy of the ensemble of conformations of the peptide on the restricted nanopore region, related to its relative axial orientation inside the nanopore.
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Affiliation(s)
| | - Aldo E Rossini
- Department of Basic and Applied Science for Engineering, Sapienza University of Rome , Via A. Scarpa14, 00161 Rome, Italy
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata , Via del Politecnico 1, 00133 Rome, Italy
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia , Via Regina Elena 291, 00161 Rome, Italy
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University , Gwangju, Korea
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107
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Taniguchi M. Single-Molecule Analysis Methods Using Nanogap Electrodes and Their Application to DNA Sequencing Technologies. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170224] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047
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108
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Albrecht T, Slabaugh G, Alonso E, Al-Arif SMMR. Deep learning for single-molecule science. NANOTECHNOLOGY 2017; 28:423001. [PMID: 28762339 DOI: 10.1088/1361-6528/aa8334] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Exploring and making predictions based on single-molecule data can be challenging, not only due to the sheer size of the datasets, but also because a priori knowledge about the signal characteristics is typically limited and poor signal-to-noise ratio. For example, hypothesis-driven data exploration, informed by an expectation of the signal characteristics, can lead to interpretation bias or loss of information. Equally, even when the different data categories are known, e.g., the four bases in DNA sequencing, it is often difficult to know how to make best use of the available information content. The latest developments in machine learning (ML), so-called deep learning (DL) offer interesting, new avenues to address such challenges. In some applications, such as speech and image recognition, DL has been able to outperform conventional ML strategies and even human performance. However, to date DL has not been applied much in single-molecule science, presumably in part because relatively little is known about the 'internal workings' of such DL tools within single-molecule science as a field. In this Tutorial, we make an attempt to illustrate in a step-by-step guide how one of those, a convolutional neural network (CNN), may be used for base calling in DNA sequencing applications. We compare it with a SVM as a more conventional ML method, and discuss some of the strengths and weaknesses of the approach. In particular, a 'deep' neural network has many features of a 'black box', which has important implications on how we look at and interpret data.
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Affiliation(s)
- Tim Albrecht
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
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109
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Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH. DNA sequencing at 40: past, present and future. Nature 2017; 550:345-353. [DOI: 10.1038/nature24286] [Citation(s) in RCA: 552] [Impact Index Per Article: 78.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/21/2017] [Indexed: 12/31/2022]
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110
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Zhou J, Wang Y, Menard LD, Panyukov S, Rubinstein M, Ramsey JM. Enhanced nanochannel translocation and localization of genomic DNA molecules using three-dimensional nanofunnels. Nat Commun 2017; 8:807. [PMID: 28993619 PMCID: PMC5634460 DOI: 10.1038/s41467-017-00951-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 08/08/2017] [Indexed: 12/13/2022] Open
Abstract
The ability to precisely control the transport of single DNA molecules through a nanoscale channel is critical to DNA sequencing and mapping technologies that are currently under development. Here we show how the electrokinetically driven introduction of DNA molecules into a nanochannel is facilitated by incorporating a three-dimensional nanofunnel at the nanochannel entrance. Individual DNA molecules are imaged as they attempt to overcome the entropic barrier to nanochannel entry through nanofunnels with various shapes. Theoretical modeling of this behavior reveals the pushing and pulling forces that result in up to a 30-fold reduction in the threshold electric field needed to initiate nanochannel entry. In some cases, DNA molecules are stably trapped and axially positioned within a nanofunnel at sub-threshold electric field strengths, suggesting the utility of nanofunnels as force spectroscopy tools. These applications illustrate the benefit of finely tuning nanoscale conduit geometries, which can be designed using the theoretical model developed here.Forcing a DNA molecule into a nanoscale channel requires overcoming the free energy barrier associated with confinement. Here, the authors show that DNA injected through a funnel-shaped entrance more efficiently enters the nanochannel, thanks to facilitating forces generated by the nanofunnel geometry.
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Affiliation(s)
- Jinsheng Zhou
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yanqian Wang
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Laurent D Menard
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Sergey Panyukov
- PN Lebedev Physical Institute, Russian Academy of Sciences, Moscow, 117924, Russia
| | - Michael Rubinstein
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - J Michael Ramsey
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA.
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111
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Restrepo-Pérez L, John S, Aksimentiev A, Joo C, Dekker C. SDS-assisted protein transport through solid-state nanopores. NANOSCALE 2017; 9:11685-11693. [PMID: 28776058 PMCID: PMC5611827 DOI: 10.1039/c7nr02450a] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Using nanopores for single-molecule sequencing of proteins - similar to nanopore-based sequencing of DNA - faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule experiments to investigate the utility of SDS (Sodium Dodecyl Sulfate) to unfold proteins for solid-state nanopore translocation, while simultaneously endowing them with a stronger electrical charge. Our simulations and experiments prove that SDS-treated proteins show a considerable loss of the protein structure during the nanopore translocation. Moreover, SDS-treated proteins translocate through the nanopore in the direction prescribed by the electrophoretic force due to the negative charge impaired by SDS. In summary, our results suggest that SDS causes protein unfolding while facilitating protein translocation in the direction of the electrophoretic force; both characteristics being advantageous for future protein sequencing applications using solid-state nanopores.
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Affiliation(s)
- Laura Restrepo-Pérez
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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112
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Abstract
Single-molecule studies of protein folding hold keys to unveiling protein folding pathways and elusive intermediate folding states-attractive pharmaceutical targets. Although conventional single-molecule approaches can detect folding intermediates, they presently lack throughput and require elaborate labeling. Here, we theoretically show that measurements of ionic current through a nanopore containing a protein can report on the protein's folding state. Our all-atom molecular dynamics (MD) simulations show that the unfolding of a protein lowers the nanopore ionic current, an effect that originates from the reduction of ion mobility in proximity to a protein. Using a theoretical model, we show that the average change in ionic current produced by a folding-unfolding transition is detectable despite the orientational and conformational heterogeneity of the folded and unfolded states. By analyzing millisecond-long all-atom MD simulations of multiple protein transitions, we show that a nanopore ionic current recording can detect folding-unfolding transitions in real time and report on the structure of folding intermediates.
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Affiliation(s)
- Wei Si
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, 210096, China
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- To whom correspondence should be addressed:
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113
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Gao R, Ying YL, Hu YX, Li YJ, Long YT. Wireless Bipolar Nanopore Electrode for Single Small Molecule Detection. Anal Chem 2017; 89:7382-7387. [DOI: 10.1021/acs.analchem.7b00729] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Rui Gao
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yong-Xu Hu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yuan-Jie Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
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114
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Detecting Single-Nucleotides by Tunneling Current Measurements at Sub-MHz Temporal Resolution. SENSORS 2017; 17:s17040885. [PMID: 28420199 PMCID: PMC5424762 DOI: 10.3390/s17040885] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 04/11/2017] [Accepted: 04/14/2017] [Indexed: 01/22/2023]
Abstract
Label-free detection of single-nucleotides was performed by fast tunneling current measurements in a polar solvent at 1 MHz sampling rate using SiO2-protected Au nanoprobes. Short current spikes were observed, suggestive of trapping/detrapping of individual nucleotides between the nanoelectrodes. The fall and rise features of the electrical signatures indicated signal retardation by capacitance effects with a time constant of about 10 microseconds. The high temporal resolution revealed current fluctuations, reflecting the molecular conformation degrees of freedom in the electrode gap. The method presented in this work may enable direct characterizations of dynamic changes in single-molecule conformations in an electrode gap in liquid.
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115
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Li WQ, Huang B, Huang ML, Peng LL, Hong ZW, Zheng JF, Chen WB, Li JF, Zhou XS. Detecting Electron Transport of Amino Acids by Using Conductance Measurement. SENSORS 2017; 17:s17040811. [PMID: 28394265 PMCID: PMC5422172 DOI: 10.3390/s17040811] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/14/2022]
Abstract
The single molecular conductance of amino acids was measured by a scanning tunneling microscope (STM) break junction. Conductance measurement of alanine gives out two conductance values at 10−1.85 G0 (1095 nS) and 10−3.7 G0 (15.5 nS), while similar conductance values are also observed for aspartic acid and glutamic acid, which have one more carboxylic acid group compared with alanine. This may show that the backbone of NH2–C–COOH is the primary means of electron transport in the molecular junction of aspartic acid and glutamic acid. However, NH2–C–COOH is not the primary means of electron transport in the methionine junction, which may be caused by the strong interaction of the Au–SMe (methyl sulfide) bond for the methionine junction. The current work reveals the important role of the anchoring group in the electron transport in different amino acids junctions.
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Affiliation(s)
- Wei-Qiong Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China.
| | - Bing Huang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China.
| | - Miao-Ling Huang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China.
| | - Lin-Lu Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China.
| | - Ze-Wen Hong
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China.
| | - Ju-Fang Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China.
| | - Wen-Bo Chen
- Shanghai Key Laboratory of Materials Protection and Advanced Materials in Electric Power, Shanghai University of Electric Power, Shanghai 200090, China.
| | - Jian-Feng Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China.
| | - Xiao-Shun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China.
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116
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Barati Farimani A, Heiranian M, Min K, Aluru NR. Antibody Subclass Detection Using Graphene Nanopores. J Phys Chem Lett 2017; 8:1670-1676. [PMID: 28325049 DOI: 10.1021/acs.jpclett.7b00385] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Solid-state nanopores are promising for label-free protein detection. The large thickness, ranging from several tens of nanometers to micrometers and larger, of solid-state nanopores prohibits atomic-scale scanning or interrogation of proteins. Here, a single-atom thick graphene nanopore is shown to be highly capable of sensing and discriminating between different subclasses of IgG antibodies despite their minor and subtle variation in atomic structure. Extensive molecular dynamics (MD) simulations, rigorous statistical analysis with a total aggregate simulation time of 2.7 μs, supervised machine learning (ML), and classification techniques are employed to distinguish IgG2 from IgG3. The water flux and ionic current during IgG translocation reveal distinct clusters for IgG subclasses facilitating an additional recognition mechanism. In addition, the histogram of ionic current for each segment of IgG can provide high-resolution spatial detection. Our results show that nanoporous graphene can be used to detect and distinguish antibody subclasses with good accuracy.
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Affiliation(s)
- Amir Barati Farimani
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Mohammad Heiranian
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Kyoungmin Min
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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117
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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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118
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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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119
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Shankla M, Aksimentiev A. Modulation of Molecular Flux Using a Graphene Nanopore Capacitor. J Phys Chem B 2017; 121:3724-3733. [PMID: 28009170 DOI: 10.1021/acs.jpcb.6b10574] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Modulation of ionic current flowing through nanoscale pores is one of the fundamental biological processes. Inspired by nature, nanopores in synthetic solid-state membranes are being developed to enable rapid analysis of biological macromolecules and to serve as elements of nanofludic circuits. Here, we theoretically investigate ion and water transport through a graphene-insulator-graphene membrane containing a single, electrolyte-filled nanopore. By means of all-atom molecular dynamics simulations, we show that the charge state of such a graphene nanopore capacitor can regulate both the selectivity and the magnitude of the nanopore ionic current. At a fixed transmembrane bias, the ionic current can be switched from being carried by an equal mixture of cations and anions to being carried almost exclusively by either cationic or anionic species, depending on the sign of the charge assigned to both plates of the capacitor. Assigning the plates of the capacitor opposite sign charges can either increase the nanopore current or reduce it substantially, depending on the polarity of the bias driving the transmembrane current. Facilitated by the changes of the nanopore surface charge, such ionic current modulations are found to occur despite the physical dimensions of the nanopore being an order of magnitude larger than the screening length of the electrolyte. The ionic current rectification is accompanied by a pronounced electro-osmotic effect that can transport neutral molecules such as proteins and drugs across the solid-state membrane and thereby serve as an interface between electronic and chemical signals.
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Affiliation(s)
- Manish Shankla
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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120
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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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121
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Chang B, Zhang B, Sun T. Smart Polymers with Special Wettability. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13. [PMID: 27008568 DOI: 10.1002/smll.201503472] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/10/2016] [Indexed: 05/16/2023]
Abstract
Surface wettability plays a key role in addressing issues ranging from basic life activities to our daily life, and thus being able to control it is an attractive goal. Learning from nature, both of its structure and function, brings us much inspiration in designing smart polymers to tackle this major challenge. Life functions particularly depend on biomolecular recognition-induced interfacial properties from the aqueous phase onto either "soft" cell and tissue or "hard" inorganic bone and tooth surfaces. The driving force is noncovalent weak interactions rather than strong covalent combinations. An overview is provided of the weak interactions that perform vital actions in mediating biological processes, which serve as a basis for elaborating multi-component polymers with special wettabilities. The role of smart polymers from molecular recognitions to macroscopic properties are highlighted. The rationale is that highly selective weak interactions are capable of creating a dynamic synergetic communication in the building components of polymers. Biomolecules could selectively induce conformational transitions of polymer chains, and then drive a switching of physicochemical properties, e.g., roughness, stiffness and compositions, which are an integrated embodiment of macroscopic surface wettabilities.
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Affiliation(s)
- Baisong Chang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, 430070, P.R. China
| | - Bei Zhang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, 430070, P.R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, 430070, P.R. China
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, P.R. China
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122
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Dubois V, Niklaus F, Stemme G. Design and fabrication of crack-junctions. MICROSYSTEMS & NANOENGINEERING 2017; 3:17042. [PMID: 31057876 PMCID: PMC6444981 DOI: 10.1038/micronano.2017.42] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/01/2017] [Accepted: 06/19/2017] [Indexed: 05/06/2023]
Abstract
Nanogap electrodes consist of pairs of electrically conducting tips that exhibit nanoscale gaps. They are building blocks for a variety of applications in quantum electronics, nanophotonics, plasmonics, nanopore sequencing, molecular electronics, and molecular sensing. Crack-junctions (CJs) constitute a new class of nanogap electrodes that are formed by controlled fracture of suspended bridge structures fabricated in an electrically conducting thin film under residual tensile stress. Key advantages of the CJ methodology over alternative technologies are that CJs can be fabricated with wafer-scale processes, and that the width of each individual nanogap can be precisely controlled in a range from <2 to >100 nm. While the realization of CJs has been demonstrated in initial experiments, the impact of the different design parameters on the resulting CJs has not yet been studied. Here we investigate the influence of design parameters such as the dimensions and shape of the notches, the length of the electrode-bridge and the design of the anchors, on the formation and propagation of cracks and on the resulting features of the CJs. We verify that the design criteria yields accurate prediction of crack formation in electrode-bridges featuring a beam width of 280 nm and beam lengths ranging from 1 to 1.8 μm. We further present design as well as experimental guidelines for the fabrication of CJs and propose an approach to initiate crack formation after release etching of the suspended electrode-bridge, thereby enabling the realization of CJs with pristine electrode surfaces.
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Affiliation(s)
- Valentin Dubois
- KTH Royal Institute of Technology, Micro and Nanosystem, Osquldas väg 10, Stockholm 100 44, Sweden
| | - Frank Niklaus
- KTH Royal Institute of Technology, Micro and Nanosystem, Osquldas väg 10, Stockholm 100 44, Sweden
| | - Göran Stemme
- KTH Royal Institute of Technology, Micro and Nanosystem, Osquldas väg 10, Stockholm 100 44, Sweden
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123
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Sacchi M, Wales DJ, Jenkins SJ. Energy landscapes and dynamics of glycine on Cu(110). Phys Chem Chem Phys 2017; 19:16600-16605. [DOI: 10.1039/c7cp02716h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Amino acids adsorbed on single-crystal metal surfaces have emerged as prototypical systems for exploring the properties that govern the development of long-range chirality in self-assembled monolayers and supramolecular 2D networks. In this study, we characterise the self-assembly mechanism for glycine on the Cu(110) surface.
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Affiliation(s)
- Marco Sacchi
- Department of Chemistry
- University of Surrey
- Guildford
- UK
| | - David J. Wales
- Department of Chemistry
- University of Cambridge
- Lensfield Road
- Cambridge
- UK
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124
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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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125
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Wen H, Li W, Chen J, He G, Li L, Olson MA, Sue ACH, Stoddart JF, Guo X. Complex formation dynamics in a single-molecule electronic device. SCIENCE ADVANCES 2016; 2:e1601113. [PMID: 28138528 PMCID: PMC5262467 DOI: 10.1126/sciadv.1601113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/21/2016] [Indexed: 05/20/2023]
Abstract
Single-molecule electronic devices offer unique opportunities to investigate the properties of individual molecules that are not accessible in conventional ensemble experiments. However, these investigations remain challenging because they require (i) highly precise device fabrication to incorporate single molecules and (ii) sufficient time resolution to be able to make fast molecular dynamic measurements. We demonstrate a graphene-molecule single-molecule junction that is capable of probing the thermodynamic and kinetic parameters of a host-guest complex. By covalently integrating a conjugated molecular wire with a pendent crown ether into graphene point contacts, we can transduce the physical [2]pseudorotaxane (de)formation processes between the electron-rich crown ether and a dicationic guest into real-time electrical signals. The conductance of the single-molecule junction reveals two-level fluctuations that are highly dependent on temperature and solvent environments, affording a nondestructive means of quantitatively determining the binding and rate constants, as well as the activation energies, for host-guest complexes. The thermodynamic processes reveal the host-guest binding to be enthalpy-driven and are consistent with conventional 1H nuclear magnetic resonance titration experiments. This electronic device opens up a new route to developing single-molecule dynamics investigations with microsecond resolution for a broad range of chemical and biochemical applications.
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Affiliation(s)
- Huimin Wen
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wengang Li
- Institute for Molecular Design and Synthesis, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jiewei Chen
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Gen He
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Longhua Li
- Scientific Research Academy, Jiangsu University, Zhenjiang 212013, China
| | - Mark A. Olson
- Institute for Molecular Design and Synthesis, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Andrew C.-H. Sue
- Institute for Molecular Design and Synthesis, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Department of Chemistry, Northwestern University, Evanston, IL 60208–3113, USA
- Corresponding author. (X.G.); (A.C.-H.S.); (J.F.S.)
| | - J. Fraser Stoddart
- Institute for Molecular Design and Synthesis, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Department of Chemistry, Northwestern University, Evanston, IL 60208–3113, USA
- Corresponding author. (X.G.); (A.C.-H.S.); (J.F.S.)
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, China
- Corresponding author. (X.G.); (A.C.-H.S.); (J.F.S.)
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126
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Li J, He G, Ueno H, Jia C, Noji H, Qi C, Guo X. Direct real-time detection of single proteins using silicon nanowire-based electrical circuits. NANOSCALE 2016; 8:16172-16176. [PMID: 27714062 DOI: 10.1039/c6nr04103e] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present an efficient strategy through surface functionalization to build a single silicon nanowire field-effect transistor-based biosensor that is capable of directly detecting protein adsorption/desorption at the single-event level. The step-wise signals in real-time detection of His-tag F1-ATPases demonstrate a promising electrical biosensing approach with single-molecule sensitivity, thus opening up new opportunities for studying single-molecule biophysics in broad biological systems.
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Affiliation(s)
- Jie Li
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China. and Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.
| | - Gen He
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China. and Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.
| | - Hiroshi Ueno
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan.
| | - Chuancheng Jia
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.
| | - Hiroyuki Noji
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan.
| | - Chuanmin Qi
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China. and Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, P. R. China
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127
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Cayer DM, Nazor KL, Schork NJ. Mission critical: the need for proteomics in the era of next-generation sequencing and precision medicine. Hum Mol Genet 2016; 25:R182-R189. [DOI: 10.1093/hmg/ddw214] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 12/14/2022] Open
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128
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Wilson J, Sloman L, He Z, Aksimentiev A. Graphene Nanopores for Protein Sequencing. ADVANCED FUNCTIONAL MATERIALS 2016; 26:4830-4838. [PMID: 27746710 PMCID: PMC5063307 DOI: 10.1002/adfm.201601272] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
An inexpensive, reliable method for protein sequencing is essential to unraveling the biological mechanisms governing cellular behavior and disease. Current protein sequencing methods suffer from limitations associated with the size of proteins that can be sequenced, the time, and the cost of the sequencing procedures. Here, we report the results of all-atom molecular dynamics simulations that investigated the feasibility of using graphene nanopores for protein sequencing. We focus our study on the biologically significant phenylalanine-glycine repeat peptides (FG-nups)-parts of the nuclear pore transport machinery. Surprisingly, we found FG-nups to behave similarly to single stranded DNA: the peptides adhere to graphene and exhibit step-wise translocation when subject to a transmembrane bias or a hydrostatic pressure gradient. Reducing the peptide's charge density or increasing the peptide's hydrophobicity was found to decrease the translocation speed. Yet, unidirectional and stepwise translocation driven by a transmembrane bias was observed even when the ratio of charged to hydrophobic amino acids was as low as 1:8. The nanopore transport of the peptides was found to produce stepwise modulations of the nanopore ionic current correlated with the type of amino acids present in the nanopore, suggesting that protein sequencing by measuring ionic current blockades may be possible.
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Affiliation(s)
- James Wilson
- Department of Physics, University of Illinois Urbana-Champaign,
Urbana, IL 61801, USA
| | - Leila Sloman
- McGill University, 845 Rue Sherbrooke O, Montreal, QC H3A 0G4,
Canada
| | - Zhiren He
- Department of Physics, University of Illinois Urbana-Champaign,
Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois Urbana-Champaign,
Urbana, IL 61801, USA
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129
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Gül OT, Pugliese KM, Choi Y, Sims PC, Pan D, Rajapakse AJ, Weiss GA, Collins PG. Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths. BIOSENSORS-BASEL 2016; 6:bios6030029. [PMID: 27348011 PMCID: PMC5039648 DOI: 10.3390/bios6030029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 01/17/2023]
Abstract
As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein’s activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF) of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF’s base-by-base activity. After measuring as few as 20 copies, the template length can be determined with <1 base pair resolution, and different template lengths can be identified and enumerated in solutions containing template mixtures.
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Affiliation(s)
- O Tolga Gül
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
- Department of Physics, Polatlı Faculty of Science and Arts, Gazi University, Polatlı 06900, Turkey
| | - Kaitlin M Pugliese
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697, USA
| | - Yongki Choi
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
- Department of Physics, North Dakota State University, Fargo, ND 58108, USA
| | - Patrick C Sims
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
| | - Deng Pan
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
| | - Arith J Rajapakse
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
| | - Gregory A Weiss
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697, USA.
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA 92697, USA.
| | - Philip G Collins
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA.
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130
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Zhang Y, Liu J, Li D, Dai X, Yan F, Conlan XA, Zhou R, Barrow CJ, He J, Wang X, Yang W. Self-Assembled Core-Satellite Gold Nanoparticle Networks for Ultrasensitive Detection of Chiral Molecules by Recognition Tunneling Current. ACS NANO 2016; 10:5096-103. [PMID: 27104661 DOI: 10.1021/acsnano.6b00216] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chirality sensing is a very challenging task. Here, we report a method for ultrasensitive detection of chiral molecule l/d-carnitine based on changes in the recognition tunneling current across self-assembled core-satellite gold nanoparticle (GNP) networks. The recognition tunneling technique has been demonstrated to work at the single molecule level where the binding between the reader molecules and the analytes in a nanojunction. This process was observed to generate a unique and sensitive change in tunneling current, which can be used to identify the analytes of interest. The molecular recognition mechanism between amino acid l-cysteine and l/d-carnitine has been studied with the aid of SERS. The different binding strength between homo- or heterochiral pairs can be effectively probed by the copper ion replacement fracture. The device resistance was measured before and after the sequential exposures to l/d-carnitine and copper ions. The normalized resistance change was found to be extremely sensitive to the chirality of carnitine molecule. The results suggested that a GNP networks device optimized for recognition tunneling was successfully built and that such a device can be used for ultrasensitive detection of chiral molecules.
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Affiliation(s)
- Yuanchao Zhang
- College of Chemistry and Chemical Engineering, Ocean University of China , Qingdao 266100, China
- School of Life and Environmental Science, Centre for Chemistry and Biotechnology, Deakin University , Geelong, Victoria 3216, Australia
| | - Jingquan Liu
- College of Chemical Science and Engineering, Qingdao University , Qingdao 266071, China
| | - Da Li
- College of Chemical Science and Engineering, Qingdao University , Qingdao 266071, China
| | - Xing Dai
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University , Suzhou 215123, China
| | - Fuhua Yan
- Nanjing Stomatological Hospital, Medical School of Nanjing University , Nanjing 210008, China
| | - Xavier A Conlan
- School of Life and Environmental Science, Centre for Chemistry and Biotechnology, Deakin University , Geelong, Victoria 3216, Australia
| | - Ruhong Zhou
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University , Suzhou 215123, China
- IBM Thomas J. Watson Research Centre , Yorktown Heights, New York 10598, United States
| | - Colin J Barrow
- School of Life and Environmental Science, Centre for Chemistry and Biotechnology, Deakin University , Geelong, Victoria 3216, Australia
| | - Jin He
- Physics Department, Biomolecular Science Institute, Florida International University , Miami, Florida 33199, United States
| | - Xin Wang
- College of Chemistry and Chemical Engineering, Ocean University of China , Qingdao 266100, China
| | - Wenrong Yang
- School of Life and Environmental Science, Centre for Chemistry and Biotechnology, Deakin University , Geelong, Victoria 3216, Australia
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131
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Dubois V, Niklaus F, Stemme G. Crack-Defined Electronic Nanogaps. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:2178-82. [PMID: 26784270 DOI: 10.1002/adma.201504569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/03/2015] [Indexed: 05/24/2023]
Abstract
Achieving near-atomic-scale electronic nanogaps in a reliable and scalable manner will facilitate fundamental advances in molecular detection, plasmonics, and nanoelectronics. Here, a method is shown for realizing crack-defined nanogaps separating TiN electrodes, allowing parallel and scalable fabrication of arrays of sub-10 nm electronic nanogaps featuring individually defined gap widths.
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Affiliation(s)
- Valentin Dubois
- Department of Micro and Nanosystems, School of Electrical Engineering, KTH Royal Institute of Technology, SE-10044, Stockholm, Sweden
| | - Frank Niklaus
- Department of Micro and Nanosystems, School of Electrical Engineering, KTH Royal Institute of Technology, SE-10044, Stockholm, Sweden
| | - Göran Stemme
- Department of Micro and Nanosystems, School of Electrical Engineering, KTH Royal Institute of Technology, SE-10044, Stockholm, Sweden
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132
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Xiang D, Wang X, Jia C, Lee T, Guo X. Molecular-Scale Electronics: From Concept to Function. Chem Rev 2016; 116:4318-440. [DOI: 10.1021/acs.chemrev.5b00680] [Citation(s) in RCA: 816] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Dong Xiang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Key
Laboratory of Optical Information Science and Technology, Institute
of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chuancheng Jia
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Takhee Lee
- Department
of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea
| | - Xuefeng Guo
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Department
of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, China
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133
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Di Ventra M, Taniguchi M. Decoding DNA, RNA and peptides with quantum tunnelling. NATURE NANOTECHNOLOGY 2016; 11:117-26. [PMID: 26839257 DOI: 10.1038/nnano.2015.320] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 12/07/2015] [Indexed: 05/25/2023]
Abstract
Drugs and treatments could be precisely tailored to an individual patient by extracting their cellular- and molecular-level information. For this approach to be feasible on a global scale, however, information on complete genomes (DNA), transcriptomes (RNA) and proteomes (all proteins) needs to be obtained quickly and at low cost. Quantum mechanical phenomena could potentially be of value here, because the biological information needs to be decoded at an atomic level and quantum tunnelling has recently been shown to be able to differentiate single nucleobases and amino acids in short sequences. Here, we review the different approaches to using quantum tunnelling for sequencing, highlighting the theoretical background to the method and the experimental capabilities demonstrated to date. We also explore the potential advantages of the approach and the technical challenges that must be addressed to deliver practical quantum sequencing devices.
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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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134
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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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135
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Biswas S, Song W, Borges C, Lindsay S, Zhang P. Click Addition of a DNA Thread to the N-Termini of Peptides for Their Translocation through Solid-State Nanopores. ACS NANO 2015; 9:9652-64. [PMID: 26364915 PMCID: PMC5648329 DOI: 10.1021/acsnano.5b04984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Foremost among the challenges facing single molecule sequencing of proteins by nanopores is the lack of a universal method for driving proteins or peptides into nanopores. In contrast to nucleic acids, the backbones of which are uniformly negatively charged nucleotides, proteins carry positive, negative and neutral side chains that are randomly distributed. Recombinant proteins carrying a negatively charged oligonucleotide or polypeptide at the C-termini can be translocated through a α-hemolysin (α-HL) nanopore, but the required genetic engineering limits the generality of these approaches. In this present study, we have developed a chemical approach for addition of a charged oligomer to peptides so that they can be translocated through nanopores. As an example, an oligonucleotide PolyT20 was tethered to peptides through first selectively functionalizing their N-termini with azide followed by a click reaction. The data show that the peptide-PolyT20 conjugates translocated through nanopores, whereas the unmodified peptides did not. Surprisingly, the conjugates with their peptides tethered at the 5'-end of PolyT20 passed the nanopores more rapidly than the PolyT20 alone. The PolyT20 also yielded a wider distribution of blockade currents. The same broad distribution was found for a conjugate with its peptide tethered at the 3'-end of PolyT20, suggesting that the larger blockades (and longer translocation times) are associated with events in which the 5'-end of the PolyT20 enters the pore first.
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Affiliation(s)
- Sudipta Biswas
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Weisi Song
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Chad Borges
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Corresponding Author: The author(s) to whom correspondence should be addressed: ;
| | - Peiming Zhang
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
- Corresponding Author: The author(s) to whom correspondence should be addressed: ;
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136
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Kudr J, Skalickova S, Nejdl L, Moulick A, Ruttkay-Nedecky B, Adam V, Kizek R. Fabrication of solid-state nanopores and its perspectives. Electrophoresis 2015; 36:2367-79. [DOI: 10.1002/elps.201400612] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/13/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Jiri Kudr
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Sylvie Skalickova
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Lukas Nejdl
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Branislav Ruttkay-Nedecky
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
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137
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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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138
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Akhterov MV, Choi Y, Olsen TJ, Sims PC, Iftikhar M, Gul OT, Corso BL, Weiss GA, Collins PG. Observing lysozyme's closing and opening motions by high-resolution single-molecule enzymology. ACS Chem Biol 2015; 10:1495-501. [PMID: 25763461 DOI: 10.1021/cb500750v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Single-molecule techniques can monitor the kinetics of transitions between enzyme open and closed conformations, but such methods usually lack the resolution to observe the underlying transition pathway or intermediate conformational dynamics. We have used a 1 MHz bandwidth carbon nanotube transistor to electronically monitor single molecules of the enzyme T4 lysozyme as it processes substrate. An experimental resolution of 2 μs allowed the direct recording of lysozyme's opening and closing transitions. Unexpectedly, both motions required 37 μs, on average. The distribution of transition durations was also independent of the enzyme's state: either catalytic or nonproductive. The observation of smooth, continuous transitions suggests a concerted mechanism for glycoside hydrolysis with lysozyme's two domains closing upon the polysaccharide substrate in its active site. We distinguish these smooth motions from a nonconcerted mechanism, observed in approximately 10% of lysozyme openings and closings, in which the enzyme pauses for an additional 40-140 μs in an intermediate, partially closed conformation. During intermediate forming events, the number of rate-limiting steps observed increases to four, consistent with four steps required in the stepwise, arrow-pushing mechanism. The formation of such intermediate conformations was again independent of the enzyme's state. Taken together, the results suggest lysozyme operates as a Brownian motor. In this model, the enzyme traces a single pathway for closing and the reverse pathway for enzyme opening, regardless of its instantaneous catalytic productivity. The observed symmetry in enzyme opening and closing thus suggests that substrate translocation occurs while the enzyme is closed.
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Affiliation(s)
- Maxim V. Akhterov
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Yongki Choi
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Tivoli J. Olsen
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Patrick C. Sims
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Mariam Iftikhar
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - O. Tolga Gul
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Brad L. Corso
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Gregory A. Weiss
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Philip G. Collins
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
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139
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Nichols RJ, Higgins SJ. Single-Molecule Electronics: Chemical and Analytical Perspectives. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:389-417. [PMID: 26048551 DOI: 10.1146/annurev-anchem-071114-040118] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.
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Affiliation(s)
- Richard J Nichols
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom;
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140
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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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141
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A theoretical justification for single molecule peptide sequencing. PLoS Comput Biol 2015; 11:e1004080. [PMID: 25714988 PMCID: PMC4341059 DOI: 10.1371/journal.pcbi.1004080] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/10/2014] [Indexed: 11/19/2022] Open
Abstract
The proteomes of cells, tissues, and organisms reflect active cellular processes and change continuously in response to intracellular and extracellular cues. Deep, quantitative profiling of the proteome, especially if combined with mRNA and metabolite measurements, should provide an unprecedented view of cell state, better revealing functions and interactions of cell components. Molecular diagnostics and biomarker discovery should benefit particularly from the accurate quantification of proteomes, since complex diseases like cancer change protein abundances and modifications. Currently, shotgun mass spectrometry is the primary technology for high-throughput protein identification and quantification; while powerful, it lacks high sensitivity and coverage. We draw parallels with next-generation DNA sequencing and propose a strategy, termed fluorosequencing, for sequencing peptides in a complex protein sample at the level of single molecules. In the proposed approach, millions of individual fluorescently labeled peptides are visualized in parallel, monitoring changing patterns of fluorescence intensity as N-terminal amino acids are sequentially removed, and using the resulting fluorescence signatures (fluorosequences) to uniquely identify individual peptides. We introduce a theoretical foundation for fluorosequencing and, by using Monte Carlo computer simulations, we explore its feasibility, anticipate the most likely experimental errors, quantify their potential impact, and discuss the broad potential utility offered by a high-throughput peptide sequencing technology. The development of next-generation DNA and RNA sequencing methods has transformed biology, with current platforms generating >1 billion sequencing reads per run. Unfortunately, no method of similar scale and throughput exists to identify and quantify specific proteins in complex mixtures, representing a critical bottleneck in many biochemical and molecular diagnostic assays. What is urgently needed is a massively parallel method, akin to next-gen DNA sequencing, for identifying and quantifying peptides or proteins in a sample. In principle, single-molecule peptide sequencing could achieve this goal, allowing billions of distinct peptides to be sequenced in parallel and thereby identifying proteins composing the sample and digitally quantifying them by direct counting of peptides. Here, we discuss theoretical considerations of single molecule peptide sequencing, suggest one possible experimental strategy, and, using computer simulations, characterize the potential utility and unusual properties of this future proteomics technology.
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142
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Carson S, Wanunu M. Challenges in DNA motion control and sequence readout using nanopore devices. NANOTECHNOLOGY 2015; 26:074004. [PMID: 25642629 PMCID: PMC4710574 DOI: 10.1088/0957-4484/26/7/074004] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nanopores are being hailed as a potential next-generation DNA sequencer that could provide cheap, high-throughput DNA analysis. In this review we present a detailed summary of the various sensing techniques being investigated for use in DNA sequencing and mapping applications. A crucial impasse to the success of nanopores as a reliable DNA analysis tool is the fast and stochastic nature of DNA translocation. We discuss the incorporation of biological motors to step DNA through a pore base-by-base, as well as the many experimental modifications attempted for the purpose of slowing and controlling DNA transport.
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143
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Juhaniewicz J, Pawlowski J, Sek S. Electron Transport Mediated by Peptides Immobilized on Surfaces. Isr J Chem 2015. [DOI: 10.1002/ijch.201400165] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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144
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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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145
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Frielinghaus R, Besson C, Houben L, Saelhoff AK, Schneider CM, Meyer C. Controlled covalent binding of antiferromagnetic tetramanganese complexes to carbon nanotubes. RSC Adv 2015. [DOI: 10.1039/c5ra14983e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tetramanganese complexes are covalently attached to carbon nanotubes such, that the magnetic properties of the antiferromagnetic molecules are preserved.
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Affiliation(s)
- R. Frielinghaus
- Peter Grünberg Institute (PGI-6)
- Forschungszentrum Jülich
- JARA-Fundamentals of Future Information Technologies
- 52425 Jülich
- Germany
| | - C. Besson
- Institute of Inorganic Chemistry
- RWTH Aachen University
- JARA-Fundamentals of Future Information Technologies
- Aachen
- Germany
| | - L. Houben
- Peter Grünberg Institute (PGI-5) and Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons
- Forschungszentrum Jülich
- 52425 Jülich
- Germany
| | - A.-K. Saelhoff
- Peter Grünberg Institute (PGI-6)
- Forschungszentrum Jülich
- JARA-Fundamentals of Future Information Technologies
- 52425 Jülich
- Germany
| | - C. M. Schneider
- Peter Grünberg Institute (PGI-6)
- Forschungszentrum Jülich
- JARA-Fundamentals of Future Information Technologies
- 52425 Jülich
- Germany
| | - C. Meyer
- Peter Grünberg Institute (PGI-6)
- Forschungszentrum Jülich
- JARA-Fundamentals of Future Information Technologies
- 52425 Jülich
- Germany
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146
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Sampath G. Amino acid discrimination in a nanopore and the feasibility of sequencing peptides with a tandem cell and exopeptidase. RSC Adv 2015. [DOI: 10.1039/c5ra02118a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Peptide sequencing in an electrolytic cell with two nanopores in tandem and exopeptidase.
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147
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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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148
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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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149
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Ivankin A, Henley RY, Larkin J, Carson S, Toscano ML, Wanunu M. Label-free optical detection of biomolecular translocation through nanopore arrays. ACS NANO 2014; 8:10774-81. [PMID: 25232895 PMCID: PMC4212781 DOI: 10.1021/nn504551d] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
In recent years, nanopores have emerged as exceptionally promising single-molecule sensors due to their ability to detect biomolecules at subfemtomole levels in a label-free manner. Development of a high-throughput nanopore-based biosensor requires multiplexing of nanopore measurements. Electrical detection, however, poses a challenge, as each nanopore circuit must be electrically independent, which requires complex nanofluidics and embedded electrodes. Here, we present an optical method for simultaneous measurements of the ionic current across an array of solid-state nanopores, requiring no additional fabrication steps. Proof-of-principle experiments are conducted that show simultaneous optical detection and characterization of ssDNA and dsDNA using an array of pores. Through a comparison with electrical measurements, we show that optical measurements are capable of accessing equivalent transmembrane current information.
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Affiliation(s)
- Andrey Ivankin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Robert Y. Henley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Joseph Larkin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Michael L. Toscano
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Address correspondence to
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150
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Larkin J, Foquet M, Turner SW, Korlach J, Wanunu M. Reversible positioning of single molecules inside zero-mode waveguides. NANO LETTERS 2014; 14:6023-9. [PMID: 25209321 PMCID: PMC4189617 DOI: 10.1021/nl503134x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/07/2014] [Indexed: 05/20/2023]
Abstract
We have developed a hybrid nanopore/zero-mode waveguide device for single-molecule fluorescence and DNA sequencing applications. The device is a freestanding solid-state membrane with sub-5 nm nanopores that reversibly delivers individual biomolecules to the base of 70 nm diameter waveguides for interrogation. Rapid and reversible molecular loading is achieved by controlling the voltage across the device. Using this device we demonstrate protein and DNA loading with efficiency that is orders of magnitude higher than diffusion-based molecular loading.
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Affiliation(s)
- Joseph Larkin
- Department
of Physics and Department of Chemistry/Chemical Biology, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
| | - Mathieu Foquet
- Pacific
Biosciences, 1380 Willow
Road, Menlo Park, California 94025, United States
| | - Stephen W. Turner
- Pacific
Biosciences, 1380 Willow
Road, Menlo Park, California 94025, United States
| | - Jonas Korlach
- Pacific
Biosciences, 1380 Willow
Road, Menlo Park, California 94025, United States
| | - Meni Wanunu
- Department
of Physics and Department of Chemistry/Chemical Biology, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
- E-mail: . Fax: (617) 373 2943
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