101
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Kletsov AA, Kosolapova KI, Chumakov AS, Glukhova VA, Mikhailov AI, Glukhovskoi EG. Identification of nucleotides by measuring their current during DNA translocation through a nanopore. Russ Chem Bull 2016. [DOI: 10.1007/s11172-015-1159-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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102
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Tanimoto S, Tsutsui M, Yokota K, Taniguchi M. Dipole effects on the formation of molecular junctions. NANOSCALE HORIZONS 2016; 1:399-406. [PMID: 32260630 DOI: 10.1039/c6nh00088f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Measuring the tunnelling current is a promising way of identifying individual molecules in a liquid, wherein molecular conformations in an electrode gap play a crucial role in the electron transport properties. Here we report that molecular dipole interactions with the electric field effectively restrict the configurational degrees of freedom in metal-molecule-metal systems. We utilized a mechanically tunable Au nanoelectrode gap to electrically detect diaminobenzene isomers. We found suppression of a variation in the single-molecule conductance of 1,2-benzenediamines (BDAs) in water suggesting a significant influence of the huge electric field created between the nanoprobes to align the molecular dipole along the potential gradient and concomitant formation of well-defined junction structures for the molecules through-space coupled to one side of the electrodes. On the other hand, the field effect was absent in 1,3- and 1,4-BDAs, which is attributed to their smaller dipole moments and the more rigid chemical connections to the electrodes via Au-amine bonds.
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Affiliation(s)
- Sachie Tanimoto
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, Japan.
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103
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Nanopore-CMOS Interfaces for DNA Sequencing. BIOSENSORS-BASEL 2016; 6:bios6030042. [PMID: 27509529 PMCID: PMC5039661 DOI: 10.3390/bios6030042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/18/2016] [Accepted: 07/28/2016] [Indexed: 12/30/2022]
Abstract
DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces.
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104
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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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105
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He Y, Tsutsui M, Scheicher RH, Miao XS, Taniguchi M. Salt-Gradient Approach for Regulating Capture-to-Translocation Dynamics of DNA with Nanochannel Sensors. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00176] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuhui He
- School
of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
| | - Makusu Tsutsui
- The
Institute of Scientific and Industrial Research, Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Ralph H. Scheicher
- Division
of Materials Theory, Department of Physics and Astronomy, Angström
Laboratory, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
| | - Xiang Shui Miao
- School
of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
| | - Masateru Taniguchi
- The
Institute of Scientific and Industrial Research, Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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106
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Zhang W, Gan S, Vezzoli A, Davidson RJ, Milan DC, Luzyanin KV, Higgins SJ, Nichols RJ, Beeby A, Low PJ, Li B, Niu L. Single-Molecule Conductance of Viologen-Cucurbit[8]uril Host-Guest Complexes. ACS NANO 2016; 10:5212-5220. [PMID: 27055002 DOI: 10.1021/acsnano.6b00786] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The local molecular environment is a critical factor which should be taken into account when measuring single-molecule electrical properties in condensed media or in the design of future molecular electronic or single molecule sensing devices. Supramolecular interactions can be used to control the local environment in molecular assemblies and have been used to create microenvironments, for instance, for chemical reactions. Here, we use supramolecular interactions to create microenvironments which influence the electrical conductance of single molecule wires. Cucurbit[8]uril (CB[8]) with a large hydrophobic cavity was used to host the viologen (bipyridinium) molecular wires forming a 1:1 supramolecular complex. Significant increases in the viologen wire single molecule conductances are observed when it is threaded into CB[8] due to large changes of the molecular microenvironment. The results were interpreted within the framework of a Marcus-type model for electron transfer as arising from a reduction in outer-sphere reorganization energy when the viologen is confined within the hydrophobic CB[8] cavity.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory of Electroanalytical Chemistry, CAS Center for Excellence in Nanoscience, c/o Engineering Laboratory for Modern Analytical Techniques, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Shiyu Gan
- State Key Laboratory of Electroanalytical Chemistry, CAS Center for Excellence in Nanoscience, c/o Engineering Laboratory for Modern Analytical Techniques, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
| | - Andrea Vezzoli
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Ross J Davidson
- Department of Chemistry, Durham University , South Road, Durham DH1 3LE, United Kingdom
| | - David C Milan
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Konstantin V Luzyanin
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Simon J Higgins
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Richard J Nichols
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Andrew Beeby
- Department of Chemistry, Durham University , South Road, Durham DH1 3LE, United Kingdom
| | - Paul J Low
- School of Chemistry and Biochemistry, University of Western Australia , 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Buyi Li
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Li Niu
- State Key Laboratory of Electroanalytical Chemistry, CAS Center for Excellence in Nanoscience, c/o Engineering Laboratory for Modern Analytical Techniques, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
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107
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Comer J, Aksimentiev A. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores. NANOSCALE 2016; 8:9600-13. [PMID: 27103233 PMCID: PMC4860951 DOI: 10.1039/c6nr01061j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequences despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25% for single-base substitutions in ultra small (1.6 nm × 1.1 nm cross section; 2 nm length) solid-state nanopores. Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purines and pyrimidines in the triplet are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length increases the ionic current noise. Thus, the sequence dependence of the nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.
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Affiliation(s)
- Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University, P-213 Mosier Hall, 1800 Denison Ave, Manhattan, Kansas, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W Green St, Urbana, IL, USA.
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108
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Gruss D, Velizhanin KA, Zwolak M. Landauer's formula with finite-time relaxation: Kramers' crossover in electronic transport. Sci Rep 2016; 6:24514. [PMID: 27094206 PMCID: PMC4837356 DOI: 10.1038/srep24514] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/30/2016] [Indexed: 12/23/2022] Open
Abstract
Landauer’s formula is the standard theoretical tool to examine ballistic transport in nano- and meso-scale junctions, but it necessitates that any variation of the junction with time must be slow compared to characteristic times of the system, e.g., the relaxation time of local excitations. Transport through structurally dynamic junctions is, however, increasingly of interest for sensing, harnessing fluctuations, and real-time control. Here, we calculate the steady-state current when relaxation of electrons in the reservoirs is present and demonstrate that it gives rise to three regimes of behavior: weak relaxation gives a contact-limited current; strong relaxation localizes electrons, distorting their natural dynamics and reducing the current; and in an intermediate regime the Landauer view of the system only is recovered. We also demonstrate that a simple equation of motion emerges, which is suitable for efficiently simulating time-dependent transport.
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Affiliation(s)
- Daniel Gruss
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.,Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA.,Department of Physics, Oregon State University, Corvallis, OR 97331, USA
| | - Kirill A Velizhanin
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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109
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Kundu S, Karmakar SN. Detection of base-pair mismatches in DNA using graphene-based nanopore device. NANOTECHNOLOGY 2016; 27:135101. [PMID: 26894508 DOI: 10.1088/0957-4484/27/13/135101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a unique way to detect base-pair mismatches in DNA, leading to a different epigenetic disorder by the method of nanopore sequencing. Based on a tight-binding formulation of a graphene-based nanopore device, using the Green's function approach we study the changes in the electronic transport properties of the device as we translocate a double-stranded DNA through the nanopore embedded in a zigzag graphene nanoribbon. In the present work we are not only successful in detecting the usual AT and GC pairs but also a set of possible mismatches in the complementary base pairing.
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Affiliation(s)
- Sourav Kundu
- Condensed Matter Physics Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India
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110
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Yanagi I, Oura T, Haga T, Ando M, Yamamoto J, Mine T, Ishida T, Hatano T, Akahori R, Yokoi T, Anazawa T. Side-gated ultrathin-channel nanopore FET sensors. NANOTECHNOLOGY 2016; 27:115501. [PMID: 26876025 DOI: 10.1088/0957-4484/27/11/115501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A side-gated, ultrathin-channel nanopore FET (SGNAFET) is proposed for fast and label-free DNA sequencing. The concept of the SGNAFET comprises the detection of changes in the channel current during DNA translocation through a nanopore and identifying the four types of nucleotides as a result of these changes. To achieve this goal, both p- and n-type SGNAFETs with a channel thicknesses of 2 or 4 nm were fabricated, and the stable transistor operation of both SGNAFETs in air, water, and a KCl buffer solution were confirmed. In addition, synchronized current changes were observed between the ionic current through the nanopore and the SGNAFET's drain current during DNA translocation through the nanopore.
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Affiliation(s)
- Itaru Yanagi
- Hitachi Ltd, Research & Development Group, Center for Technology Innovation-Healthcare, 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8603, Japan
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111
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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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112
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Heerema SJ, Dekker C. Graphene nanodevices for DNA sequencing. NATURE NANOTECHNOLOGY 2016; 11:127-36. [PMID: 26839258 DOI: 10.1038/nnano.2015.307] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 11/23/2015] [Indexed: 05/24/2023]
Abstract
Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.
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Affiliation(s)
- Stephanie J Heerema
- Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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113
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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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114
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Krstic P. Response of a DNA Hydrogen Bond to a Force in Liquid. ADVANCES IN QUANTUM CHEMISTRY 2016. [DOI: 10.1016/bs.aiq.2015.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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115
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U-shaped relationship between current and pitch in helicene molecules. Sci Rep 2015; 5:16731. [PMID: 26581650 PMCID: PMC4652163 DOI: 10.1038/srep16731] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 10/19/2015] [Indexed: 01/16/2023] Open
Abstract
The helicene is constructed by twisted benzene or other aromatic rings, exhibiting a helical structure. Using first-principles calculations, we investigate the electronic transport of helicenes under stretching or compressing. Interestingly, a U-shaped curve of the current against d (the pitch of a helicene) is observed. Further analysis shows that, it is the result of the nonmonotonic change of HOMO-LUMO gap with d. The change of overlap between orbitals induced by conformational deformation is found to be the underlying mechanism. Moreover, the U-curve phenomenon is an intrinsic feature of the helicene molecules, being robust to the electrode materials or doping. This U-curve behavior is expected to be extended to helical graphene or other related structures, showing great application potential.
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116
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Ab initio electron propagator calculations of transverse conduction through DNA nucleotide bases in 1-nm nanopore corroborate third generation sequencing. Biochim Biophys Acta Gen Subj 2015; 1860:140-5. [PMID: 26525735 DOI: 10.1016/j.bbagen.2015.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/16/2015] [Indexed: 11/20/2022]
Abstract
BACKGROUND The conduction properties of DNA molecule, particularly its transverse conductance (electron transfer through nucleotide bridges), represent a point of interest for DNA chemistry community, especially for DNA sequencing. However, there is no fully developed first-principles theory for molecular conductance and current that allows one to analyze the transverse flow of electrical charge through a nucleotide base. METHODS We theoretically investigate the transverse electron transport through all four DNA nucleotide bases by implementing an unbiased ab initio theoretical approach, namely, the electron propagator theory. RESULTS The electrical conductance and current through DNA nucleobases (guanine [G], cytosine [C], adenine [A] and thymine [T]) inserted into a model 1-nm Ag-Ag nanogap are calculated. The magnitudes of the calculated conductance and current are ordered in the following hierarchies: gA>gG>gC>gT and IG>IA>IT>IC correspondingly. The new distinguishing parameter for the nucleobase identification is proposed, namely, the onset bias magnitude. Nucleobases exhibit the following hierarchy with respect to this parameter: Vonset(A)<Vonset(T)<Vonset(G)<Vonset(C). CONCLUSIONS The difference in current magnitudes and onset voltages implies the possibility of nucleobases electrical identification by virtue of DNA translocation through an electrode-equipped nanopore. GENERAL SIGNIFICANCE The results represent interest for the theorists and practitioners in the field of third generation sequencing techniques as well as in the field of DNA chemistry.
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117
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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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118
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Li J, Yu D, Zhao Q. Solid-state nanopore-based DNA single molecule detection and sequencing. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1542-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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119
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Li Z, Guo H. A molecular dynamics simulation study of sucking a single polymer chain into nanopores: blockage and memory effects. POLYM INT 2015. [DOI: 10.1002/pi.4929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ziqi Li
- Beijing National Laboratory for Molecular Sciences, Joint Laboratory of Polymer Sciences and Materials, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Hongxia Guo
- Beijing National Laboratory for Molecular Sciences, Joint Laboratory of Polymer Sciences and Materials, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
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120
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Fyta M. Threading DNA through nanopores for biosensing applications. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:273101. [PMID: 26061408 DOI: 10.1088/0953-8984/27/27/273101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This review outlines the recent achievements in the field of nanopore research. Nanopores are typically used in single-molecule experiments and are believed to have a high potential to realize an ultra-fast and very cheap genome sequencer. Here, the various types of nanopore materials, ranging from biological to 2D nanopores are discussed together with their advantages and disadvantages. These nanopores can utilize different protocols to read out the DNA nucleobases. Although, the first nanopore devices have reached the market, many still have issues which do not allow a full realization of a nanopore sequencer able to sequence the human genome in about a day. Ways to control the DNA, its dynamics and speed as the biomolecule translocates the nanopore in order to increase the signal-to-noise ratio in the reading-out process are examined in this review. Finally, the advantages, as well as the drawbacks in distinguishing the DNA nucleotides, i.e., the genetic information, are presented in view of their importance in the field of nanopore sequencing.
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Affiliation(s)
- Maria Fyta
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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121
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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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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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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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Shi J, Hou J, Fang Y. Recent advances in nanopore-based nucleic acid analysis and sequencing. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1503-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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125
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Harrer S, Kim SC, Schieber C, Kannam S, Gunn N, Moore S, Scott D, Bathgate R, Skafidas S, Wagner JM. Label-free screening of single biomolecules through resistive pulse sensing technology for precision medicine applications. NANOTECHNOLOGY 2015; 26:182502. [PMID: 25875197 DOI: 10.1088/0957-4484/26/18/182502] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Employing integrated nano- and microfluidic circuits for detecting and characterizing biological compounds through resistive pulse sensing technology is a vibrant area of research at the interface of biotechnology and nanotechnology. Resistive pulse sensing platforms can be customized to study virtually any particle of choice which can be threaded through a fluidic channel and enable label-free single-particle interrogation with the primary read-out signal being an electric current fingerprint. The ability to perform label-free molecular screening with single-molecule and even single binding site resolution makes resistive pulse sensing technology a powerful tool for analyzing the smallest units of biological systems and how they interact with each other on a molecular level. This task is at the core of experimental systems biology and in particular 'omics research which in combination with next-generation DNA-sequencing and next-generation drug discovery and design forms the foundation of a novel disruptive medical paradigm commonly referred to as personalized medicine or precision medicine. DNA-sequencing has approached the 1000-Dollar-Genome milestone allowing for decoding a complete human genome with unmatched speed and at low cost. Increased sequencing efficiency yields massive amounts of genomic data. Analyzing this data in combination with medical and biometric health data eventually enables understanding the pathways from individual genes to physiological functions. Access to this information triggers fundamental questions for doctors and patients alike: what are the chances of an outbreak for a specific disease? Can individual risks be managed and if so how? Which drugs are available and how should they be applied? Could a new drug be tailored to an individual's genetic predisposition fast and in an affordable way? In order to provide answers and real-life value to patients, the rapid evolvement of novel computing approaches for analyzing big data in systems genomics has to be accompanied by an equally strong effort to develop next-generation DNA-sequencing and next-generation drug screening and design platforms. In that context lab-on-a-chip devices utilizing nanopore- and nanochannel based resistive pulse-sensing technology for DNA-sequencing and protein screening applications occupy a key role. This paper describes the status quo of resistive pulse sensing technology for these two application areas with a special focus on current technology trends and challenges ahead.
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Affiliation(s)
- S Harrer
- IBM Research-Australia, 204 Lygon Street, 3053 Carlton, VIC, Australia. University of Melbourne, 3010 Parkville, VIC, Australia
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Ribot JC, Chatterjee A, Nagpal P. Measurements of single nucleotide electronic states as nanoelectronic fingerprints for identification of DNA nucleobases, their protonated and unprotonated states, isomers, and tautomers. J Phys Chem B 2015; 119:4968-74. [PMID: 25793310 DOI: 10.1021/acs.jpcb.5b01403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several nanoelectronic techniques have been explored to distinguish the sequence of nucleic acids in DNA macromolecules. Identification of unique electronic signatures using nanopore conductance, tunneling spectroscopy, or other nanoelectronic techniques depends on electronic states of the DNA nucleotides. While several experimental and computational studies have focused on interaction of nucleobases with different substrates, the effect of nucleic acid biochemistry on its electronic properties has been largely unexplored. Here, we present correlated measurements of frontier molecular orbitals and higher-order electronic states for four DNA nucleobases (adenine, cytosine, thymine, and guanine), and first-principle quantum chemical density functional theoretical (DFT) computations. Using different pH conditions in our experiments, we show that small changes in the biochemical state of these nucleic acids strongly affect the intrinsic electronic structure, measured using scanning tunneling spectroscopy (STS). In our experimental measurements and computations, significant differences were observed between the position of frontier orbitals and higher-energy states between protonated and unprotonated nucleic acids, isomers, and different keto-enol tautomer's formed in these nucleotides, leading to their facile identification. Furthermore, we show unique "electronic fingerprints" for all nucleotides (A, G, T, C) using STS, with most distinct states identified at acidic pH. These results can have important implications for identification of nucleic acid sequences in DNA molecules using a high-throughput nanoelectronic identification technique.
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Affiliation(s)
- Josep Casamada Ribot
- †Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute, §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado, Boulder, Colorado, 80309, United States
| | - Anushree Chatterjee
- †Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute, §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado, Boulder, Colorado, 80309, United States
| | - Prashant Nagpal
- †Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute, §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado, Boulder, Colorado, 80309, United States
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128
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Buyukdagli S, Blossey R, Ala-Nissila T. Ionic current inversion in pressure-driven polymer translocation through nanopores. PHYSICAL REVIEW LETTERS 2015; 114:088303. [PMID: 25768784 DOI: 10.1103/physrevlett.114.088303] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Indexed: 05/24/2023]
Abstract
We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics. In the presence of multivalent counterions, electrostatic many-body effects result in the reversal of the DNA charge. The attraction of anions to the charge-inverted DNA molecule reverses the sign of the ionic current through the pore. Our theory allows for a comprehensive understanding of the complex features of the resulting streaming currents. The underlying mechanism is an efficient way to detect DNA charge reversal in pressure-driven translocation experiments with multivalent cations.
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Affiliation(s)
- Sahin Buyukdagli
- Department of Physics, Bilkent University, Ankara 06800, Turkey
- Institut de Recherche Interdisciplinaire USR3078 CNRS and Université Lille I, Parc de la Haute Borne, 52 Avenue de Halley, 59658 Villeneuve d'Ascq, France
| | - Ralf Blossey
- Institut de Recherche Interdisciplinaire USR3078 CNRS and Université Lille I, Parc de la Haute Borne, 52 Avenue de Halley, 59658 Villeneuve d'Ascq, France
| | - T Ala-Nissila
- Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
- Department of Physics, Brown University, Providence, Box 1843, Rhode Island 02912-1843, USA
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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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130
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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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131
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Kim HS, Kim YH. Recent progress in atomistic simulation of electrical current DNA sequencing. Biosens Bioelectron 2015; 69:186-98. [PMID: 25744599 DOI: 10.1016/j.bios.2015.02.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 10/24/2022]
Abstract
We review recent advances in the DNA sequencing method based on measurements of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major (Mode I) or perturbing (Mode II) current signals. Scanning tunneling microscope and tunneling electrode gap configurations belong to the former category, while the nanochannels with or without an embedded nanopore belong to the latter. The molecular sensing mechanisms of Modes I and II roughly correspond to the electron tunneling and electrochemical gating, respectively. Special emphasis will be given on the computer simulation studies, which have been playing a critical role in the initiation and development of the field. We also highlight low-dimensional nanomaterials such as carbon nanotubes, graphene, and graphene nanoribbons that allow the novel Mode II approach. Finally, several issues in previous computational studies are discussed, which points to future research directions toward more reliable simulation of electrical current DNA sequencing devices.
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Affiliation(s)
- Han Seul Kim
- School of Energy, Environment, Water, and Sustaibability, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Yong-Hoon Kim
- School of Energy, Environment, Water, and Sustaibability, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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132
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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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133
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Foroushani A, Zhang Y, Li D, Mathesh M, Wang H, Yan F, Barrow CJ, He J, Yang W. Tunnelling current recognition through core–satellite gold nanoparticles for ultrasensitive detection of copper ions. Chem Commun (Camb) 2015; 51:2921-4. [DOI: 10.1039/c4cc09451d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The addition of copper ions induces the formation of GNP/l-cysteine/Cu2+/l-cysteine/GNP molecular junctions and generates a significant decrease in the resistance through the networks.
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Affiliation(s)
- Alireza Foroushani
- School of Life and Environmental Sciences
- Deakin University
- Victoria-3217
- Australia
| | - Yuanchao Zhang
- School of Life and Environmental Sciences
- Deakin University
- Victoria-3217
- Australia
- College of Chemistry and Chemical Engineering
| | - Da Li
- School of Life and Environmental Sciences
- Deakin University
- Victoria-3217
- Australia
| | - Motilal Mathesh
- School of Life and Environmental Sciences
- Deakin University
- Victoria-3217
- Australia
| | - Hongbin Wang
- School of Chemistry and Biotechnology
- Yunnan Minzu University
- Kunming 650500
- China
| | - Fuhua Yan
- Institute and Hospital of Stomatology
- Nanjing University Medical School
- Nanjing
- China
| | - Colin J. Barrow
- School of Life and Environmental Sciences
- Deakin University
- Victoria-3217
- Australia
| | - Jin He
- Physics Department
- Florida International University
- Miami
- USA
| | - Wenrong Yang
- School of Life and Environmental Sciences
- Deakin University
- Victoria-3217
- Australia
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134
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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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135
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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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136
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Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A. Close encounters with DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:413101. [PMID: 25238560 PMCID: PMC4207370 DOI: 10.1088/0953-8984/26/41/413101] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.
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Affiliation(s)
- C Maffeo
- Department of Physics, University of Illinois, Urbana, IL, USA
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137
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Huang S. Nanopore-based sensing devices and applications to genome sequencing: a brief history and the missing pieces. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0641-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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138
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Li Z, Smeu M, Park TH, Rawson J, Xing Y, Therien MJ, Ratner MA, Borguet E. Hapticity-dependent charge transport through carbodithioate-terminated [5,15-bis(phenylethynyl)porphinato]zinc(II) complexes in metal-molecule-metal junctions. NANO LETTERS 2014; 14:5493-5499. [PMID: 25255444 DOI: 10.1021/nl502466a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Single molecule break junction experiments and nonequilibrium Green's function calculations using density functional theory (NEGF-DFT) of carbodithioate- and thiol-terminated [5,15-bis(phenylethynyl)-10,20-diarylporphinato]zinc(II) complexes reveal the impact of the electrode-linker coordination mode on charge transport at the single-molecule level. Replacement of thiolate (-S(-)) by the carbodithioate (-CS2(-)) anchoring motif leads to an order of magnitude increase of single molecule conductance. In contrast to thiolate-terminated structures, metal-molecule-metal junctions that exploit the carbodithioate linker manifest three distinct conductance values. We hypothesize that the magnitudes of these conductances depend upon carbodithoate linker hapticity with measured conductances across Au-[5,15-bis(4'-(dithiocarboxylate)phenylethynyl)-10,20-diarylporphinato]zinc(II)-Au junctions the greatest when both anchoring groups attach to the metal surface in a bidentate fashion. We support this hypothesis with NEGF-DFT calculations, which consider the electron transport properties for specific binding geometries. These results provide new insights into the origin of molecule-to-molecule conductance heterogeneity in molecular charge transport measurements and the factors that optimize electrode-molecule-electrode electronic coupling and maximize the conductance for charge transport.
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Affiliation(s)
- Zhihai Li
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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139
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Kim Y, Kim ES, Lee Y, Kim JH, Shim BC, Cho SM, Lee JS, Park JW. Reading single DNA with DNA polymerase followed by atomic force microscopy. J Am Chem Soc 2014; 136:13754-60. [PMID: 25203438 DOI: 10.1021/ja5063983] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The importance of DNA sequencing in the life sciences and personalized medicine is continually increasing. Single-molecule sequencing methods have been developed to analyze DNA directly without the need for amplification. Here, we present a new approach to sequencing single DNA molecules using atomic force microscopy (AFM). In our approach, four surface-conjugated nucleotides were examined sequentially with a DNA polymerase-immobilized AFM tip. By observing the specific rupture events upon examination of a matching nucleotide, we could determine the template base bound in the polymerase's active site. The subsequent incorporation of the complementary base in solution enabled the next base to be read. Additionally, we observed that the DNA polymerase could incorporate the surface-conjugated dGTP when the applied force was controlled by employing the force-clamp mode.
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Affiliation(s)
- Youngkyu Kim
- School of Interdisciplinary Bioscience and Bioengineering, ‡Department of Chemistry, and §Department of Life Sciences, Pohang University of Science and Technology , San 31 Hyoja-dong, Pohang, 790-784, Korea
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140
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Artés JM, López-Martínez M, Díez-Pérez I, Sanz F, Gorostiza P. Nanoscale charge transfer in redox proteins and DNA: Towards biomolecular electronics. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2014.05.089] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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141
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Luan B, Wang C, Royyuru A, Stolovitzky G. Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages. NANOTECHNOLOGY 2014; 25:265101. [PMID: 24920303 DOI: 10.1088/0957-4484/25/26/265101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A nanofluidic channel, with a pair of perpendicularly aligned nanoelectrodes, is proposed to electrically control the motion of DNA molecules. Using all-atom molecular dynamics simulations, we studied electrostatic responses of a charged DNA molecule in the nanochannel and investigated optimized operating conditions for controlling the DNA molecule. When the transversal electric field was periodically turned on and off, the DNA molecule was correspondingly immobilized on and released from the channel surface. Under simultaneously applied longitudinal biasing and transversal trapping electric fields, the DNA molecule moved forward in a 'ratchet'-like fashion. It is expected that achieving the controlled motion of DNA in the channel can advance studies and applications of a nanochannel-based sensor for analyzing DNA (e.g., DNA sequencing).
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Affiliation(s)
- Binquan Luan
- IBM T J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, 10598, USA
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142
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Resolving the molecular mechanism of cadherin catch bond formation. Nat Commun 2014; 5:3941. [PMID: 24887573 DOI: 10.1038/ncomms4941] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/23/2014] [Indexed: 11/09/2022] Open
Abstract
Classical cadherin Ca(2+)-dependent cell-cell adhesion proteins play key roles in embryogenesis and in maintaining tissue integrity. Cadherins mediate robust adhesion by binding in multiple conformations. One of these adhesive states, called an X-dimer, forms catch bonds that strengthen and become longer lived in the presence of mechanical force. Here we use single-molecule force-clamp spectroscopy with an atomic force microscope along with molecular dynamics and steered molecular dynamics simulations to resolve the molecular mechanisms underlying catch bond formation and the role of Ca(2+) ions in this process. Our data suggest that tensile force bends the cadherin extracellular region such that they form long-lived, force-induced hydrogen bonds that lock X-dimers into tighter contact. When Ca(2+) concentration is decreased, fewer de novo hydrogen bonds are formed and catch bond formation is eliminated.
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143
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Zhao Y, Ashcroft B, Zhang P, Liu H, Sen S, Song W, Im J, Gyarfas B, Manna S, Biswas S, Borges C, Lindsay S. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling. NATURE NANOTECHNOLOGY 2014; 9:466-73. [PMID: 24705512 PMCID: PMC4047173 DOI: 10.1038/nnano.2014.54] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 02/18/2014] [Indexed: 05/18/2023]
Abstract
The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic 'fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore.
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Affiliation(s)
- Yanan Zhao
- 1] Department of Physics, Arizona State University, PO Box 871504 Tempe, Arizona 85287, USA [2] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [3]
| | - Brian Ashcroft
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2]
| | - Peiming Zhang
- Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA
| | - Hao Liu
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Suman Sen
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Weisi Song
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - JongOne Im
- 1] Department of Physics, Arizona State University, PO Box 871504 Tempe, Arizona 85287, USA [2] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA
| | - Brett Gyarfas
- Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA
| | - Saikat Manna
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Sovan Biswas
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Chad Borges
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- 1] Department of Physics, Arizona State University, PO Box 871504 Tempe, Arizona 85287, USA [2] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [3] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
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144
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Rajan AC, Rezapour MR, Yun J, Cho Y, Cho WJ, Min SK, Lee G, Kim KS. Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition. ACS NANO 2014; 8:1827-1833. [PMID: 24446806 DOI: 10.1021/nn4062148] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.
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Affiliation(s)
- Arunkumar Chitteth Rajan
- Department of Chemistry and ‡Department of Physics, Pohang University of Science and Technology , Pohang 790-784, Korea
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145
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Yokota K, Tsutsui M, Taniguchi M. Electrode-embedded nanopores for label-free single-molecule sequencing by electric currents. RSC Adv 2014. [DOI: 10.1039/c4ra00933a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Electrode-embedded nanopores have been developed to realize label-free, low-cost, and high-throughput DNA sequencers.
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Affiliation(s)
- Kazumichi Yokota
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki, Japan
| | - Makusu Tsutsui
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki, Japan
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146
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Bui PT, Nishino T. Electron transfer through coordination bond interaction between single molecules: conductance switching by a metal ion. Phys Chem Chem Phys 2014; 16:5490-4. [DOI: 10.1039/c4cp00051j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal-coordination bond interaction within molecular junctions was revealed to significantly facilitate electron transfer between single molecules. Such facilitation was utilized to construct bistable molecular switches activated by a single metal ion.
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Affiliation(s)
- Phuc Tan Bui
- Department of Materials Science
- Osaka Prefecture University
- Sakai, Japan
| | - Tomoaki Nishino
- Department of Applied Chemistry
- Osaka Prefecture University
- Sakai, Japan
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147
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Krishnakumar P, Gyarfas B, Song W, Sen S, Zhang P, Krstić P, Lindsay S. Slowing DNA translocation through a nanopore using a functionalized electrode. ACS NANO 2013; 7:10319-26. [PMID: 24161197 PMCID: PMC3875158 DOI: 10.1021/nn404743f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanopores were fabricated with an integrated microscale Pd electrode coated with either a hydrogen-bonding or hydrophobic monolayer. Bare pores, or those coated with octanethiol, translocated single-stranded DNA with times of a few microseconds per base. Pores functionalized with 4(5)-(2-mercaptoethyl)-1H-imidazole-2-carboxamide slowed average translocation times, calculated as the duration of the event divided by the number of bases translocated, to about 100 μs per base at biases in the range of 50 to 80 mV.
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Affiliation(s)
- Padmini Krishnakumar
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Brett Gyarfas
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Weisi Song
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Suman Sen
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
| | - Peiming Zhang
- Department of Physics, Arizona State University, Tempe, AZ 85287
| | - Predrag Krstić
- Joint Institute of Computational Science, University of Tennessee, Oak Ridge, TN 37831
- TheoretiK, Knoxville, TN 37921, USA
| | - Stuart Lindsay
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
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148
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Belkin M, Maffeo C, Wells DB, Aksimentiev A. Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores. ACS NANO 2013; 7:6816-24. [PMID: 23876013 PMCID: PMC3812943 DOI: 10.1021/nn403575n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated via a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4-8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA.
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149
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Chen X. Theoretical electrical conductivity of hydrogen-bonded benzamide-derived molecules and single DNA bases. J Biol Phys 2013; 39:607-24. [PMID: 23996406 DOI: 10.1007/s10867-013-9321-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022] Open
Abstract
A benzamide molecule is used as a "reader" molecule to form hydrogen bonds with five single DNA bases, i.e., four normal single DNA bases A,T,C,G and one for 5methylC. The whole molecule is then attached to the gold surface so that a meta-molecule junction is formed. We calculate the transmission function and conductance for the five metal-molecule systems, with the implementation of density functional theory-based non-equilibrium Green function method. Our results show that each DNA base exhibits a unique conductance and most of them are on the pS level. The distinguishable conductance of each DNA base provides a way for the fast sequencing of DNA. We also investigate the dependence of conductivity of such a metal-molecule system on the hydrogen bond length between the "reader" molecule and DNA base, which shows that conductance follows an exponential decay as the hydrogen bond length increases, i.e., the conductivity is highly sensitive to the change in hydrogen bond length.
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Affiliation(s)
- Xiang Chen
- Department of Physics, Center for Biological Physics Arizona State University, Tempe, AZ 85287-1504, USA.
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150
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Liang F, Lindsay S, Zhang P. 1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling. Org Biomol Chem 2013; 10:8654-9. [PMID: 23038027 DOI: 10.1039/c2ob26529j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A : T and G : C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs.
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Affiliation(s)
- Feng Liang
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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