51
|
Wang HY, Gu Z, Cao C, Wang J, Long YT. Analysis of a single α-synuclein fibrillation by the interaction with a protein nanopore. Anal Chem 2013; 85:8254-61. [PMID: 23899046 DOI: 10.1021/ac401496x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The formation of an α-synuclein fibril is critical in the pathogenesis of Parkinson's disease. The native unfolded α-synuclein monomer will translocate through an α-hemolysin nanopore by applied potential at physiological conditions in vitro. Applying a potential transformed α-synuclein into a partially folded intermediate, which was monitored by capture inside the vestibule of an α-hemolysin nanopore with a capture current of 20 ± 1.0 pA. The procedure involves the critical early stage of α-synuclein structural transformation. Further elongation of the intermediate produces a block current to 5 ± 0.5 pA. It is revealed that the early stage fibril of α-synuclein inside the nanopore is affected by intrapeptide electrostatic interaction. In addition, trehalose cleared the fibrillation by changing the surface hydrophobic interaction of A53T α-synuclein, which did not show any inhibition effect from WT α-synuclein. The results proved that the interpeptide hydrophobic interactions in the elongation of A53T α-synuclein protofilaments can be greatly weakened by trehalose. This suggests that trehalose inhibits the interpeptide interaction involved in protein secondary structure. The hydrophobic and electrostatic interactions are associated with an increase in α-synuclein fibrillation propensity. This work provides unique insights into the earliest steps of the α-synuclein aggregation pathway and provides the potential basis for the development of drugs that can prevent α-synuclein aggregation at the initial stage.
Collapse
Affiliation(s)
- Hai-Yan Wang
- Shanghai Key Laboratory of Functional Materials Chemistry and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | | | | | | | | |
Collapse
|
52
|
Pizzolato N, Fiasconaro A, Adorno DP, Spagnolo B. Translocation dynamics of a short polymer driven by an oscillating force. J Chem Phys 2013; 138:054902. [PMID: 23406144 DOI: 10.1063/1.4789016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We study the translocation dynamics of a short polymer moving in a noisy environment and driven by an oscillating force. The dynamics is numerically investigated by solving a Langevin equation in a two-dimensional domain. We consider a phenomenological cubic potential with a metastable state to model the polymer-pore interaction and the entropic free energy barrier characterizing the translocation process. The mean first translocation time of the center of inertia of polymers shows a nonmonotonic behavior, with a minimum, as a function of the number of the monomers. The dependence of the mean translocation time on the polymer chain length shows a monotonically increasing behavior for high values of the number of monomers. Moreover, the translocation time shows a minimum as a function of the frequency of the oscillating forcing field for all the polymer lengths investigated. This finding represents the evidence of the resonant activation phenomenon in the dynamics of polymer translocation, whose occurrence is maintained for different values of the noise intensity.
Collapse
Affiliation(s)
- Nicola Pizzolato
- Dipartimento di Fisica e Chimica, Università di Palermo and CNISM, Viale delle Scienze edificio 18, I-90128 Palermo, Italy
| | | | | | | |
Collapse
|
53
|
Freedman KJ, Bastian AR, Chaiken I, Kim MJ. Solid-state nanopore detection of protein complexes: applications in healthcare and protein kinetics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:750-759. [PMID: 23074081 DOI: 10.1002/smll.201201423] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 09/12/2012] [Indexed: 06/01/2023]
Abstract
Protein conjugation provides a unique look into many biological phenomena and has been used for decades for molecular recognition purposes. In this study, the use of solid-state nanopores for the detection of gp120-associated complexes are investigated. They exhibit monovalent and multivalent binding to anti-gp120 antibody monomer and dimers. In order to investigate the feasibility of many practical applications related to nanopores, detection of specific protein complexes is attempted within a heterogeneous protein sample, and the role of voltage on complexed proteins is researched. It is found that the electric field within the pore can result in unbinding of a freely translocating protein complex within the transient event durations measured experimentally. The strong dependence of the unbinding time with voltage can be used to improve the detection capability of the nanopore system by adding an additional level of specificity that can be probed. These data provide a strong framework for future protein-specific detection schemes, which are shown to be feasible in the realm of a 'real-world' sample and an automated multidimensional method of detecting events.
Collapse
Affiliation(s)
- Kevin J Freedman
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | | | | | | |
Collapse
|
54
|
Reiner JE, Robertson JWF, Burden DL, Burden LK, Balijepalli A, Kasianowicz JJ. Temperature sculpting in yoctoliter volumes. J Am Chem Soc 2013; 135:3087-94. [PMID: 23347384 DOI: 10.1021/ja309892e] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ability to perturb large ensembles of molecules from equilibrium led to major advances in understanding reaction mechanisms in chemistry and biology. Here, we demonstrate the ability to control, measure, and make use of rapid temperature changes in fluid volumes that are commensurate with the size of single molecules. The method is based on attaching gold nanoparticles to a single nanometer-scale pore formed by a protein ion channel. Visible laser light incident on the nanoparticles causes a rapid and large increase of the adjacent solution temperature, which is estimated from the change in the nanopore ionic conductance. The temperature shift also affects the ability of individual molecules to enter into and interact with the nanopore. This technique could significantly improve sensor systems and force measurements based on single nanopores, thereby enabling a method for single molecule thermodynamics and kinetics.
Collapse
Affiliation(s)
- Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, USA.
| | | | | | | | | | | |
Collapse
|
55
|
Affiliation(s)
| | - Sergey M. Bezrukov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, U.S.A
| |
Collapse
|
56
|
Reiner JE, Balijepalli A, Robertson JWF, Campbell J, Suehle J, Kasianowicz JJ. Disease Detection and Management via Single Nanopore-Based Sensors. Chem Rev 2012; 112:6431-51. [DOI: 10.1021/cr300381m] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Joseph E. Reiner
- Department of Physics, Virginia
Commonwealth University, 701 W. Grace Street, Richmond, Virginia 23284,
United States
| | - Arvind Balijepalli
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
- Laboratory of Computational Biology,
National Heart Lung and Blood Institute, Rockville, Maryland 20852,
United States
| | - Joseph W. F. Robertson
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - Jason Campbell
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - John Suehle
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - John J. Kasianowicz
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| |
Collapse
|
57
|
Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
| |
Collapse
|
58
|
Kumar S, Tao C, Chien M, Hellner B, Balijepalli A, Robertson JWF, Li Z, Russo JJ, Reiner JE, Kasianowicz JJ, Ju J. PEG-labeled nucleotides and nanopore detection for single molecule DNA sequencing by synthesis. Sci Rep 2012; 2:684. [PMID: 23002425 PMCID: PMC3448304 DOI: 10.1038/srep00684] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 08/29/2012] [Indexed: 02/01/2023] Open
Abstract
We describe a novel single molecule nanopore-based sequencing by synthesis (Nano-SBS) strategy that can accurately distinguish four bases by detecting 4 different sized tags released from 5'-phosphate-modified nucleotides. The basic principle is as follows. As each nucleotide is incorporated into the growing DNA strand during the polymerase reaction, its tag is released and enters a nanopore in release order. This produces a unique ionic current blockade signature due to the tag's distinct chemical structure, thereby determining DNA sequence electronically at single molecule level with single base resolution. As proof of principle, we attached four different length PEG-coumarin tags to the terminal phosphate of 2'-deoxyguanosine-5'-tetraphosphate. We demonstrate efficient, accurate incorporation of the nucleotide analogs during the polymerase reaction, and excellent discrimination among the four tags based on nanopore ionic currents. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.
Collapse
Affiliation(s)
- Shiv Kumar
- Center for Genome Technology & Biomolecular Engineering, Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
59
|
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
|
60
|
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
|
61
|
Nelson EM, Kurz V, Shim J, Timp W, Timp G. Using a nanopore for single molecule detection and single cell transfection. Analyst 2012; 137:3020-7. [PMID: 22645737 DOI: 10.1039/c2an35571j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We assert that it is possible to trap and identify proteins, and even (conceivably) manipulate proteins secreted from a single cell (i.e. the secretome) through transfection via electroporation by exploiting the exquisite control over the electrostatic potential available in a nanopore. These capabilities may be leveraged for single cell analysis and transfection with single molecule resolution, ultimately enabling a careful scrutiny of tissue heterogeneity.
Collapse
|
62
|
Zhang K, Luo K. Dynamics of polymer translocation into a circular nanocontainer through a nanopore. J Chem Phys 2012; 136:185103. [DOI: 10.1063/1.4712618] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
63
|
Rudenko MI, Holmes MR, Ermolenko DN, Lunt EJ, Gerhardt S, Noller HF, Deamer DW, Hawkins A, Schmidt H. Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip. Biosens Bioelectron 2011; 29:34-9. [DOI: 10.1016/j.bios.2011.07.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 07/17/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022]
|
64
|
Bacri L, Oukhaled A, Hémon E, Bassafoula FB, Auvray L, Daniel R. Discrimination of neutral oligosaccharides through a nanopore. Biochem Biophys Res Commun 2011; 412:561-4. [PMID: 21839725 DOI: 10.1016/j.bbrc.2011.07.121] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 07/28/2011] [Indexed: 10/17/2022]
Abstract
The detection of oligosaccharides at the single-molecule level was investigated using a protein nanopore device. Neutral oligosaccharides of various molecular weights were translocated through a single α-hemolysin nanopore and their nano-transit recorded at the single-molecule level. The translocation of maltose and dextran oligosaccharides featured by 1→4 and 1→6 glycosidic bonds respectively was studied in an attempt to discriminate oligosaccharides according to their polymerization degree and glycosidic linkages. Oligosaccharides were translocated through a free diffusion regime indicating that they adopted an extended conformation during their translocation in the nanopore. The dwell time increased with molecular mass, suggesting the usefulness of nanopore as a molecular sizing device.
Collapse
Affiliation(s)
- Laurent Bacri
- CNRS UMR 8587, Laboratoire Analyse et Environnement, Université d'Évry Val d'Essonne, Évry, France.
| | | | | | | | | | | |
Collapse
|
65
|
Ying YL, Li DW, Li Y, Lee JS, Long YT. Enhanced translocation of poly(dt)45 through an α-hemolysin nanopore by binding with antibody. Chem Commun (Camb) 2011; 47:5690-2. [PMID: 21491051 DOI: 10.1039/c0cc05787h] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The translocation time of poly(dT)(45) through an α-hemolysin pore was reduced in the presence of a DNA-binding Fab fragment. The Fab acts as a rudder to steer the DNA into the pore.
Collapse
Affiliation(s)
- Yi-Lun Ying
- Shanghai Key Laboratory of Functional Materials Chemistry & Department of Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai, PR China
| | | | | | | | | |
Collapse
|
66
|
Asandei A, Apetrei A, Luchian T. Uni-molecular detection and quantification of selected β-lactam antibiotics with a hybrid α-hemolysin protein pore. J Mol Recognit 2011; 24:199-207. [DOI: 10.1002/jmr.1038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
67
|
He J, Liu H, Pang P, Cao D, Lindsay S. Translocation events in a single walled carbon nanotube. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454112. [PMID: 21179393 PMCID: PMC3004237 DOI: 10.1088/0953-8984/22/45/454112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Translocation of DNA oligomers through a single walled carbon nanotube was demonstrated recently. Translocation events are accompanied by giant current pulses, the origin of which remains obscure. Here, we show that introduction of a nucleotide alone, guanosine triphosphate into the input reservoir of a carbon nanotube nanofluidic also gives giant current pulses. Taken together with data on oligomer translocation, theses new results suggest that pulse width has a non-linear, power-law dependence on the number of nucleotides in a DNA molecule. We have also measured the time for the onset of DNA translocation pulses after bias reversal, finding that the time for the onset of translocation is directly proportional to the period of bias reversal.
Collapse
Affiliation(s)
- Jin He
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | | | | | | | | |
Collapse
|
68
|
Zilman A, Bel G. Crowding effects in non-equilibrium transport through nano-channels. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454130. [PMID: 21339616 DOI: 10.1088/0953-8984/22/45/454130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Transport through nano-channels plays an important role in many biological processes and industrial applications. Gaining insights into the functioning of biological transport processes and the design of man-made nano-devices requires an understanding of the basic physics of such transport. A simple exclusion process has proven to be very useful in explaining the properties of several artificial and biological nano-channels. It is particularly useful for modeling the influence of inter-particle interactions on transport characteristics. In this paper, we explore several models of the exclusion process using a mean field approach and computer simulations. We examine the effects of crowding inside the channel and in its immediate vicinity on the mean flux and the transport times of single molecules. Finally, we discuss the robustness of the theory's predictions with respect to the crucial characteristics of the hindered diffusion in nano-channels that need to be included in the model.
Collapse
Affiliation(s)
- A Zilman
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | |
Collapse
|
69
|
Yusko EC, Billeh YN, Mayer M. Current oscillations generated by precipitate formation in the mixing zone between two solutions inside a nanopore. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454127. [PMID: 21339613 DOI: 10.1088/0953-8984/22/45/454127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Unlike biological protein pores in lipid membranes, nanopores fabricated in synthetic materials can withstand a wide range of environmental conditions including the presence of organic solvents. This capability expands the potential of synthetic nanopores to monitor chemical reactions occurring at the interface between solutions of organic and aqueous character. In this work, nanopores fabricated in borosilicate glass or silicon nitride connected a predominantly organic solvent to an aqueous solvent, thereby generating a mixing zone between these solutions inside the pore. This configuration was exploited to precipitate small organic molecules with low aqueous solubility inside the nanopores, and concomitantly, to monitor this precipitation by the decrease of the ionic conductance through the nanopores over time. Hence, this method provides a means to induce and investigate the formation of nanoprecipitates or nanoparticles. Interestingly, precipitates with a slight electric charge were cleared from the pore, causing the conductance of the pore to return to its original value. This process repeated, resulting in stable oscillations of the ionic current. Although such oscillations might be useful in fluidic logic circuits, few conditions capable of generating oscillations in ionic currents have been reported. The frequency and amplitude of oscillations could be tuned by changing the concentration of the precipitating molecule, the pH of the electrolyte, and the applied potential bias. In addition to generating oscillations, nanopores that separate two different solutions may be useful for monitoring and mediating chemical reactions in the mixing zone between two solutions.
Collapse
Affiliation(s)
- Erik C Yusko
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Lurie Biomedical Engineering Building, Room 2174, Ann Arbor, MI 48109-2110, USA
| | | | | |
Collapse
|
70
|
Majd S, Yusko EC, Billeh YN, Macrae MX, Yang J, Mayer M. Applications of biological pores in nanomedicine, sensing, and nanoelectronics. Curr Opin Biotechnol 2010; 21:439-76. [PMID: 20561776 PMCID: PMC3121537 DOI: 10.1016/j.copbio.2010.05.002] [Citation(s) in RCA: 237] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 05/03/2010] [Accepted: 05/06/2010] [Indexed: 12/29/2022]
Abstract
Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.
Collapse
Affiliation(s)
- Sheereen Majd
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110, USA
| | | | | | | | | | | |
Collapse
|
71
|
Luo K, Metzler R. Polymer translocation into a fluidic channel through a nanopore. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:021922. [PMID: 20866852 DOI: 10.1103/physreve.82.021922] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Indexed: 05/29/2023]
Abstract
Using two-dimensional Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a fluidic channel with diameter R through a nanopore under a driving force F . Due to the crowding effect induced by the partially translocated monomers, the translocation dynamics is significantly altered in comparison to an unconfined environment, namely, we observe a nonuniversal dependence of the translocation time τ on the chain length N . τ initially decreases rapidly and then saturates with increasing R , and a dependence of the scaling exponent α of τ with N on the channel width R is observed. The otherwise inverse linear scaling of τ with F breaks down and we observe a minimum of α as a function of F . These behaviors are interpreted in terms of the waiting time of an individual segment passing through the pore during translocation.
Collapse
Affiliation(s)
- Kaifu Luo
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui Province, People's Republic of China.
| | | |
Collapse
|
72
|
Japrung D, Henricus M, Li Q, Maglia G, Bayley H. Urea facilitates the translocation of single-stranded DNA and RNA through the alpha-hemolysin nanopore. Biophys J 2010; 98:1856-63. [PMID: 20441749 DOI: 10.1016/j.bpj.2009.12.4333] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 12/14/2009] [Accepted: 12/29/2009] [Indexed: 11/15/2022] Open
Abstract
The staphylococcal alpha-hemolysin (alphaHL) protein nanopore is under investigation as a fast, cheap detector for nucleic acid analysis and sequencing. Although discrimination of all four bases of DNA by the alphaHL pore has been demonstrated, analysis of single-stranded DNAs and RNAs containing secondary structure mediated by basepairing is prevented because these nucleic acids cannot be translocated through the pore. Here, we show that a structured 95-nucleotide single-stranded DNA and its RNA equivalent are translocated through the alphaHL pore in the presence of 4 M urea, a concentration that denatures the secondary structure of the polynucleotides. The alphaHL pore is functional even in 7 M urea, and therefore it is easily stable enough for analyses of challenging DNA and RNA species.
Collapse
Affiliation(s)
- Deanpen Japrung
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | | | | | | |
Collapse
|
73
|
|
74
|
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
|
75
|
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
|
76
|
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: 130] [Impact Index Per Article: 9.3] [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
|
77
|
Affiliation(s)
- Long Ma
- School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, UK
| | | |
Collapse
|
78
|
Nanotechnology for early cancer detection. SENSORS 2010; 10:428-55. [PMID: 22315549 PMCID: PMC3270850 DOI: 10.3390/s100100428] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 12/14/2009] [Accepted: 12/29/2009] [Indexed: 12/19/2022]
Abstract
Vast numbers of studies and developments in the nanotechnology area have been conducted and many nanomaterials have been utilized to detect cancers at early stages. Nanomaterials have unique physical, optical and electrical properties that have proven to be very useful in sensing. Quantum dots, gold nanoparticles, magnetic nanoparticles, carbon nanotubes, gold nanowires and many other materials have been developed over the years, alongside the discovery of a wide range of biomarkers to lower the detection limit of cancer biomarkers. Proteins, antibody fragments, DNA fragments, and RNA fragments are the base of cancer biomarkers and have been used as targets in cancer detection and monitoring. It is highly anticipated that in the near future, we might be able to detect cancer at a very early stage, providing a much higher chance of treatment.
Collapse
|
79
|
|
80
|
Liu H, He J, Tang J, Liu H, Pang P, Cao D, Krstic P, Joseph S, Lindsay S, Nuckolls C. Translocation of single-stranded DNA through single-walled carbon nanotubes. Science 2010; 327:64-7. [PMID: 20044570 PMCID: PMC2801077 DOI: 10.1126/science.1181799] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
We report the fabrication of devices in which one single-walled carbon nanotube spans a barrier between two fluid reservoirs, enabling direct electrical measurement of ion transport through the tube. A fraction of the tubes pass anomalously high ionic currents. Electrophoretic transport of small single-stranded DNA oligomers through these tubes is marked by large transient increases in ion current and was confirmed by polymerase chain reaction analysis. Each current pulse contains about 10(7) charges, an enormous amplification of the translocated charge. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurements, and may open avenues for control of DNA translocation.
Collapse
Affiliation(s)
- Haitao Liu
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Jin He
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Jinyao Tang
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Hao Liu
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
| | - Pei Pang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- Department of Physics, Arizona State University, Tempe, AZ 85287
| | - Di Cao
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- Department of Physics, Arizona State University, Tempe, AZ 85287
| | - Predrag Krstic
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Sony Joseph
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Department of Physics, Arizona State University, Tempe, AZ 85287
| | - Colin Nuckolls
- Department of Chemistry, Columbia University, New York, NY 10027
| |
Collapse
|
81
|
Abstract
We present a Langevin dynamics simulation study of enzyme-modulated translocation of a single-stranded DNA molecule through a cylindrical nanopore. The toroidal-shaped enzyme placed along the axis of the pore, threads a DNA molecule at a constant rate. As a result of this controlled release process, the length of DNA available for translocation varies with time. We examine the effect of time-dependent conformational entropy of the DNA on the translocation process. In addition, we also examine the effects of both the separation between the exonuclease and the pore, and the rate at which DNA is released by the enzyme. Our results indicate that the separation distance primarily influences the entry of the DNA into the pore. The length of the DNA released by the exonuclease that is most likely to enter the pore is nearly equal to separation distance between the pore and the exonuclease despite the flexibility of the polymer. However, the speed at which the DNA translocates through the nanopore is solely determined by the rate at which the exonuclease releases the DNA. We find that the translocation velocity is directly proportional to the rate of release.
Collapse
Affiliation(s)
- Ajay S. Panwar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003
| | - M. Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003
| |
Collapse
|
82
|
Perry M, Vissing T, Boesen TP, Hansen JS, Emnéus J, Nielsen CH. Automated sampling and data processing derived from biomimetic membranes. BIOINSPIRATION & BIOMIMETICS 2009; 4:044001. [PMID: 19901449 DOI: 10.1088/1748-3182/4/4/044001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recent advances in biomimetic membrane systems have resulted in an increase in membrane lifetimes from hours to days and months. Long-lived membrane systems demand the development of both new automated monitoring equipment capable of measuring electrophysiological membrane characteristics and new data processing software to analyze and organize the large amounts of data generated. In this work, we developed an automated instrumental voltage clamp solution based on a custom-designed software controller application (the WaveManager), which enables automated on-line voltage clamp data acquisition applicable to long-time series experiments. We designed another software program for off-line data processing. The automation of the on-line voltage clamp data acquisition and off-line processing was furthermore integrated with a searchable database (DiscoverySheet) for efficient data management. The combined solution provides a cost efficient and fast way to acquire, process and administrate large amounts of voltage clamp data that may be too laborious and time consuming to handle manually.
Collapse
Affiliation(s)
- M Perry
- Aquaporin A/S, Diplomvej 377, DK-2800 Kgs. Lyngby, Denmark
| | | | | | | | | | | |
Collapse
|
83
|
Purnell RF, Schmidt JJ. Discrimination of single base substitutions in a DNA strand immobilized in a biological nanopore. ACS NANO 2009; 3:2533-8. [PMID: 19694456 DOI: 10.1021/nn900441x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nanopores have been explored as highly sensitive sensors for detection and rapid sequencing of single molecules of DNA. To sequence DNA with a nanopore requires that adenine (A), cytosine (C), thymine (T), and guanine (G) produce distinct current signals as they traverse the pore. Recently, we demonstrated that homopolymers of adenine, cytosine, and thymine immobilized in the nanopore protein alpha-hemolysin (alphaHL) produced distinct current blockades dependent on their chemical orientation. To probe the detection limit of alphaHL, we examined immobilized single strands of T(40) DNA (polyT) with single base substitutions of A, C, and G at 12 positions on the strand occupying the stem region of alphaHL. We find blockade currents sensitive to base identity over most of these positions with the most sensitive region near the pore constriction. Adenine substitutions increase the measured blockade current to values intermediate to the polyT and polyA currents at a number of positions, while C substitutions increase the current to a level intermediate to polyT and polyC values in some positions, but decrease it below polyT in others. These changes in blockade current were also observed for G substitutions. These results indicate that total blockade currents measured in alphaHL arise from nucleotides at multiple locations and thus are not uniquely attributable to an individual base in a specific position, a finding consistent with a recently published study. The measurements of C and G substitutions also suggest that blockade current may be modulated through interactions between nucleotides and the pore interior at multiple sites in alphaHL.
Collapse
Affiliation(s)
- Robert F Purnell
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
| | | |
Collapse
|
84
|
Hansen JS, Perry M, Vogel J, Groth JS, Vissing T, Larsen MS, Geschke O, Emneús J, Bohr H, Nielsen CH. Large scale biomimetic membrane arrays. Anal Bioanal Chem 2009; 395:719-27. [DOI: 10.1007/s00216-009-3010-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 07/22/2009] [Accepted: 07/23/2009] [Indexed: 10/20/2022]
|
85
|
Borsenberger V, Mitchell N, Howorka S. Chemically labeled nucleotides and oligonucleotides encode DNA for sensing with nanopores. J Am Chem Soc 2009; 131:7530-1. [PMID: 19441786 DOI: 10.1021/ja902004s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The labeling of nucleotides and oligonucleotides with reporter groups is an important tool in the sequence-specific sensing of DNA, as exemplified by fluorescence tags. Here we show that chemical tags can encode sequence information for electrical nanopore recordings. In nanopore recordings, individual DNA strands are electrophoretically driven through a nanoscale pore leading to detectable blockades of ionic current. The tags cause characteristic electrical signatures in the current blockades of translocating DNA strands and thereby encode sequence information. The viability of the strategy is demonstrated by discriminating between drug resistance-conferring point mutations. By being independent of pore engineering, the new approach can potentially enhance the sensing repertoire of durable solid-state nanopores for which alternative sensing strategies developed for protein pores are not easily accessible.
Collapse
Affiliation(s)
- Vinciane Borsenberger
- Department of Chemistry, University College London, Christopher Ingold Building, 20 Gordon Street, London WC1H OAJ, UK
| | | | | |
Collapse
|
86
|
Hurt N, Wang H, Akeson M, Lieberman KR. Specific nucleotide binding and rebinding to individual DNA polymerase complexes captured on a nanopore. J Am Chem Soc 2009; 131:3772-8. [PMID: 19275265 DOI: 10.1021/ja809663f] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanoscale pores are a tool for single molecule analysis of DNA or RNA processing enzymes. Monitoring catalytic activity in real time using this technique requires that these enzymes retain function while held atop a nanopore in an applied electric field. Using an alpha-hemolysin nanopore, we measured the dwell time for complexes of DNA with the Klenow fragment of Escherichia coli DNA polymerase I (KF) as a function of the concentration of deoxynucleoside triphosphate (dNTP) substrate. We analyzed these dwell time measurements in the framework of a two-state model for captured complexes (DNA-KF binary and DNA-KF-dNTP ternary states). Average nanopore dwell time increased without saturating as a function of correct dNTP concentration across 4 orders of magnitude. This arises from two factors that are proportional to dNTP concentration: (1) The fraction of complexes that are in the ternary state when initially captured predominantly affects dwell time at low dNTP concentrations. (2) The rate of binding and rebinding of dNTP to captured complexes affects dwell time at higher dNTP concentrations. Thus there are two regimes that display a linear relationship between average dwell time and dNTP concentration. The transition from one linear regime to the other occurs near the equilibrium dissociation constant (K(d)) for dNTP binding to KF-DNA complexes in solution. We conclude from the combination of titration experiments and modeling that DNA-KF complexes captured atop the nanopore retain iterative, sequence-specific dNTP binding, as required for catalysis and fidelity in DNA synthesis.
Collapse
Affiliation(s)
- Nicholas Hurt
- Department of Chemistry and Biochemistry, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA
| | | | | | | |
Collapse
|
87
|
Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proc Natl Acad Sci U S A 2009; 106:7702-7. [PMID: 19380741 DOI: 10.1073/pnas.0901054106] [Citation(s) in RCA: 311] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The sequencing of individual DNA strands with nanopores is under investigation as a rapid, low-cost platform in which bases are identified in order as the DNA strand is transported through a pore under an electrical potential. Although the preparation of solid-state nanopores is improving, biological nanopores, such as alpha-hemolysin (alphaHL), are advantageous because they can be precisely manipulated by genetic modification. Here, we show that the transmembrane beta-barrel of an engineered alphaHL pore contains 3 recognition sites that can be used to identify all 4 DNA bases in an immobilized single-stranded DNA molecule, whether they are located in an otherwise homopolymeric DNA strand or in a heteropolymeric strand. The additional steps required to enable nanopore DNA sequencing are outlined.
Collapse
|
88
|
|
89
|
Enhanced translocation of single DNA molecules through alpha-hemolysin nanopores by manipulation of internal charge. Proc Natl Acad Sci U S A 2008; 105:19720-5. [PMID: 19060213 DOI: 10.1073/pnas.0808296105] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both protein and solid-state nanopores are under intense investigation for the analysis of nucleic acids. A crucial advantage of protein nanopores is that site-directed mutagenesis permits precise tuning of their properties. Here, by augmenting the internal positive charge within the alpha-hemolysin pore and varying its distribution, we increase the frequency of translocation of a 92-nt single-stranded DNA through the pore at +120 mV by approximately 10-fold over the wild-type protein and dramatically lower the voltage threshold at which translocation occurs, e.g., by 50 mV for 1 event.s(-1).muM(-1). Further, events in which DNA enters the pore, but is not immediately translocated, are almost eliminated. These experiments provide a basis for improved nucleic acid analysis with protein nanopores, which might be translated to solid-state nanopores by using chemical surface modification.
Collapse
|
90
|
Kececi K, Sexton LT, Buyukserin F, Martin CR. Resistive-pulse detection of short dsDNAs using a chemically functionalized conical nanopore sensor. Nanomedicine (Lond) 2008; 3:787-96. [DOI: 10.2217/17435889.3.6.787] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To develop nanopore resistive-pulse sensors for the detection of short (50 base-pair [bp] and 100 bp) DNAs. Materials & methods: Conically shaped nanopores were chemical etched into polyethylene terphthalate membranes. The as-etched membrane had anionic carboxylate sites on the pore walls. Neutral and hydrophilic ethanolamine functional groups were attached to these carboxylate sites using well-established EDC (1-ethyl-3-[3-dimethylaminopropyl] carbodiimide hydrochloride) chemistry. Results & discussion: The ethanolamine-functionalized pores were used to detect 50 and 100 bp DNAs via the resistive-pulse method. The resistive-pulse signature produced by the 50 bp DNA could be distinguished from that of the 100 bp DNA with these sensors. Conclusions: Attachment of ethanolamine to the carboxylate groups on the pore wall lowered the anionic charge density on the wall. This mitigated the problem of electrostatic rejection of the anionic DNAs from the pore and enabled the detection of these DNA analytes.
Collapse
Affiliation(s)
- Kaan Kececi
- Departments of Chemistry & Anesthesiology, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| | - Lindsay T Sexton
- Departments of Chemistry & Anesthesiology, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| | - Fatih Buyukserin
- Departments of Chemistry & Anesthesiology, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| | - Charles R Martin
- Departments of Chemistry & Anesthesiology, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| |
Collapse
|
91
|
Luo K, Ala-Nissila T, Ying SC, Bhattacharya A. Translocation dynamics with attractive nanopore-polymer interactions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:061918. [PMID: 19256879 DOI: 10.1103/physreve.78.061918] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 08/15/2008] [Indexed: 05/27/2023]
Abstract
Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time tau approximately tau1+tau2+tau3 corresponding to the initial filling of the pore, transfer of polymer from the cis side to the trans side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from nonactivated to activated in nature as the strength of the attractive interaction increases, and tau3 becomes the dominant contribution to the total translocation time for strong attraction. This leads to nonuniversal dependence of tau as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a plausible explanation for the different scaling behavior observed in solid state nanopores vs that for the natural alpha-hemolysin channel.
Collapse
Affiliation(s)
- Kaifu Luo
- Physics Department, Technical University of Munich, D-85748 Garching, Germany.
| | | | | | | |
Collapse
|
92
|
Abstract
The mechanisms of KCl-induced enhancement in identification of individual molecules of poly(ethylene glycol) using solitary alpha-hemolysin nanoscale pores are described. The interaction of single molecules with the nanopore causes changes in the ionic current flowing through the pore. We show that the on-rate constant of the process is several hundred times larger and that the off-rate is several hundred times smaller in 4 M KCl than in 1 M KCl. These shifts dramatically improve detection and make single molecule identification feasible. KCl also changes the solubility of poly(ethylene glycol) by the same order of magnitude as it changes the rate constants. In addition, the polymer-nanopore interaction is determined to be a strong non-monotonic function of voltage, indicating that the flexible, nonionic poly(ethylene glycol) acts as a charged molecule. Therefore, salting-out and Coulombic interactions are responsible for the KCl-induced enhancement. These results will advance the development of devices with sensor elements based on single nanopores.
Collapse
|
93
|
Murray RW. Nanoelectrochemistry: Metal Nanoparticles, Nanoelectrodes, and Nanopores. Chem Rev 2008; 108:2688-720. [DOI: 10.1021/cr068077e] [Citation(s) in RCA: 963] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
94
|
Ervin EN, Kawano R, White RJ, White HS. Simultaneous Alternating and Direct Current Readout of Protein Ion Channel Blocking Events Using Glass Nanopore Membranes. Anal Chem 2008; 80:2069-76. [DOI: 10.1021/ac7021103] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Eric N. Ervin
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112
| | - Ryuji Kawano
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112
| | - Ryan J. White
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112
| | - Henry S. White
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112
| |
Collapse
|
95
|
Wang J, Martin CR. A new drug-sensing paradigm based on ion-current rectification in a conically shaped nanopore. Nanomedicine (Lond) 2008; 3:13-20. [DOI: 10.2217/17435889.3.1.13] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To utilize the ion-current rectification phenomenon observed for conically shaped nanopores as the basis for designing sensors for drug molecules that adsorb to the walls of the nanopore. Methods: The conically shaped nanopore was prepared by the well-known track-etch method in a polyimide (Kapton) membrane. The ion current flowing through the nanopore was measured as a function of applied transmembrane potential in the presence of the analyte drug molecule, Hoechst 33258. Results: The pore walls in the Kapton membrane are hydrophobic yet have fixed carboxylate groups that give the walls a net negative charge. This fixed anionic surface charge causes the nanopore to rectify the ion current flowing through it. The analyte drug molecule, Hoechst 33258, is cationic yet also hydrophobic. When the membrane is exposed to this molecule, it adsorbs to the pore walls and neutralizes the anionic surface charge, thus lowering the extent of ion-current rectification. The change in rectification is proportional to the concentration of the drug. Conclusions: This nanopore sensor is selective for hydrophobic cations relative to anions, neutral molecules and less hydrophobic cations. Future work will explore ways of augmenting this hydrophobic effect-based selectivity so that more highly selective sensors can be obtained.
Collapse
Affiliation(s)
- JiaHai Wang
- University of Florida, Department of Chemistry & Center for Research at the Bio/Nano Interface, Gainesville, FL 32605, USA
| | - Charles R Martin
- University of Florida, Department of Chemistry & Center for Research at the Bio/Nano Interface, Gainesville, FL 32605, USA
| |
Collapse
|
96
|
Abstract
The crucial step in the intrinsic, or mitochondrial, apoptotic pathway is permeabilization of the mitochondrial outer membrane. Permeabilization triggers release of apoptogenic factors, such as cytochrome c, from the mitochondrial intermembrane space into the cytosol where these factors ensure propagation of the apoptotic cascade and execution of cell death. However, the mechanism(s) underlying permeabilization of the outer membrane remain controversial. Two mechanisms, involving opening of two different mitochondrial channels, have been proposed to be responsible for the permeabilization; the permeability transition pore (PTP) in the inner membrane and the mitochondrial apoptosis-induced channel (MAC) in the outer membrane. Opening of PTP would lead to matrix swelling, subsequent rupture of the outer membrane, and an unspecific release of intermembrane proteins into the cytosol. However, many believe PTP opening is a consequence of apoptosis and this channel is thought to principally play a role in necrosis, not apoptosis. Activation of MAC is exquisitely regulated by Bcl-2 family proteins, which are the sentinels of apoptosis. MAC provides specific pores in the outer membrane for the passage of intermembrane proteins, in particular cytochrome c, to the cytosol. The electrophysiological characteristics of MAC are very similar to Bax channels and depletion of Bax significantly diminishes MAC activity, suggesting that Bax is an essential constituent of MAC in some systems. The characteristics of various mitochondrial channels and Bax are compared. The involvement of MAC and PTP activities in apoptosis of disease and their pharmacology are discussed.
Collapse
Affiliation(s)
- Kathleen W Kinnally
- Department of Basic Sciences, New York University College of Dentistry, 345 East 24th Street, New York, NY 10010, USA.
| | | |
Collapse
|
97
|
Kasianowicz JJ, Robertson JWF, Chan ER, Reiner JE, Stanford VM. Nanoscopic porous sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:737-766. [PMID: 20636096 DOI: 10.1146/annurev.anchem.1.031207.112818] [Citation(s) in RCA: 217] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
There are thousands of different nanometer-scale pores in biology, many of which act as sensors for specific chemical agents. Recent work suggests that protein and solid-state nanopores have many potential uses in a wide variety of analytical applications. In this review we survey this field of research and discuss the prospects for advances that could be made in the near future.
Collapse
Affiliation(s)
- John J Kasianowicz
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, USA.
| | | | | | | | | |
Collapse
|
98
|
Healy K, Schiedt B, Morrison AP. Solid-state nanopore technologies for nanopore-based DNA analysis. Nanomedicine (Lond) 2007; 2:875-97. [DOI: 10.2217/17435889.2.6.875] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nanopore-based DNA analysis is a new single-molecule technique that involves monitoring the flow of ions through a narrow pore, and detecting changes in this flow as DNA molecules also pass through the pore. It has the potential to carry out a range of laboratory and medical DNA analyses, orders of magnitude faster than current methods. Initial experiments used a protein channel for its pre-defined, precise structure, but since then several approaches for the fabrication of solid-state pores have been developed. These aim to match the capabilities of biochannels, while also providing increased durability, control over pore geometry and compatibility with semiconductor and microfluidics fabrication techniques. This review summarizes each solid-state nanopore fabrication technique reported to date, and compares their advantages and disadvantages. Methods and applications for nanopore surface modification are also presented, followed by a discussion of approaches used to measure pore size, geometry and surface properties. The review concludes with an outlook on the future of solid-state nanopores.
Collapse
Affiliation(s)
- Ken Healy
- University College Cork, Department of Electrical and Electronic Engineering, Ireland
- University of Pennsylvania, Department of Physics and Astronomy, 209 S 33rd Street, Philadelphia, PA 19104, USA
| | - Birgitta Schiedt
- Gesellschaft für Schwerionenforschung, Planckstr. 1, D-64291, Darmstadt, Germany
- Centre National de la Recherche Scientifique, Laboratory for Photonics and Nanostructures, Route de Nozay, F-91460 Marcoussis, France
- Université d’Évry Val d’Essonne, Laboratoire MPI, Bd. François Mitterrand, F-91025 Évry, France
| | - Alan P Morrison
- University College Cork, Department of Electrical and Electronic Engineering, Ireland
| |
Collapse
|
99
|
|
100
|
Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| |
Collapse
|