151
|
Kasianowicz JJ, Reiner JE, Robertson JWF, Henrickson SE, Rodrigues C, Krasilnikov OV. Detecting and characterizing individual molecules with single nanopores. Methods Mol Biol 2012; 870:3-20. [PMID: 22528255 DOI: 10.1007/978-1-61779-773-6_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Single-nanometer-scale pores have demonstrated the capability for the detection, identification, and characterization of individual molecules. This measurement method could soon extend the existing commercial instrumentation or provide solutions to niche applications in many fields, including health care and the basic sciences. However, that paradigm shift requires a significantly better understanding of the physics and chemistry that govern the interactions between nanopores and analytes. We describe herein some of our methods and approaches to address this issue.
Collapse
Affiliation(s)
- John J Kasianowicz
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
| | | | | | | | | | | |
Collapse
|
152
|
Single-molecule electrical random resequencing of DNA and RNA. Sci Rep 2012; 2:501. [PMID: 22787559 PMCID: PMC3392642 DOI: 10.1038/srep00501] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 06/22/2012] [Indexed: 11/08/2022] Open
Abstract
Two paradigm shifts in DNA sequencing technologies—from bulk to single molecules and from optical to electrical detection—are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5′-UGAGGUA-3′ from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes.
Collapse
|
153
|
Tian Y, Wen L, Hou X, Hou G, Jiang L. Bioinspired Ion-Transport Properties of Solid-State Single Nanochannels and Their Applications in Sensing. Chemphyschem 2012; 13:2455-70. [DOI: 10.1002/cphc.201200057] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Indexed: 12/27/2022]
|
154
|
Abstract
Much more than ever, nucleic acids are recognized as key building blocks in many of life's processes, and the science of studying these molecular wonders at the single-molecule level is thriving. A new method of doing so has been introduced in the mid 1990's. This method is exceedingly simple: a nanoscale pore that spans across an impermeable thin membrane is placed between two chambers that contain an electrolyte, and voltage is applied across the membrane using two electrodes. These conditions lead to a steady stream of ion flow across the pore. Nucleic acid molecules in solution can be driven through the pore, and structural features of the biomolecules are observed as measurable changes in the trans-membrane ion current. In essence, a nanopore is a high-throughput ion microscope and a single-molecule force apparatus. Nanopores are taking center stage as a tool that promises to read a DNA sequence, and this promise has resulted in overwhelming academic, industrial, and national interest. Regardless of the fate of future nanopore applications, in the process of this 16-year-long exploration, many studies have validated the indispensability of nanopores in the toolkit of single-molecule biophysics. This review surveys past and current studies related to nucleic acid biophysics, and will hopefully provoke a discussion of immediate and future prospects for the field.
Collapse
Affiliation(s)
- Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, United States.
| |
Collapse
|
155
|
Transverse electric field dragging of DNA in a nanochannel. Sci Rep 2012; 2:394. [PMID: 22558512 PMCID: PMC3342585 DOI: 10.1038/srep00394] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 04/23/2012] [Indexed: 11/08/2022] Open
Abstract
Nanopore analysis is an emerging single-molecule strategy for non-optical and high-throughput DNA sequencing, the principle of which is based on identification of each constituent nucleobase by measuring trans-membrane ionic current blockade or transverse tunnelling current as it moves through the pore. A crucial issue for nanopore sequencing is the fact that DNA translocates a nanopore too fast for addressing sequence with a single base resolution. Here we report that a transverse electric field can be used to slow down the translocation. We find 400-fold decrease in the DNA translocation speed by adding a transverse field of 10 mV/nm in a gold-electrode-embedded silicon dioxide channel. The retarded flow allowed us to map the local folding pattern in individual DNA from trans-pore ionic current profiles. This field dragging approach may provide a new way to control the polynucleotide translocation kinetics.
Collapse
|
156
|
Sen YH, Jain T, Aguilar CA, Karnik R. Enhanced discrimination of DNA molecules in nanofluidic channels through multiple measurements. LAB ON A CHIP 2012; 12:1094-101. [PMID: 22298224 PMCID: PMC3341097 DOI: 10.1039/c2lc20771k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nanofluidic sensing elements have been the focus of recent experiments for numerous applications ranging from nucleic acid fragment sizing to single-molecule DNA sequencing. These applications critically rely on high measurement fidelity, and methods to increase resolution are required. Herein, we describe fabrication and testing of a nanochannel device that enhances measurement resolution by performing multiple measurements (>100) on single DNA molecules. The enhanced measurement resolution enabled length discrimination between a mixture of λ-DNA (48.5 kbp) and T7 DNA (39.9 kbp) molecules, which were detected as transient current changes during translocation of the molecules through the nanochannel. As long DNA molecules are difficult to resolve quickly and with high fidelity with conventional electrophoresis, this approach may yield potentially portable, direct electrical sizing of DNA fragments with high sensitivity and resolution.
Collapse
Affiliation(s)
- Yi-Heng Sen
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Tarun Jain
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Rohit Karnik
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
157
|
Raillon C, Cousin P, Traversi F, Garcia-Cordero E, Hernandez N, Radenovic A. Nanopore detection of single molecule RNAP-DNA transcription complex. NANO LETTERS 2012; 12:1157-1164. [PMID: 22372476 DOI: 10.1021/nl3002827] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In the past decade, a number of single-molecule methods have been developed with the aim of investigating single protein and nucleic acid interactions. For the first time we use solid-state nanopore sensing to detect a single E. coli RNAP-DNA transcription complex and single E. coli RNAP enzyme. On the basis of their specific conductance translocation signature, we can discriminate and identify between those two types of molecular translocations and translocations of bare DNA. This opens up a new perspectives for investigating transcription processes at the single-molecule level.
Collapse
Affiliation(s)
- C Raillon
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | | | | | | | | | | |
Collapse
|
158
|
Li Q, Zhao Q, Lu B, Zhang H, Liu S, Tang Z, Qu L, Zhu R, Zhang J, You L, Yang F, Yu D. Size evolution and surface characterization of solid-state nanopores in different aqueous solutions. NANOSCALE 2012; 4:1572-1576. [PMID: 22314312 DOI: 10.1039/c2nr12040b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The stability and surface evolution of solid-state nanopores in aqueous solutions are extremely important since they would get immersed in solutions during DNA translocation experiment for DNA analyses. In this work, we systematically studied the size evolution of SiN nanopores in ethanol, deionized water and potassium chloride (KCl) solutions by careful surface characterization and composition analyses using a transmission electron microscope. Surprisingly, we found that nanopores closed up completely in ethanol in an hour and showed a 30% and 20% size decrease in deionized water and KCl solutions, respectively. Strong evidence of surface oxidation was found by composition analyses in the nanopore area. Nanopore size evolution was strongly dependent on initial pore size and solution pH value. In pH = 13 KCl solution, SiN nanopores were observed to increase in size instead of decrease. The results not only provide useful information for DNA detection based on solid-state nanopores, but can also guide design and application of other nanodevices exposed to electrolyte-solvent systems such as cell-on-a-chip devices and biosensors.
Collapse
Affiliation(s)
- Qingtao Li
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
159
|
Edmonds CM, Hudiono YC, Ahmadi AG, Hesketh PJ, Nair S. Polymer translocation in solid-state nanopores: Dependence of scaling behavior on pore dimensions and applied voltage. J Chem Phys 2012; 136:065105. [DOI: 10.1063/1.3682777] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
160
|
Melnikov DV, Nikolaev A, Leburton JP, Gracheva ME. Polymer translocation through an electrically tunable nanopore in a multilayered semiconductor membrane. Methods Mol Biol 2012; 870:187-207. [PMID: 22528265 DOI: 10.1007/978-1-61779-773-6_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have developed a two-level computational model that enables us to calculate electrostatic fields created by a semiconductor membrane submerged in electrolytic solution and investigate the effects of these fields on the dynamics of a polymer translocating through a nanopore in the membrane. In order to calculate the electrostatic potentials and the ionic concentrations in a solid-state nanopore, we have self-consistently solved Poisson equation within the semiclassical approximation for charge carrier statistics in the membrane and electrolyte. The electrostatic potentials obtained from these simulations are then used in conjunction with Langevin (Brownian) dynamics to model polymer translocation through the nanopore. In this work, we consider single-stranded DNA (ssDNA) translocation through semiconductor membranes consisting of heavily doped p- and n-layers of silicon forming a pn-junction which is capable of creating strong electric fields. We show that the membrane electric field controls dynamics of a biomolecule inside the channel, to either momentarily trap it, slow it down, or allow it to translocate at will.
Collapse
|
161
|
Di Ventra M, Krems M, Wilson J, Pershin YV. DNA characterization by transverse electrical current in a nanochannel. Methods Mol Biol 2012; 870:149-63. [PMID: 22528263 DOI: 10.1007/978-1-61779-773-6_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We review an approach for the characterization of single-stranded DNA based on the statistical identification of single bases via transverse electronic transport while DNA translocates in a nanopore or nanochannel. We describe the theoretical methods used to demonstrate this method for experimentally realizable systems and discuss the different physical processes involved. Recent experimental reports have shown the validity of this approach, although further work is necessary to make this a practical fast sequencing tool.
Collapse
|
162
|
Abstract
Solid-state nanopores are emerging as robust single molecule electronic measurement devices and as platforms for confining biomolecules for further analysis. The first silicon nitride nanopore to detect individual DNA molecules was fabricated using ion beam sculpting (IBS), a method that uses broad, low-energy ion beams to create nanopores with dimensions ranging from 2 to 20 nm. In this chapter, we discuss the fabrication, characterization, and use of IBS-sculpted nanopores as well as efficient uses of pClamp and MATLAB software suites for data acquisition and analysis. The fabrication section covers the repeatability and the pore size limits. The characterization discussion focuses on the geometric properties as measured by low- and high-resolution transmission electron microscopy (TEM), electron energy loss spectroscopy, and energy-filtered TEM. The section on translocation experiments focuses on how to use tools commonly available to the nanopore experimenter to determine whether a pore will be useful for experimentation or if it should be abandoned. A memory-efficient method of taking data using Clampex's event-driven mode and dual-channel recording is presented, followed by an easy-to-implement multithreshold event detection and classification method using MATLAB software.
Collapse
Affiliation(s)
- Ryan C. Rollings
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| | - David S. McNabb
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jiali Li
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| |
Collapse
|
163
|
Ellis JS, Strutwolf J, Arrigan DWM. Finite-element simulations of the influence of pore wall adsorption on cyclic voltammetry of ion transfer across a liquid–liquid interface formed at a micropore. Phys Chem Chem Phys 2012; 14:2494-500. [DOI: 10.1039/c2cp23052f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
164
|
Hall AR, Keegstra JM, Duch MC, Hersam MC, Dekker C. Measuring single-wall carbon nanotubes with solid-state nanopores. Methods Mol Biol 2012; 870:227-239. [PMID: 22528267 DOI: 10.1007/978-1-61779-773-6_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Solid-state nanopores have been used widely to study biological polymers. Here, we expand the technique to analyze single-wall carbon nanotubes. By wrapping them in an amphiphilic layer, individual tubes can be translocated electrically through a nanopore, resulting in temporary interruptions in the trans-pore current reminiscent of measurements on DNA, RNA, and proteins. The technique may find use in discriminating nanotubes by size and thus electrical structure, facilitating their inclusion in electrical devices.
Collapse
Affiliation(s)
- Adam R Hall
- Kavli Institute of Nanoscience, Delft Technical University, Delft, The Netherlands
| | | | | | | | | |
Collapse
|
165
|
Biomimetic nanopores: learning from and about nature. Trends Biotechnol 2011; 29:607-14. [DOI: 10.1016/j.tibtech.2011.07.006] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 07/29/2011] [Accepted: 07/29/2011] [Indexed: 11/23/2022]
|
166
|
Sathe C, Zou X, Leburton JP, Schulten K. Computational investigation of DNA detection using graphene nanopores. ACS NANO 2011; 5:8842-51. [PMID: 21981556 PMCID: PMC3222720 DOI: 10.1021/nn202989w] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nanopore-based single-molecule detection and analysis have been pursued intensively over the past decade. One of the most promising applications in this regard is DNA sequencing achieved through DNA translocation-induced blockades in ionic current. Recently, nanopores fabricated in graphene sheets were used to detect double-stranded DNA. Due to its subnanometer thickness, graphene nanopores show great potential to realize DNA sequencing at single-base resolution. Resolving at the atomic level electric field-driven DNA translocation through graphene nanopores is crucial to guide the design of graphene-based sequencing devices. Molecular dynamics simulations, in principle, can achieve such resolution and are employed here to investigate the effects of applied voltage, DNA conformation, and sequence as well as pore charge on the translocation characteristics of DNA. We demonstrate that such simulations yield current characteristics consistent with recent measurements and suggest that under suitable bias conditions A-T and G-C base pairs can be discriminated using graphene nanopores.
Collapse
|
167
|
Luan B, Martyna G, Stolovitzky G. Characterizing and controlling the motion of ssDNA in a solid-state nanopore. Biophys J 2011; 101:2214-22. [PMID: 22067161 DOI: 10.1016/j.bpj.2011.08.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 08/23/2011] [Accepted: 08/25/2011] [Indexed: 10/15/2022] Open
Abstract
Sequencing DNA in a synthetic solid-state nanopore is potentially a low-cost and high-throughput method. Essential to the nanopore-based DNA sequencing method is the ability to control the motion of a single-stranded DNA (ssDNA) molecule at single-base resolution. Experimental studies showed that the average translocation speed of DNA driven by a biasing electric field can be affected by ionic concentration, solvent viscosity, or temperature. Even though it is possible to slow down the average translocation speed, instantaneous motion of DNA is too diffusive to allow each DNA base to stay in front of a sensor site for its measurement. Using extensive all-atom molecular dynamics simulations, we study the diffusion constant, friction coefficient, electrophoretic mobility, and effective charge of ssDNA in a solid-state nanopore. Simulation results show that the spatial fluctuation of ssDNA in 1 ns is comparable to the spacing between neighboring nucleotides in ssDNA, which makes the sensing of a DNA base very difficult. We demonstrate that the recently proposed DNA transistor could potentially solve this problem by electrically trapping ssDNA inside the DNA transistor and ratcheting ssDNA base-by-base in a biasing electric field. When increasing the biasing electric field, we observed that the translocation of ssDNA changes from ratcheting to steady-sliding. The simulated translocation of ssDNA in the DNA transistor was theoretically characterized using Fokker-Planck analysis.
Collapse
Affiliation(s)
- Binquan Luan
- IBM T. J. Watson Research Center, Yorktown Heights, New York, USA.
| | | | | |
Collapse
|
168
|
Lu B, Albertorio F, Hoogerheide DP, Golovchenko JA. Origins and consequences of velocity fluctuations during DNA passage through a nanopore. Biophys J 2011; 101:70-9. [PMID: 21723816 DOI: 10.1016/j.bpj.2011.05.034] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 05/09/2011] [Accepted: 05/13/2011] [Indexed: 10/18/2022] Open
Abstract
We describe experiments and modeling results that reveal and explain the distribution of times that identical double-stranded DNA (dsDNA) molecules take to pass through a voltage-biased solid-state nanopore. We show that the observed spread in this distribution is caused by viscous-drag-induced velocity fluctuations that are correlated with the initial conformation of nanopore-captured molecules. This contribution exceeds that due to diffusional Brownian motion during the passage. Nevertheless, and somewhat counterintuitively, the diffusional Brownian motion determines the fundamental limitations of rapid DNA strand sequencing with a nanopore. We model both diffusional and conformational fluctuations in a Langevin description. It accounts well for passage time variations for DNA molecules of different lengths, and predicts conditions required for low-error-rate nanopore-strand DNA sequencing with nanopores.
Collapse
Affiliation(s)
- Bo Lu
- Department of Physics, Harvard University, Cambridge, Massachusetts, USA
| | | | | | | |
Collapse
|
169
|
de Zoysa RSS, Krishantha DMM, Zhao Q, Gupta J, Guan X. Translocation of single-stranded DNA through the α-hemolysin protein nanopore in acidic solutions. Electrophoresis 2011; 32:3034-41. [PMID: 21997574 DOI: 10.1002/elps.201100216] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 06/02/2011] [Accepted: 06/09/2011] [Indexed: 11/12/2022]
Abstract
The effect of acidic pH on the translocation of single-stranded DNA through the α-hemolysin pore is investigated. Two significantly different types of events, i.e. deep blockades and shallow blockades, are observed at low pH. The residence times of the shallow blockades are not significantly different from those of the DNA translocation events obtained at or near physiological pH, whereas the deep blockades have much larger residence times and blockage amplitudes. With a decrease in the pH of the electrolyte solution, the percentage of the deep blockades in the total events increases. Furthermore, the mean residence time of these long-lived events is dependent on the length of DNA, and also varies with the nucleotide base, suggesting that they are appropriate for use in DNA analysis. In addition to being used as an effective approach to affect DNA translocation in the nanopore, manipulation of the pH of the electrolyte solution provides a potential means to greatly enhance the sensitivity of nanopore stochastic sensing.
Collapse
Affiliation(s)
- Ranulu S S de Zoysa
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019-0065, USA
| | | | | | | | | |
Collapse
|
170
|
Ali M, Nasir S, Nguyen QH, Sahoo JK, Tahir MN, Tremel W, Ensinger W. Metal Ion Affinity-based Biomolecular Recognition and Conjugation inside Synthetic Polymer Nanopores Modified with Iron–Terpyridine Complexes. J Am Chem Soc 2011; 133:17307-14. [DOI: 10.1021/ja205042t] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mubarak Ali
- Technische Universität Darmstadt, Department of Material- and Geo-Sciences, Petersenstrasse 23, D-64287 Darmstadt, Germany
- Materials Research Department, GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Saima Nasir
- Technische Universität Darmstadt, Department of Material- and Geo-Sciences, Petersenstrasse 23, D-64287 Darmstadt, Germany
- Materials Research Department, GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Quoc Hung Nguyen
- Technische Universität Darmstadt, Department of Material- and Geo-Sciences, Petersenstrasse 23, D-64287 Darmstadt, Germany
- Materials Research Department, GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Jugal Kishore Sahoo
- Department of Chemistry, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55099 Mainz, Germany
| | - Muhammad Nawaz Tahir
- Department of Chemistry, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55099 Mainz, Germany
| | - Wolfgang Tremel
- Department of Chemistry, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55099 Mainz, Germany
| | - Wolfgang Ensinger
- Technische Universität Darmstadt, Department of Material- and Geo-Sciences, Petersenstrasse 23, D-64287 Darmstadt, Germany
- Materials Research Department, GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| |
Collapse
|
171
|
Shendure JA, Porreca GJ, Church GM, Gardner AF, Hendrickson CL, Kieleczawa J, Slatko BE. Overview of DNA Sequencing Strategies. ACTA ACUST UNITED AC 2011; Chapter 7:Unit7.1. [DOI: 10.1002/0471142727.mb0701s96] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jay A. Shendure
- Department of Genome Sciences, University of Washington Seattle Washington
| | | | - George M. Church
- Department of Genetics, Harvard Medical School Boston Massachusetts
| | | | | | | | | |
Collapse
|
172
|
Mondaini F, Moriconi L. Markov chain modeling of polymer translocation through pores. J Chem Phys 2011; 135:114902. [PMID: 21950882 DOI: 10.1063/1.3637039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We solve the Chapman-Kolmogorov equation and study the exact splitting probabilities of the general stochastic process which describes polymer translocation through membrane pores within the broad class of Markov chains. Transition probabilities, which satisfy a specific balance constraint, provide a refinement of the Chuang-Kantor-Kardar relaxation picture of translocation, allowing us to investigate finite size effects in the evaluation of dynamical scaling exponents. We find that (i) previous Langevin simulation results can be recovered only if corrections to the polymer mobility exponent are taken into account and (ii) the dynamical scaling exponents have a slow approach to their predicted asymptotic values as the polymer's length increases. We also address, along with strong support from additional numerical simulations, a critical discussion which points in a clear way the viability of the Markov chain approach put forward in this work.
Collapse
Affiliation(s)
- Felipe Mondaini
- Instituto de Física, Universidade Federal do Rio de Janeiro, C.P. 68528, Rio de Janeiro, 21945-970 RJ, Brazil
| | | |
Collapse
|
173
|
van den Hout M, Skinner GM, Klijnhout S, Krudde V, Dekker NH. The passage of homopolymeric RNA through small solid-state nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:2217-2224. [PMID: 21638785 DOI: 10.1002/smll.201100265] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 03/14/2011] [Indexed: 05/30/2023]
Abstract
Solid-state nanopores are widely acknowledged as tools with which to study local structure in biological molecules. Individual molecules are forced through a nanopore, causing a characteristic change in an ionic current that depends on the molecules' local diameter and charge distribution. Here, the translocation measurements of long (~5-30 kilobases) single-stranded poly(U) and poly(A) molecules through nanopores ranging from 1.5 to 8 nm in diameter are presented. Individual molecules are found to be able to cause multiple levels of conductance blockade upon traversing the pore. By analyzing these conductance blockades and their relative incidence as a function of nanopore diameter, it is concluded that the smallest conductance blockades likely correspond to molecules that translocate through the pore in predominantly head-to-tail fashion. The larger conductance blockades are likely caused by molecules that arrive at the nanopore entrance with many strands simultaneously. These measurements constitute the first demonstration that single-stranded RNA can be captured in solid-state nanopores that are smaller than the diameter of double-stranded RNA. These results further the understanding of the conductance blockades caused by nucleic acids in solid-state nanopores, relevant for future applications, such as the direct determination of RNA secondary structure.
Collapse
Affiliation(s)
- Michiel van den Hout
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | | | | | | | | |
Collapse
|
174
|
Fyta M, Melchionna S, Succi S. Translocation of biomolecules through solid-state nanopores: Theory meets experiments. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/polb.22284] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
175
|
Freedman KJ, Jürgens M, Prabhu A, Ahn CW, Jemth P, Edel JB, Kim MJ. Chemical, Thermal, and Electric Field Induced Unfolding of Single Protein Molecules Studied Using Nanopores. Anal Chem 2011; 83:5137-44. [DOI: 10.1021/ac2001725] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Maike Jürgens
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Chi Won Ahn
- NEMS-BIO Team, National Nanofab Center, Deajeon, Korea
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Joshua B. Edel
- Department of Chemistry, Imperial College London, South Kensington, London, United Kingdom
| | | |
Collapse
|
176
|
Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE. Landscape of next-generation sequencing technologies. Anal Chem 2011; 83:4327-41. [PMID: 21612267 DOI: 10.1021/ac2010857] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
177
|
Asghar W, Ilyas A, Billo JA, Iqbal SM. Shrinking of Solid-state Nanopores by Direct Thermal Heating. NANOSCALE RESEARCH LETTERS 2011; 6:372. [PMID: 21711885 PMCID: PMC3211463 DOI: 10.1186/1556-276x-6-372] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 05/04/2011] [Indexed: 05/28/2023]
Abstract
Solid-state nanopores have emerged as useful single-molecule sensors for DNA and proteins. A novel and simple technique for solid-state nanopore fabrication is reported here. The process involves direct thermal heating of 100 to 300 nm nanopores, made by focused ion beam (FIB) milling in free-standing membranes. Direct heating results in shrinking of the silicon dioxide nanopores. The free-standing silicon dioxide membrane is softened and adatoms diffuse to a lower surface free energy. The model predicts the dynamics of the shrinking process as validated by experiments. The method described herein, can process many samples at one time. The inbuilt stress in the oxide film is also reduced due to annealing. The surface composition of the pore walls remains the same during the shrinking process. The linear shrinkage rate gives a reproducible way to control the diameter of a pore with nanometer precision.
Collapse
Affiliation(s)
- Waseem Asghar
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
- Nanotechnology Research and Teaching Facility, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Azhar Ilyas
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
- Nanotechnology Research and Teaching Facility, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Joseph Anthony Billo
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
- Nanotechnology Research and Teaching Facility, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Samir Muzaffar Iqbal
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
- Nanotechnology Research and Teaching Facility, University of Texas at Arlington, Arlington, TX 76019, USA
- Joint Graduate Committee of Bioengineering Program, University of Texas at Arlington and University of Texas Southwestern Medical Center at Dallas, University of Texas at Arlington, Arlington, TX 76019, USA
| |
Collapse
|
178
|
Nikolaev A, Gracheva ME. Simulation of ionic current through the nanopore in a double-layered semiconductor membrane. NANOTECHNOLOGY 2011; 22:165202. [PMID: 21393823 DOI: 10.1088/0957-4484/22/16/165202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We study the effects of different nanopore geometries (double-conical, single-conical, cylindrical) on the electrostatic potential distribution and ionic conductivity in a double-layered semiconductor nanopore device as functions of the applied membrane bias. Ionic current-voltage characteristics as well as their rectification ratios are calculated using a simple ion transport model. Based on our calculations, we find that the double-layered semiconductor membrane with a single-conical nanopore with a narrow opening in the n-Si layer exhibits the largest range of available potential variations in the pore and, thus, may be better suited for control of polymer translocation through the nanopore.
Collapse
Affiliation(s)
- Alexey Nikolaev
- Department of Physics, Clarkson University, Potsdam, NY 13699, USA
| | | |
Collapse
|
179
|
Patterson N, Hodges VC, Vasile MJ, Adams DP, Chen Z, Brinker CJ. Direct Focused Ion Beam Drilling of Nanopores. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-983-0983-ll05-05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractFocused 30keV gallium ion beam, single-pixel drilling combined with backside particle detection is used to fabricate pores having exit diameters as small as ~11 nm in 200 nm-thick silicon nitride membranes. The backside channelplate detector response obtained about the onset of breakthrough is interpreted by plan-view transmission electron microscopy investigations of hole morphology. Immediately prior to breakthrough, there is a rise in detector signal as the local membrane thickness is reduced. This likely occurs as a result of ion transmission and, possibly, forward sputtering. At the dose required for breakthrough a maximum detector signal is obtained thus providing a potential method for end point detection. The focused ion drilling technique avoids broad area beam exposure methods that are often used to reduce hole diameter to nanometer dimension. In addition, the current approach overcomes difficulties in determining a required dose for breakthrough such as those that arise from an inhomogeneous membrane thickness, redeposition, or ion channeling.
Collapse
|
180
|
Holden DA, Hendrickson G, Lyon LA, White HS. Resistive Pulse Analysis of Microgel Deformation During Nanopore Translocation. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2011; 115:2999-3004. [PMID: 27347278 PMCID: PMC4920357 DOI: 10.1021/jp111244v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Deformation of 570-nm radius poly(N-isopropylacrylamide-co-acrylic acid) microgels passing through individual 375- to 915-nm radius nanopores in glass has been investigated by the resistive-pulse method. Particle translocation through nanopores of dimensions smaller than the microgel yields electrical signatures reflecting the dynamics of microgel deformation. Translocation rates, and event duration and peak shape, are functions of the conductivities of microgel and electrolyte. Our results demonstrate that nanopore resistive-pulse methods provide new fundamental insights into microgel permeation through porous membranes.
Collapse
Affiliation(s)
- Deric A. Holden
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112
| | - Grant Hendrickson
- Georgia Institute of Technology, School of Chemistry and Biochemistry and Petit Institute for Bioengineering & Bioscience, 901 Atlantic Drive, NW, Atlanta, GA 30332-0400
| | - L. Andrew Lyon
- Georgia Institute of Technology, School of Chemistry and Biochemistry and Petit Institute for Bioengineering & Bioscience, 901 Atlantic Drive, NW, Atlanta, GA 30332-0400
| | - Henry S. White
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112
| |
Collapse
|
181
|
Holden DA, Hendrickson G, Lyon LA, White HS. Resistive Pulse Analysis of Microgel Deformation During Nanopore Translocation. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2011. [PMID: 27347278 DOI: 10.1021/jp204839j] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Deformation of 570-nm radius poly(N-isopropylacrylamide-co-acrylic acid) microgels passing through individual 375- to 915-nm radius nanopores in glass has been investigated by the resistive-pulse method. Particle translocation through nanopores of dimensions smaller than the microgel yields electrical signatures reflecting the dynamics of microgel deformation. Translocation rates, and event duration and peak shape, are functions of the conductivities of microgel and electrolyte. Our results demonstrate that nanopore resistive-pulse methods provide new fundamental insights into microgel permeation through porous membranes.
Collapse
Affiliation(s)
- Deric A Holden
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112
| | - Grant Hendrickson
- Georgia Institute of Technology, School of Chemistry and Biochemistry and Petit Institute for Bioengineering & Bioscience, 901 Atlantic Drive, NW, Atlanta, GA 30332-0400
| | - L Andrew Lyon
- Georgia Institute of Technology, School of Chemistry and Biochemistry and Petit Institute for Bioengineering & Bioscience, 901 Atlantic Drive, NW, Atlanta, GA 30332-0400
| | - Henry S White
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112
| |
Collapse
|
182
|
Rincon-Restrepo M, Mikhailova E, Bayley H, Maglia G. Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes. NANO LETTERS 2011; 11:746-50. [PMID: 21222450 PMCID: PMC3391008 DOI: 10.1021/nl1038874] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Protein nanopores may provide a cheap and fast technology to sequence individual DNA molecules. However, the electrophoretic translocation of ssDNA molecules through protein nanopores has been too rapid for base identification. Here, we show that the translocation of DNA molecules through the α-hemolysin protein nanopore can be slowed controllably by introducing positive charges into the lumen of the pore by site directed mutagenesis. Although the residual ionic current during DNA translocation is insufficient for direct base identification, we propose that the engineered pores might be used to slow down DNA in hybrid systems, for example, in combination with solid-state nanopores.
Collapse
|
183
|
Ali M, Tahir MN, Siwy Z, Neumann R, Tremel W, Ensinger W. Hydrogen Peroxide Sensing with Horseradish Peroxidase-Modified Polymer Single Conical Nanochannels. Anal Chem 2011; 83:1673-80. [DOI: 10.1021/ac102795a] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Mubarak Ali
- Technische Universität Darmstadt, Fachbereich Material-u. Geowissenschaften, Fachgebiet Materialanalytik, Petersenstrasse 23, D-64287 Darmstadt, Germany
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Muhammad Nawaz Tahir
- Department of Chemistry, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55099 Mainz, Germany
| | - Zuzanna Siwy
- Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Reinhard Neumann
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Wolfgang Tremel
- Department of Chemistry, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55099 Mainz, Germany
| | - Wolfgang Ensinger
- Technische Universität Darmstadt, Fachbereich Material-u. Geowissenschaften, Fachgebiet Materialanalytik, Petersenstrasse 23, D-64287 Darmstadt, Germany
| |
Collapse
|
184
|
Sanmiguel P. Next-generation sequencing and potential applications in fungal genomics. Methods Mol Biol 2011; 722:51-60. [PMID: 21590412 DOI: 10.1007/978-1-61779-040-9_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the first fungal genome was sequenced in 1996, sequencing technologies have advanced dramatically. In recent years, it has become possible to cost-effectively generate vast amounts of DNA sequence data using a number of cell- and electrophoresis-free sequencing technologies, commonly known as "next" or "second" generation. In this chapter, we present a brief overview of next-generation sequencers that are commercially available now. Their potential applications in fungal genomics studies are discussed.
Collapse
Affiliation(s)
- Phillip Sanmiguel
- Purdue Genomics Core Facility, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
185
|
Zhou K, Perry JM, Jacobson SC. Transport and sensing in nanofluidic devices. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:321-41. [PMID: 21456970 DOI: 10.1146/annurev-anchem-061010-113938] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Ion transport and sensing in nanofluidic devices are receiving a great deal of attention because of their unique transport properties and potential analytical applications. Some aspects of microscale transport transfer directly to the nanoscale, but nanofluidic systems can be significantly influenced by phenomena such as double-layer overlap, surface charge, ion-current rectification, diffusion, and entropic forces, which are either insignificant or absent in larger microchannels. Micro- and nanofabrication techniques create features with a wide range of well-defined geometries and dimensions in synthetic and solid-state substrates. Moreover, these techniques permit coupling of multiple nano- and microscale elements, which can execute various functions. We discuss basic nanofluidic architectures, material transport properties through single and multiple nanochannels, and characterization of single particles by resistive-pulse sensing.
Collapse
Affiliation(s)
- Kaimeng Zhou
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA
| | | | | |
Collapse
|
186
|
Schibel AEP, An N, Jin Q, Fleming AM, Burrows CJ, White HS. Nanopore detection of 8-oxo-7,8-dihydro-2'-deoxyguanosine in immobilized single-stranded DNA via adduct formation to the DNA damage site. J Am Chem Soc 2010; 132:17992-5. [PMID: 21138270 PMCID: PMC3021242 DOI: 10.1021/ja109501x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to detect DNA damage within the context of the surrounding sequence is an important goal in medical diagnosis and therapies, but there are no satisfactory methods available to detect a damaged base while providing sequence information. One of the most common base lesions is 8-oxo-7,8-dihydroguanine, which occurs during oxidation of guanine. In the work presented here, we demonstrate the detection of a single oxidative damage site using ion channel nanopore methods employing α-hemolysin. Hydantoin lesions produced from further oxidation of 8-oxo-7,8-dihydroguanine, as well as spirocyclic adducts produced from covalently attaching a primary amine to the spiroiminodihydantoin lesion, were detected by tethering the damaged DNA to streptavidin via a biotin linkage and capturing the DNA inside an α-hemolysin ion channel. Spirocyclic adducts, in both homo- and heteropolymer background single-stranded DNA sequences, produced current blockage levels differing by almost 10% from those of native base current blockage levels. These preliminary studies show the applicability of ion channel recordings not only for DNA sequencing, which has recently received much attention, but also for detecting DNA damage, which will be an important component to any sequencing efforts.
Collapse
Affiliation(s)
- Anna E. P. Schibel
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850
| | - Na An
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850
| | - Qian Jin
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850
| | - Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850
| | - Henry S. White
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850
| |
Collapse
|
187
|
Ali M, Neumann R, Ensinger W. Sequence-specific recognition of DNA oligomer using peptide nucleic acid (PNA)-modified synthetic ion channels: PNA/DNA hybridization in nanoconfined environment. ACS NANO 2010; 4:7267-74. [PMID: 21082785 DOI: 10.1021/nn102119q] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Here we demonstrate the design and construction of a simple, highly sensitive and selective nanofluidic sensing device, based on a single synthetic conical nanochannel for the sequence specific detection of single-stranded DNA oligonucleotides. The biosensing performance of the device depends sensitively on the surface charge and chemical groups incorporated on the inner channel wall that act as binding sites for different analytes. Uncharged peptide nucleic acid (PNA) probes are covalently immobilized on the channel surface through carbodiimide coupling chemistry. This diminishes the channel surface charge, leading to a significant decrease in the rectified ion current flowing through the channel. The PNA-modified channel acts as a highly specific and selective device for the detection of a complementary single-stranded DNA sequence. Upon PNA/DNA hybridization, the channel surface charge density increased due to the presence of the negatively charged DNA strand. The changes in the surface charge-dependent current-voltage (I-V) curves and rectification ratio of the channel confirm the success of immobilization and PNA/DNA hybridization within a confined space at the nanoscale. In addition, a control experiment indicated that the biosensor exhibits remarkable specificity toward a cDNA strand and also has the ability to discriminate single-base mismatch DNA sequences on the basis of rectified ion flux through the nanochannel. In this context, we envision that the single conical nanochannels functionalized with a PNA probe will provide a biosensing platform for the detection and discrimination of short single-stranded DNA oligomer of unknown sequence.
Collapse
Affiliation(s)
- Mubarak Ali
- Technische Universität Darmstadt, Fachbereich Material- u. Geowissenschaften, Fachgebiet Materialanalytik, Petersenstrasse 23, D-64287 Darmstadt, Germany.
| | | | | |
Collapse
|
188
|
Singer A, Kuhn H, Frank-Kamenetskii M, Meller A. Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454111. [PMID: 21339599 DOI: 10.1088/0953-8984/22/45/454111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The ability to detect and measure dsDNA thermal fluctuations is of immense importance in understanding the underlying mechanisms responsible for transcription and replication regulation. We describe here the ability of solid-state nanopores to detect sub-nanometer changes in DNA structure as a result of chemically enhanced thermal fluctuations. In this study, we investigate the subtle changes in the mean effective diameter of a dsDNA molecule with 3-5 nm solid-state nanopores as a function of urea concentration and the DNA's AT content. Our studies reveal an increase in the mean effective diameter of a DNA molecule of approximately 0.6 nm at 8.7 M urea. In agreement with the mechanism of DNA local denaturation, we observe a sigmoid dependence of these effects on urea concentration. We find that the translocation times in urea are markedly slower than would be expected if the dynamics were governed primarily by viscous effects. Furthermore, we find that the sensitivity of the nanopore is sufficient to statistically differentiate between DNA molecules of nearly identical lengths differing only in sequence and AT content when placed in 3.5 M urea. Our results demonstrate that nanopores can detect subtle structural changes and are thus a valuable tool for detecting differences in biomolecules' environment.
Collapse
Affiliation(s)
- Alon Singer
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | | | | |
Collapse
|
189
|
Abelow AE, Schepelina O, White RJ, Vallée-Bélisle A, Plaxco KW, Zharov I. Biomimetic glass nanopores employing aptamer gates responsive to a small molecule. Chem Commun (Camb) 2010; 46:7984-6. [PMID: 20865192 DOI: 10.1039/c0cc02649b] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the preparation of 20 and 65 nm radii glass nanopores whose surface is modified with DNA aptamers controlling the molecular transport through the nanopores in response to small molecule binding.
Collapse
Affiliation(s)
- Alexis E Abelow
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, USA
| | | | | | | | | | | |
Collapse
|
190
|
Nelson T, Zhang B, Prezhdo OV. Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device. NANO LETTERS 2010; 10:3237-42. [PMID: 20722409 DOI: 10.1021/nl9035934] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We report an ab initio density functional theory study of the interaction of four nucleobases, cytosine, thymine, adenine, and guanine, with a novel graphene nanopore device for detecting the base sequence of a single-stranded nucleic acid (ssDNA or RNA). The nucleobases were inserted into a pore in a graphene nanoribbon, and the electrical current and conductance spectra were calculated as functions of voltage applied across the nanoribbon. The conductance spectra and charge densities were analyzed in the presence of each nucleobase in the graphene nanopore. The results indicate that due to significant differences in the conductance spectra the proposed device has adequate sensitivity to discriminate between different nucleotides. Moreover, we show that the nucleotide conductance spectrum is affected little by its orientation inside the graphene nanopore. The proposed technique may be extremely useful for real applications in developing ultrafast, low-cost DNA sequencing methods.
Collapse
Affiliation(s)
- Tammie Nelson
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | | | | |
Collapse
|
191
|
George HB, Tang Y, Chen X, Li J, Hutchinson JW, Golovchenko JA, Aziz MJ. Nanopore fabrication in amorphous Si: Viscous flow model and comparison to experiment. JOURNAL OF APPLIED PHYSICS 2010; 108:14310. [PMID: 20680096 PMCID: PMC2912934 DOI: 10.1063/1.3452390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 05/19/2010] [Indexed: 05/06/2023]
Abstract
Nanopores fabricated in free-standing amorphous silicon thin films were observed to close under 3 keV argon ion irradiation. The closing rate, measured in situ, exhibited a memory effect: at the same instantaneous radius, pores that started larger close more slowly. An ion-stimulated viscous flow model is developed and solved in both a simple analytical approximation for the small-deformation limit and in a finite element solution for large deformations. The finite-element solution exhibits surprising changes in cross-section morphology, which may be extremely valuable for single biomolecule detection, and are untested experimentally. The finite-element solution reproduces the shape of the measured nanopore radius versus fluence behavior and the sign and magnitude of the measured memory effect. We discuss aspects of the experimental data not reproduced by the model, and successes and failures of the competing adatom diffusion model.
Collapse
|
192
|
Das AK, Hong PD. Forced translocation of polymer chains through a nanotube: A case of ultrafiltration. POLYMER 2010. [DOI: 10.1016/j.polymer.2010.03.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
193
|
Sexton LT, Mukaibo H, Katira P, Hess H, Sherrill SA, Horne LP, Martin CR. An Adsorption-Based Model for Pulse Duration in Resistive-Pulse Protein Sensing. J Am Chem Soc 2010; 132:6755-63. [DOI: 10.1021/ja100693x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lindsay T. Sexton
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Hitomi Mukaibo
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Parag Katira
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Henry Hess
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Stefanie A. Sherrill
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Lloyd P. Horne
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Charles R. Martin
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| |
Collapse
|
194
|
Kowalczyk SW, Tuijtel MW, Donkers SP, Dekker C. Unraveling single-stranded DNA in a solid-state nanopore. NANO LETTERS 2010; 10:1414-20. [PMID: 20235508 DOI: 10.1021/nl100271c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Solid-state nanopores are an emerging class of single-molecule sensors. Whereas most studies so far focused on double-stranded DNA (dsDNA) molecules, exploration of single-stranded DNA (ssDNA) is of great interest as well, for example to employ such a nanopore device to read out the sequence. Here, we study the translocation of long random-sequence ssDNA through nanopores. Using atomic force microscopy, we observe the ssDNA to hybridize into a random coil, forming blobs of around 100 nm in diameter for 7 kb ssDNA. These large entangled structures have to unravel, when they arrive at the pore entrance. Indeed, we observe strong blockade events with a translocation time that is exponentially dependent on voltage, tau approximately e(-V/V(0)). Interestingly, this is very different than for dsDNA, for which tau approximately 1/V. We report translocations of ssDNA but also of ssDNA-dsDNA constructs where we compare the conductance-blockade levels for ssDNA versus dsDNA as a function of voltage.
Collapse
Affiliation(s)
- Stefan W Kowalczyk
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | | | | |
Collapse
|
195
|
Henrickson SE, DiMarzio EA, Wang Q, Stanford VM, Kasianowicz JJ. Probing single nanometer-scale pores with polymeric molecular rulers. J Chem Phys 2010; 132:135101. [PMID: 20387958 PMCID: PMC4108643 DOI: 10.1063/1.3328875] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 01/04/2010] [Indexed: 11/14/2022] Open
Abstract
We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus alpha-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the alpha-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.
Collapse
Affiliation(s)
- Sarah E Henrickson
- Semiconductor Electronics Division, NIST, Bldg. 225, Room B326, Gaithersburg, Maryland 20899-8120, USA
| | | | | | | | | |
Collapse
|
196
|
Aksimentiev A. Deciphering ionic current signatures of DNA transport through a nanopore. NANOSCALE 2010; 2:468-83. [PMID: 20644747 PMCID: PMC2909628 DOI: 10.1039/b9nr00275h] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Within just a decade from the pioneering work demonstrating the utility of nanopores for molecular sensing, nanopores have emerged as versatile systems for single-molecule manipulation and analysis. In a typical setup, a gradient of the electrostatic potential captures charged solutes from the solution and forces them to move through a single nanopore, across an otherwise impermeable membrane. The ionic current blockades resulting from the presence of a solute in a nanopore can reveal the type of the solute, for example, the nucleotide makeup of a DNA strand. Despite great success, the microscopic mechanisms underlying the functionality of such stochastic sensors remain largely unknown, as it is not currently possible to characterize the microscopic conformations of single biomolecules directly in a nanopore and thereby unequivocally establish the causal relationship between the observables and the microscopic events. Such a relationship can be determined using molecular dynamics-a computational method that can accurately predict the time evolution of a molecular system starting from a given microscopic state. This article describes recent applications of this method to the process of DNA transport through biological and synthetic nanopores.
Collapse
Affiliation(s)
- Aleksei Aksimentiev
- Department of Physics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.
| |
Collapse
|
197
|
Tsutsui M, Taniguchi M, Yokota K, Kawai T. Identifying single nucleotides by tunnelling current. NATURE NANOTECHNOLOGY 2010; 5:286-290. [PMID: 20305643 DOI: 10.1038/nnano.2010.42] [Citation(s) in RCA: 239] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 02/12/2010] [Indexed: 05/29/2023]
Abstract
A major goal in medical research is to develop a DNA sequencing technique that is capable of reading an entire human genome at low cost. Recently, it was proposed that DNA sequencing could be performed by measuring the electron transport properties of the individual nucleotides in a DNA molecule. Here, we report electrical detection of single nucleotides using two configurable nanoelectrodes and show that electron transport through single nucleotides occurs by tunnelling. We also demonstrate statistical identification of the nucleotides based on their electrical conductivity, thereby providing an experimental basis for a DNA sequencing technology based on measurements of electron transport.
Collapse
Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | | | | | | |
Collapse
|
198
|
Progress of Research on Nanopore-macromolecule Detection. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.3724/sp.j.1096.2010.00280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
199
|
Zhou X, Ren L, Li Y, Zhang M, Yu Y, Yu J. The next-generation sequencing technology: a technology review and future perspective. SCIENCE CHINA-LIFE SCIENCES 2010; 53:44-57. [PMID: 20596955 DOI: 10.1007/s11427-010-0023-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 12/16/2009] [Indexed: 10/19/2022]
Abstract
As one of the most powerful tools in biomedical research, DNA sequencing not only has been improving its productivity in an exponential growth rate but also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades. In this technical review, we look into technical characteristics of the next-gen sequencers and provide prospective insights into their future development and applications. We envisage that some of the emerging platforms are capable of supporting the $1000 genome and $100 genome goals if given a few years for technical maturation. We also suggest that scientists from China should play an active role in this campaign that will have profound impact on both scientific research and societal healthcare systems.
Collapse
Affiliation(s)
- XiaoGuang Zhou
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China.
| | - LuFeng Ren
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - YunTao Li
- Institute of Semiconductor, Chinese Academy of Sciences, Beijing, 100083, China
| | - Meng Zhang
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - YuDe Yu
- Institute of Semiconductor, Chinese Academy of Sciences, Beijing, 100083, China
| | - Jun Yu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China.
| |
Collapse
|
200
|
DING KJ, ZHANG HY, HU HG, ZHAO HM, Guan WJ, Ma YH. Progress of Research on Nanopore-macromolecule Detection. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1016/s1872-2040(09)60022-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|