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Chen S, He W, Li J, Xu D, Zhao R, Zhu L, Wu H, Xu F. Pulley Effect in the Capture of DNA Translocation through Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:5799-5808. [PMID: 38501264 DOI: 10.1021/acs.langmuir.3c03596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Nanopores are powerful single-molecule sensors for analyzing biomolecules such as DNA and proteins. Understanding the dynamics of DNA capture and translocation through nanopores is essential for optimizing their performance. In this study, we examine the effects of applied voltage and pore diameter on current blockage, translocation time, collision, and capture location by translocating λ-DNA through 5.7 and 16 nm solid-state nanopores. Ionic current changes are used to infer DNA conformations during translocation. We find that translocation time increases with pore diameter, which can be attributed to the decrease of the stall force. Linear and exponential decreases of collision frequency with voltage are observed in the 16 and 5.7 nm pores, respectively, indicating a free energy barrier in the small pore. Moreover, the results reveal a voltage-dependent bias in the capture location toward the DNA ends, which is explained by a "pulley effect" deforming the DNA as it approaches the pore. This study provides insights into the physics governing DNA capture and translocation, which can be useful for promoting single-file translocation to enhance nanopore sensing.
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Affiliation(s)
- Shulan Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang 330029, China
| | - Wen He
- Analysis and Testing Center, Nanchang Hangkong University, Nanchang 330063, China
| | - Jun Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Derong Xu
- Jiangxi Institute of Translational Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Rui Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Libo Zhu
- School of Medical Imageology, Wannan Medical College, Wuhu 241002, China
| | - Hongwen Wu
- Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Fei Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- National Regional Center for Respiratory Medicine, China-Japan Friendship Jiangxi Hospital, Nanchang 330006, China
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2
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Wu J, Choi J, Uba FI, Soper SA, Park S. Engineering inlet structures to enhance DNA capture into nanochannels in a polymer nanofluidic device produced via nanoimprint lithography. MICRO AND NANO ENGINEERING 2023; 21:100230. [PMID: 38737190 PMCID: PMC11085012 DOI: 10.1016/j.mne.2023.100230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Operating nanofluidic biosensors requires threading single molecules to be analyzed from microfluidic networks into nanostructures, mostly nanochannels or nanopores. Different inlet structures have been employed as a means of enhancing the number of the capture events into nanostructures. Here, we systematically investigated the effects of various engineered inlet structures formed at the micro/nanochannel interface on the capture of single λ-DNA molecules into the nanochannels. Different inlet geometries were evaluated and ranked in order of their effectiveness. Adding an inlet structure prior to a nanochannel effectively improved the DNA capture rate by 190 - 700 % relative to that for the abrupt micro/nanochannel interface. The capture of DNA from the microchannel to various inlets was determined mainly by the capture volumes of the inlet structures and the geometrically modified electric field in the inlet structure. However, as the width of the inlet structure increased, the hydrodynamic flow existing in the microchannel negatively influenced the DNA capture by dragging some DNA molecules deep into the inlet structure back to the microchannel. Our results indicate that engineering inlet structures is an effective means of controlling the capture of DNA molecules into nanostructures, which is important for operation of nanofluidic biosensors.
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Affiliation(s)
- Jiahao Wu
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Junseo Choi
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Franklin I. Uba
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sunggook Park
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
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3
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Farajpour N, Lastra LS, Sharma V, Freedman KJ. Calibration-Less DNA Concentration Measurements Using EOF Volumetric Flow and Single Molecule Counting. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.689584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nanopore sensing is a promising tool well suited to capture and detect DNA and other single molecules. DNA is a negatively charged biomolecule that can be captured and translocated through a constricted nanopore aperture under an applied electric field. Precise assessment of DNA concentration is of crucial importance in many analytical processes and medical diagnostic applications. Recently, we found that hydrodynamic forces can lead to DNA motion against the electrophoretic force (EPF) at low ionic strength. This study utilized glass nanopores to investigate the DNA capture mechanism and detect DNA molecules due to volumetric flow at these low ionic strength conditions. We measured the DNA capture rate at five different pico-molar concentrations. Our findings indicated that the translocation rate is proportional to the concentration of DNA molecules and requires no calibration due to the volumetric flow rate and DNA counting directly correlates with concentration. Using finite element analysis, we calculated the volumetric flow and proposed a simple, straightforward approach for accurate DNA quantification. Furthermore, these experiments explore a unique transport mechanism where one of the most highly charged molecules enters a pore against electric field forces. This quantitative technique has the potential to provide distinct insight into nanopore-based biosensing and further enhance the nanopore’s capability as a biomolecule concentration sensor.
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4
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Wang C, Sensale S, Pan Z, Senapati S, Chang HC. Slowing down DNA translocation through solid-state nanopores by edge-field leakage. Nat Commun 2021; 12:140. [PMID: 33420061 PMCID: PMC7794543 DOI: 10.1038/s41467-020-20409-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/23/2020] [Indexed: 01/26/2023] Open
Abstract
Solid-state nanopores allow high-throughput single-molecule detection but identifying and even registering all translocating small molecules remain key challenges due to their high translocation speeds. We show here the same electric field that drives the molecules into the pore can be redirected to selectively pin and delay their transport. A thin high-permittivity dielectric coating on bullet-shaped polymer nanopores permits electric field leakage at the pore tip to produce a voltage-dependent surface field on the entry side that can reversibly edge-pin molecules. This mechanism renders molecular entry an activated process with sensitive exponential dependence on the bias voltage and molecular rigidity. This sensitivity allows us to selectively prolong the translocation time of short single-stranded DNA molecules by up to 5 orders of magnitude, to as long as minutes, allowing discrimination against their double-stranded duplexes with 97% confidence.
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Affiliation(s)
- Ceming Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Sebastian Sensale
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Zehao Pan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA.
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, USA.
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Kundu P, Saha S, Gangopadhyay G. Stochastic Kinetic Approach to the Escape of DNA Hairpins from an α-Hemolysin Channel. J Phys Chem B 2020; 124:6575-6584. [DOI: 10.1021/acs.jpcb.0c05122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Prasanta Kundu
- S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Soma Saha
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Gautam Gangopadhyay
- S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
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6
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Fedorenko OA, Kaufman IK, Gibby WAT, Barabash ML, Luchinsky DG, Roberts SK, McClintock PVE. Ionic Coulomb blockade and the determinants of selectivity in the NaChBac bacterial sodium channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183301. [PMID: 32360369 DOI: 10.1016/j.bbamem.2020.183301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 01/30/2020] [Accepted: 03/29/2020] [Indexed: 10/24/2022]
Abstract
Mutation-induced transformations of conductivity and selectivity in NaChBac bacterial channels are studied experimentally and interpreted within the framework of ionic Coulomb blockade (ICB), while also taking account of resonant quantised dehydration (QD) and site protonation. Site-directed mutagenesis and whole-cell patch-clamp experiments are used to investigate how the fixed charge Qf at the selectivity filter (SF) affects both valence selectivity and same-charge selectivity. The new ICB/QD model predicts that increasing ∣Qf∣ should lead to a shift in selectivity sequences toward larger ion sizes, in agreement with the present experiments and with earlier work. Comparison of the model with experimental data leads to the introduction of an effective charge Qf∗ at the SF, which was found to differ between Aspartate and Glutamate charged rings, and also to depend on position within the SF. It is suggested that protonation of the residues within the restricted space of the SF is important in significantly reducing the effective charge of the EEEE ring. Values of Qf∗ derived from experiments on divalent blockade agree well with expectations based on the ICB/QD model and have led to the first demonstration of ICB oscillations in Ca2+ conduction as a function of the fixed charge. Preliminary studies of the dependence of Ca2+ conduction on pH are qualitatively consistent with the predictions of the model.
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Affiliation(s)
- O A Fedorenko
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YQ, UK; School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
| | - I Kh Kaufman
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - W A T Gibby
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK.
| | - M L Barabash
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK.
| | - D G Luchinsky
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK; SGT, Inc., Greenbelt, MD 20770, USA.
| | - S K Roberts
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YQ, UK.
| | - P V E McClintock
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK.
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7
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8
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Sun LZ, Wang CH, Luo MB, Li H. Trapped and non-trapped polymer translocations through a spherical pore. J Chem Phys 2019; 150:024904. [PMID: 30646715 DOI: 10.1063/1.5063331] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The polymer translocation through a spherical pore is studied using the Langevin dynamics simulation. The translocation events are classified into two types: one is the trapped translocation in which the entire polymer is trapped in the pore and the other is the non-trapped translocation where the pore cannot hold the whole polymer. We find that the trapped translocation is favored at large spheres and small external voltages. However, the monomer-pore attraction would lead to the non-monotonic behavior of the trapped translocation possibility out of all translocation events. Moreover, both the trapped and non-trapped translocation times are dependent on the polymer length, pore size, external voltage, and the monomer-pore attraction. There exist two pathways for the polymer in the trapped translocation: an actively trapped pathway for the polymer trapped in the pore before the head monomer arrives at the pore exit, and a passively trapped pathway for the polymer trapped in the pore while the head monomer is struggling to move out of the pore. The studies of trapped pathways can provide a deep understanding of the polymer translocation behavior.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Chang-Hui Wang
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Haibin Li
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
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9
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Buyukdagli S, Sarabadani J, Ala-Nissila T. Theoretical Modeling of Polymer Translocation: From the Electrohydrodynamics of Short Polymers to the Fluctuating Long Polymers. Polymers (Basel) 2019; 11:E118. [PMID: 30960102 PMCID: PMC6401762 DOI: 10.3390/polym11010118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 01/08/2023] Open
Abstract
The theoretical formulation of driven polymer translocation through nanopores is complicated by the combination of the pore electrohydrodynamics and the nonequilibrium polymer dynamics originating from the conformational polymer fluctuations. In this review, we discuss the modeling of polymer translocation in the distinct regimes of short and long polymers where these two effects decouple. For the case of short polymers where polymer fluctuations are negligible, we present a stiff polymer model including the details of the electrohydrodynamic forces on the translocating molecule. We first show that the electrohydrodynamic theory can accurately characterize the hydrostatic pressure dependence of the polymer translocation velocity and time in pressure-voltage-driven polymer trapping experiments. Then, we discuss the electrostatic correlation mechanisms responsible for the experimentally observed DNA mobility inversion by added multivalent cations in solid-state pores, and the rapid growth of polymer capture rates by added monovalent salt in α -Hemolysin pores. In the opposite regime of long polymers where polymer fluctuations prevail, we review the iso-flux tension propagation (IFTP) theory, which can characterize the translocation dynamics at the level of single segments. The IFTP theory is valid for a variety of polymer translocation and pulling scenarios. We discuss the predictions of the theory for fully flexible and rodlike pore-driven and end-pulled translocation scenarios, where exact analytic results can be derived for the scaling of the translocation time with chain length and driving force.
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Affiliation(s)
- Sahin Buyukdagli
- Department of Physics, Bilkent University, Ankara 06800, Turkey.
| | - Jalal Sarabadani
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran.
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK.
| | - Tapio Ala-Nissila
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK.
- Department of Applied Physics and QTF Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland.
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10
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Sun LZ, Li H, Xu X, Luo MB. Simulation study on the translocation of polyelectrolyte through conical nanopores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:495101. [PMID: 30431017 DOI: 10.1088/1361-648x/aaeb19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Experiments have suggested that the conical nanopore may be a reasonable sensor for the biopolymer analysis as it can provide high-resolution current signal. In this paper, we use Langevin dynamics simulation to study the translocation of charged polymer (polyelectrolyte) through three different conical nanopores, a single-conical nanopore with large entry and small exit (pore I), a single-conical nanopore with small entry and large exit (pore II), and a double-conical nanopore with the tip (narrowest place) at the middle (pore III). Simulation shows that the detailed translocation behaviors are of pore structure dependence. Pore I might be the most reasonable one for the polyelectrolyte analysis, especially at strong monomer-pore attraction, since it can efficiently reduce the polyelectrolyte speed at the tip. The simulation results are interpreted by the free energy profiles of the polyelectrolyte translocation through different pores and the time of individual monomer passing through the tips.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, People's Republic of China
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11
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Jia Z, Choi J, Park S. Surface Charge Density-Dependent DNA Capture through Polymer Planar Nanopores. ACS APPLIED MATERIALS & INTERFACES 2018; 10:40927-40937. [PMID: 30371050 DOI: 10.1021/acsami.8b14423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Surface charge density of nanopore walls plays a critical role in DNA capture in nanopore-based sensing platforms. This paper studied the effect of surface charge density on the capture of double-stranded (ds) DNA molecules into a polymer planar nanopore numerically and experimentally. First, we simulated the effective driving force ( Feff) for the translocation of a dsDNA through a planar nanopore with different sizes and surface charge densities. Focus was given on the capture stage from the nanopore mouth into the nanopore by placing a rodlike DNA at the nanopore mouth rather than inside the nanopore. For negatively charged DNA and nanopore walls, electrophoretic driving force ( FEP) under an electric field is opposed by the viscous drag force by electroosmotic flow ( FEOF). As the surface charge density of the nanopore wall becomes more negative, FEOF exceeds FEP beyond a threshold surface charge density, σthreshold, where DNA molecules cannot be driven through the nanopore via electrophoretic motion. For a 10 nm diameter nanopore filled with 1× TE buffer, σthreshold was determined to be -50 mC/m2. The simulation results were verified by performing dsDNA translocation experiments using a planar nanopore with 10 nm equivalent diameter imprinted on three polymer substrates with different surface charge densities. Both fluorescence observation and ionic current measurement confirmed that only nanopore devices with the surface charge density less negative than σthreshold allowed DNA translocation, indicating that the simulated σthreshold value can be used as a parameter to estimate the translocation of biopolymers in the design of nanopore devices.
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Affiliation(s)
- Zheng Jia
- Mechanical & Industrial Engineering Department and Center for BioModular Multiscale Systems for Precision Medicine , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Junseo Choi
- Mechanical & Industrial Engineering Department and Center for BioModular Multiscale Systems for Precision Medicine , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Sunggook Park
- Mechanical & Industrial Engineering Department and Center for BioModular Multiscale Systems for Precision Medicine , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
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12
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Buyukdagli S, Sarabadani J, Ala-Nissila T. Dielectric Trapping of Biopolymers Translocating through Insulating Membranes. Polymers (Basel) 2018; 10:polym10111242. [PMID: 30961167 PMCID: PMC6401742 DOI: 10.3390/polym10111242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 01/10/2023] Open
Abstract
Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires an extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time can be extended via the dielectric trapping of the polymer. In dilute salt conditions, the dielectric contrast between the low permittivity membrane and large permittivity solvent gives rise to attractive interactions between the cis and trans portions of the polymer. This self-attraction acts as a dielectric trap that can enhance the translocation time by orders of magnitude. We also find that electrostatic interactions result in the piecewise scaling of the translocation time τ with the polymer length L. In the short polymer regime L≲10 nm where the external drift force dominates electrostatic polymer interactions, the translocation is characterized by the drift behavior τ∼L2. In the intermediate length regime 10nm≲L≲κb−1 where κb is the Debye–Hückel screening parameter, the dielectric trap takes over the drift force. As a result, increasing polymer length leads to quasi-exponential growth of the translocation time. Finally, in the regime of long polymers L≳κb−1 where salt screening leads to the saturation of the dielectric trap, the translocation time grows linearly as τ∼L. This strong departure from the drift behavior highlights the essential role played by electrostatic interactions in polymer translocation.
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Affiliation(s)
- Sahin Buyukdagli
- Department of Physics, Bilkent University, Ankara 06800, Turkey.
| | - Jalal Sarabadani
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran.
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK.
| | - Tapio Ala-Nissila
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK.
- Department of Applied Physics and QTF Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland.
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13
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Buyukdagli S. Enhanced polymer capture speed and extended translocation time in pressure-solvation traps. Phys Rev E 2018; 97:062406. [PMID: 30011511 DOI: 10.1103/physreve.97.062406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Indexed: 12/29/2022]
Abstract
The efficiency of nanopore-based biosequencing techniques requires fast anionic polymer capture by like-charged pores followed by a prolonged translocation process. We show that this condition can be achieved by setting a pressure-solvation trap. Polyvalent cation addition to the KCl solution triggers the like-charge polymer-pore attraction. The attraction speeds-up the pressure-driven polymer capture but also traps the molecule at the pore exit, reducing the polymer capture time and extending the polymer escape time by several orders of magnitude. By direct comparison with translocation experiments [D. P. Hoogerheide et al., ACS Nano 8, 7384 (2014)1936-085110.1021/nn5025829], we characterize as well the electrohydrodynamics of polymers transport in pressure-voltage traps. We derive scaling laws that can accurately reproduce the pressure dependence of the experimentally measured polymer translocation velocity and time. We also find that during polymer capture, the electrostatic barrier on the translocating molecule slows down the liquid flow. This prediction identifies the streaming current measurement as a potential way to probe electrostatic polymer-pore interactions.
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Affiliation(s)
- Sahin Buyukdagli
- Department of Physics, Bilkent University, Ankara 06800, Turkey and QTF Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
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14
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Sun LZ, Luo MB, Cao WP, Li H. Theoretical study on the polymer translocation into an attractive sphere. J Chem Phys 2018; 149:024901. [PMID: 30007381 DOI: 10.1063/1.5025609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report a non-sampling model, combining the blob method with the standard lattice-based approximation, to calculate the free energy for the polymer translocation into an attractive sphere (i.e., spherical confined trans side) through a small pore. The translocation time is then calculated by the Fokker-Planck equation based on the free energy profile. There is a competition between the confinement effect of the sphere and the polymer-sphere attraction. The translocation time is increased due to the confinement effect of the sphere, whereas it is reduced by the polymer-sphere attraction. The two effects offset each other at a special polymer-sphere attraction which is dependent on the sphere size, the polymer length, and the driving force. Moreover, the entire translocation process can be divided into an uncrowded stage where the polymer does not experience the confinement effect of the sphere and a crowded stage where the polymer is confined by the sphere. At the critical sphere radius, the durations of the two (uncrowded and crowded) stages are the same. The critical sphere radius R* has a scaling relation with the polymer length N as R* ∼ Nβ. The calculation results show that the current model can effectively treat the translocation of a three-dimensional self-avoiding polymer into the spherical confined trans side.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Wei-Ping Cao
- Institute of Optoelectronic Technology, Lishui University, Lishui 323000, China
| | - Haibin Li
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
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15
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Pastoriza-Gallego M, Thiébot B, Bacri L, Auvray L, Pelta J. Dynamics of a polyelectrolyte through aerolysin channel as a function of applied voltage and concentration ⋆. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:58. [PMID: 29748865 DOI: 10.1140/epje/i2018-11661-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
We describe the behaviour of a polyelectrolyte in confined geometry. The transport of a polyelectrolyte, dextran sulfate, through a recombinant protein channel, aerolysin, inserted into a planar lipid bilayer is studied as a function of applied voltage and polyelectrolyte concentration and chain length. The aerolysin pore has a weak geometry asymmetry, a high number of charged residues and the polyelectrolyte is strongly negatively charged. The resulting current blockades were characterized by short and long dwelling times. Their frequency varies exponentially as a function of applied voltage and linearly as a function of polyelectrolyte concentration. The long blockade duration decreases exponentially when the electrical force increases. The ratio of the population of short events to the one of long events decreases when the applied voltage increases and displays an exponential variation. The long residence time increases with the polyelectrolyte chain length. We measure a reduction of the effective charge of the polyelectrolyte at the pore entry and inside the channel. For a fixed applied voltage, + / - 100 mV, at both sides of the protein pore entrance, the events frequency is similar as a function of dextran sulfate concentration. The mean blockade durations are independent of polyelectrolyte concentration and are similar for both entrances of the pore and remain constant as a function of the electrical force.
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Affiliation(s)
| | - Bénédicte Thiébot
- LAMBE UMR 8587, Université Cergy-Pontoise, Université Paris-Seine, 95302, Cergy-Pontoise, France
| | - Laurent Bacri
- LAMBE UMR 8587, Université Evry, CNRS, CEA, Université Paris-Saclay, 91025, Evry, France
| | - Loïc Auvray
- Laboratoire Matière et Systèmes Complexes, Université Paris Diderot, F-75205, Paris, France
| | - Juan Pelta
- LAMBE UMR 8587, Université Evry, CNRS, CEA, Université Paris-Saclay, 91025, Evry, France.
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16
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Buyukdagli S. Facilitated polymer capture by charge inverted electroosmotic flow in voltage-driven polymer translocation. SOFT MATTER 2018; 14:3541-3549. [PMID: 29682666 DOI: 10.1039/c8sm00620b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The optimal functioning of nanopore-based biosensing tools necessitates rapid polymer capture from the ion reservoir. We identify an ionic correlation-induced transport mechanism that provides this condition without the chemical modification of the polymer or the pore surface. In the typical experimental configuration where a negatively charged silicon-based pore confines a 1 : 1 electrolyte solution, anionic polymer capture is limited by electrostatic polymer-membrane repulsion and the electroosmotic (EO) flow. Added multivalent cations suppress the electrostatic barrier and reverse the pore charge, inverting the direction of the EO flow that drags the polymer to the trans side. This inverted EO flow can be used to speed up polymer capture from the reservoir and to transport weakly or non-uniformly charged polymers that cannot be controlled by electrophoresis.
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Affiliation(s)
- Sahin Buyukdagli
- Department of Physics, Bilkent University, Ankara 06800, Turkey.
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17
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Buyukdagli S, Ala-Nissila T. Multivalent cation induced attraction of anionic polymers by like-charged pores. J Chem Phys 2017; 147:144901. [DOI: 10.1063/1.4994018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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18
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Buyukdagli S, Ala-Nissila T. Controlling polymer capture and translocation by electrostatic polymer-pore interactions. J Chem Phys 2017; 147:114904. [DOI: 10.1063/1.5004182] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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19
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Nosik VL, Rudakova EB. Multilevel description of the DNA molecule translocation in solid-state synthetic nanopores. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516040155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Sun LZ, Luo MB. Langevin dynamics simulation on the translocation of polymer through α-hemolysin pore. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:415101. [PMID: 25192215 DOI: 10.1088/0953-8984/26/41/415101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The forced translocation of a polymer through an α-hemolysin pore under an electrical field is studied using a Langevin dynamics simulation. The α-hemolysin pore is modelled as a connection of a spherical vestibule and a cylindrical β-barrel and polymer-pore attraction is taken into account. The results show that polymer-pore attraction can help the polymer enter the vestibule and the β-barrel as well; however, a strong attraction will slow down the translocation of the polymer through the β-barrel. The mean translocation time for the polymer to thread through the β-barrel increases linearly with the polymer length. By comparing our results with that of a simple pore without a vestibule, we find that the vestibule helps the polymer enter and thread through the β-barrel. Moreover, we find that it is easier for the polymer to thread through the β-barrel if the polymer is located closer to the surface of the vestibule. Some simulation results are explained qualitatively by theoretically analyzing the free-energy landscape of polymer translocation.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Zhejiang University, Hangzhou 310027, People's Republic of China. Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, People's Republic of China
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21
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Wang Y, Tian K, Hunter LL, Ritzo B, Gu LQ. Probing molecular pathways for DNA orientational trapping, unzipping and translocation in nanopores by using a tunable overhang sensor. NANOSCALE 2014; 6:11372-9. [PMID: 25144935 PMCID: PMC6201287 DOI: 10.1039/c4nr03195d] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nanopores provide a unique single-molecule platform for genetic and epigenetic detection. The target nucleic acids can be accurately analyzed by characterizing their specific electric fingerprints or signatures in the nanopore. Here we report a series of novel nanopore signatures generated by target nucleic acids that are hybridized with a probe. A length-tunable overhang appended to the probe functions as a sensor to specifically modulate the nanopore current profile. The resulting signatures can reveal multiple mechanisms for the orientational trapping, unzipping, escaping and translocation of nucleic acids in the nanopore. This universal approach can be used to program various molecular movement pathways, elucidate their kinetics, and enhance the sensitivity and specificity of the nanopore sensor for nucleic acid detection.
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Affiliation(s)
- Yong Wang
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA.
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22
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Rodriguez-Larrea D, Bayley H. Protein co-translocational unfolding depends on the direction of pulling. Nat Commun 2014; 5:4841. [PMID: 25197784 PMCID: PMC4164780 DOI: 10.1038/ncomms5841] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/29/2014] [Indexed: 11/21/2022] Open
Abstract
Protein unfolding and translocation through pores occurs during trafficking between organelles, protein degradation and bacterial toxin delivery. In vivo, co-translocational unfolding can be affected by the end of the polypeptide that is threaded into the pore first. Recently, we have shown that co-translocational unfolding can be followed in a model system at the single-molecule level, thereby unravelling molecular steps and their kinetics. Here, we show that the unfolding kinetics of the model substrate thioredoxin, when pulled through an α-haemolysin pore, differ markedly depending on whether the process is initiated from the C terminus or the N terminus. Further, when thioredoxin is pulled from the N terminus, the unfolding pathway bifurcates: some molecules finish unfolding quickly, while others finish ~100 times slower. Our findings have important implications for the understanding of biological unfolding mechanisms and in the application of nanopore technology for the detection of proteins and their modifications. Protein unfolding and translocation through membrane pores occurs in several biological processes and has implications in nanopore technologies. Here, the authors show that the kinetics of unfolding differ depending on which end of the chain enters the pore first.
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Affiliation(s)
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
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23
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Galla L, Meyer AJ, Spiering A, Sischka A, Mayer M, Hall AR, Reimann P, Anselmetti D. Hydrodynamic slip on DNA observed by optical tweezers-controlled translocation experiments with solid-state and lipid-coated nanopores. NANO LETTERS 2014; 14:4176-4182. [PMID: 24935198 DOI: 10.1021/nl501909t] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We use optical tweezers to investigate the threading force on a single dsDNA molecule inside silicon-nitride nanopores between 6 and 70 nm in diameter, as well as lipid-coated solid-state nanopores. We observe a strong increase of the threading force for decreasing nanopore size that can be attributed to a significant reduction in the electroosmotic flow (EOF), which opposes the electrophoresis. Additionally, we show that the EOF can also be reduced by coating the nanopore wall with an electrically neutral lipid bilayer, resulting in an 85% increase in threading force. All experimental findings can be described by a quantitative theoretical model that incorporates a hydrodynamic slip effect on the DNA surface with a slip length of 0.5 nm.
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Affiliation(s)
- Lukas Galla
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University , 33615 Bielefeld, Germany
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24
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Briggs K, Kwok H, Tabard-Cossa V. Automated fabrication of 2-nm solid-state nanopores for nucleic acid analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2077-86. [PMID: 24585682 DOI: 10.1002/smll.201303602] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/14/2014] [Indexed: 05/25/2023]
Abstract
We demonstrate the automated and reproducible fabrication of sub-2-nm nanopores in 10-nm thick silicon nitride membranes, through controlled dielectric breakdown in solution. Our results reveal that under the appropriate conditions, nanopores can be fabricated with a size no larger than 2.0 ± 0.5-nm in diameter for a sample of N = 23 nanopores, with an average and standard deviation of 1.3 ± 0.6-nm. The dimensions of these nanopores are confirmed by using individual translocating DNA molecules as molecular rulers. We show that a 2.0-nm and a 2.1-nm diameter nanopore are capable of distinguishing single-stranded DNA versus double-stranded DNA, and that a 2.4-nm diameter nanopore can be used to investigate the overstretching transition in short dsDNA fragments. These results highlight the reliability and precision of the automated fabrication of nanopores via controlled dielectric breakdown, showing great promise for the manufacturing of future nanopore-based technologies.
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Affiliation(s)
- Kyle Briggs
- University of Ottawa, Ottawa, Ontario, Canada
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25
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Kesselheim S, Müller W, Holm C. Origin of current blockades in nanopore translocation experiments. PHYSICAL REVIEW LETTERS 2014; 112:018101. [PMID: 24483933 DOI: 10.1103/physrevlett.112.018101] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Indexed: 06/03/2023]
Abstract
We present a detailed investigation of the ionic current in a cylindrical model nanopore in the absence and the presence of a double stranded DNA homopolymer. Our atomistic simulations are capable of reproducing almost exactly the experimental data obtained by Smeets et al., including notably the crossover salt concentration that yields equal current measurements in both situations. We can rule out that the observed current blockade is due to the steric exclusion of charge carriers from the DNA, since for all investigated salt concentrations the charge carrier density is higher when the DNA is present. Calculations using a mean-field electrokinetic model proposed by van Dorp et al. fail quantitatively in predicting this effect. We can relate the shortcomings of the mean-field model to a surface related molecular drag that the ions feel in the presence of the DNA. This drag is independent of the salt concentration and originates from electrostatic, hydrodynamic, and excluded volume interactions.
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Affiliation(s)
- Stefan Kesselheim
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Wojciech Müller
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Christian Holm
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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26
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Gong X, Patil AV, Ivanov AP, Kong Q, Gibb T, Dogan F, deMello AJ, Edel JB. Label-Free In-Flow Detection of Single DNA Molecules using Glass Nanopipettes. Anal Chem 2013; 86:835-41. [DOI: 10.1021/ac403391q] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Amol V. Patil
- Department
of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Qingyuan Kong
- Department
of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Thomas Gibb
- Department
of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Fatma Dogan
- Department
of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Andrew J. deMello
- Institute
for
Chemical and Bioengineering, Department of Chemistry
and Applied Biosciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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27
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Sun LZ, Luo MB. Study on the polymer translocation induced blockade ionic current inside a nanopore by Langevin dynamics simulation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:465101. [PMID: 24099747 DOI: 10.1088/0953-8984/25/46/465101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The blockade ionic current inside a nanopore due to polymer translocation is studied using a three-dimensional Langevin dynamics method. The blockade current IB is dependent on the polymer length N, polymer configuration, polymer-pore interaction, and charge of the polymer. The behavior of IB can be explained using four factors: (1) the volume vacancy fraction fV inside the pore; (2) the conformation of the polymer; (3) the location of the polymer inside the pore; and (4) the total charge Ztot inside the pore. We find that IB increases with fV but decreases with increasing |Ztot|. The influence of the polymer's conformation is complex, dependent on the size of polymer RG and the cross-sectional size of the pore s. A compact conformation can decrease IB when RG > s but increase IB when RG < s. For the latter case, the conformation of the polymer is too small to block the pore, thus providing a broad passage for the ions. At the same fV, monomers will locate close to the surface with a large polymer-pore attraction, which also provides a large IB.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Zhejiang University, Hangzhou 310027, People's Republic of China
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28
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Getfert S, Töws T, Reimann P. Reluctance of a neutral nanoparticle to enter a charged pore. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:052710. [PMID: 24329299 DOI: 10.1103/physreve.88.052710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/06/2013] [Indexed: 06/03/2023]
Abstract
We consider the translocation of a neutral (uncharged) nanoparticle through a pore in a thin membrane with constant surface charge density. If the concomitant Debye screening layer is sufficiently thin, the resulting forces experienced by the particle on its way through the pore are negligible. But when the Debye length becomes comparable to the pore diameter, the particle encounters a quite significant potential barrier while approaching and entering the pore, and symmetrically upon exiting the pore. The main reason is an increasing pressure, which acts on the particle when it intrudes into the counter ion cloud of the Debye screening layer. In case the polarizability of the particle is different (usually smaller) than that of the ambient fluid, a second, much smaller contribution to the potential barrier is due to self-energy effects. Our numerical treatment of the problem is complemented by analytical approximations for sufficiently long cylindrical particles and pores, which agree very well with the numerics.
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Affiliation(s)
- Sebastian Getfert
- Fakultät für Physik, Universität Bielefeld, 33615 Bielefeld, Germany
| | - Thomas Töws
- Fakultät für Physik, Universität Bielefeld, 33615 Bielefeld, Germany
| | - Peter Reimann
- Fakultät für Physik, Universität Bielefeld, 33615 Bielefeld, Germany
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29
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Rowghanian P, Grosberg AY. Two cases of reciprocal relations for electric and hydrodynamic currents: A rigid polymer in a nano-channel and a polyelectrolyte gel. J Chem Phys 2013; 139:024902. [DOI: 10.1063/1.4812693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Getfert S, Töws T, Reimann P. Opposite translocation of long and short oligomers through a nanopore. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062710. [PMID: 23848718 DOI: 10.1103/physreve.87.062710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 05/09/2013] [Indexed: 06/02/2023]
Abstract
We consider elongated cylindrical particles, modeling, e.g., DNA fragments or nanorods, while they translocate under the action of an externally applied voltage through a solid state nanopore. Particular emphasis is put on the concomitant potential energy landscape encountered by the particle on its passage through the pore due to the complex interplay of various electrohydrodynamic effects beyond the realm of small Debye lengths. We find that the net potential energy difference across the membrane may be of opposite sign for short and long particles of equal diameters and charge densities (e.g., oligomers). Thermal noise thus leads to biased diffusion through the pore in opposite directions. By means of an additional membrane gate electrode it is even possible to control the specific particle length at which this transport inversion occurs.
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Affiliation(s)
- Sebastian Getfert
- Fakultät für Physik, Universität Bielefeld, 33615 Bielefeld, Germany
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31
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Qiao BF, Olvera de la Cruz M. Driving Force for Crystallization of Anionic Lipid Membranes Revealed by Atomistic Simulations. J Phys Chem B 2013; 117:5073-80. [DOI: 10.1021/jp401767c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bao Fu Qiao
- Department
of Materials Science and Engineering, and ‡Department of Chemistry, Northwestern University, Evanston, Illinois
60208, United States
| | - Monica Olvera de la Cruz
- Department
of Materials Science and Engineering, and ‡Department of Chemistry, Northwestern University, Evanston, Illinois
60208, United States
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32
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Rowghanian P, Grosberg AY. Electrophoretic capture of a DNA chain into a nanopore. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:042722. [PMID: 23679464 DOI: 10.1103/physreve.87.042722] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Indexed: 05/28/2023]
Abstract
Based on our formulation of the DNA electrophoresis near a pore [Rowghanian and Grosberg, Phys. Rev. E (to be published)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption to a sink placed on top of an energy barrier. Reproducing the previously observed diffusion-limited and barrier-limited regimes as two different limits of the particle absorption process and matching the data, our model suggests a slower growth of the capture rate with the DNA length for very large DNA molecules than the previous model, motivating more experiments beyond the current range of electric field and DNA length. At moderately weak electric fields, our model predicts a different effect, stating that the DNA length dependence of the capture rate first disappears as the field is reduced and eventually reverses to a decreasing trend with N.
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Affiliation(s)
- Payam Rowghanian
- Department of Physics and Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York 10003, USA.
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33
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Rodriguez-Larrea D, Bayley H. Multistep protein unfolding during nanopore translocation. NATURE NANOTECHNOLOGY 2013; 8:288-95. [PMID: 23474543 PMCID: PMC4830145 DOI: 10.1038/nnano.2013.22] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 01/25/2013] [Indexed: 05/18/2023]
Abstract
Cells are divided into compartments and separated from the environment by lipid bilayer membranes. Essential molecules are transported back and forth across the membranes. We have investigated how folded proteins use narrow transmembrane pores to move between compartments. During this process, the proteins must unfold. To examine co-translocational unfolding of individual molecules, we tagged protein substrates with oligonucleotides to enable potential-driven unidirectional movement through a model protein nanopore, a process that differs fundamentally from extension during force spectroscopy measurements. Our findings support a four-step translocation mechanism for model thioredoxin substrates. First, the DNA tag is captured by the pore. Second, the oligonucleotide is pulled through the pore, causing local unfolding of the C terminus of the thioredoxin adjacent to the pore entrance. Third, the remainder of the protein unfolds spontaneously. Finally, the unfolded polypeptide diffuses through the pore into the recipient compartment. The unfolding pathway elucidated here differs from those revealed by denaturation experiments in solution, for which two-state mechanisms have been proposed.
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Affiliation(s)
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
- Correspondence should be addressed to H. Bayley ()
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34
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Wu J, Zhao SL, Gao L, Wu J, Gao D. Sorting short fragments of single-stranded DNA with an evolving electric double layer. J Phys Chem B 2013; 117:2267-72. [PMID: 23356906 DOI: 10.1021/jp3096715] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate a new procedure for separation of single-stranded DNA (ssDNA) fragments that are anchored to the surface of a gold electrode by end hybridization. The new separation procedure takes advantage of the strong yet evolving nonuniform electric field near the gold surface in contact with a buffer solution gradually being diluted with deionized water. Separation of short ssDNA fragments is demonstrated by monitoring the DNA at the gold surface with in situ fluorescence measurement. The experimental results can be rationalized with a simple theoretical model of electric double layer that relates the strength of the surface pulling force to the ionic concentration of the changing buffer solution.
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Affiliation(s)
- Jiamin Wu
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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35
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Reimann P, Meyer A, Getfert S. On the Lubensky-Nelson model of polymer translocation through nanopores. Biophys J 2013; 103:889-97. [PMID: 23009838 DOI: 10.1016/j.bpj.2012.07.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 06/27/2012] [Accepted: 07/24/2012] [Indexed: 11/16/2022] Open
Abstract
We revisit the one-dimensional stochastic model of an earlier study by D. K. Lubensky and D. R. Nelson for the electrically driven translocation of polynucleotides through α-hemolysin pores. We show that the model correctly describes two further important properties of the experimentally observed translocation time distributions, namely their spread (width) and their exponential decay. The resulting overall agreement between theoretical and experimental translocation time distributions is thus very good.
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Affiliation(s)
- Peter Reimann
- Universität Bielefeld, Fakultät für Physik, Bielefeld, Germany.
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36
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Liu Q, Wu H, Wu L, Xie X, Kong J, Ye X, Liu L. Voltage-driven translocation of DNA through a high throughput conical solid-state nanopore. PLoS One 2012; 7:e46014. [PMID: 23029365 PMCID: PMC3454345 DOI: 10.1371/journal.pone.0046014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 08/27/2012] [Indexed: 11/18/2022] Open
Abstract
Nanopores have become an important tool for molecule detection at single molecular level. With the development of fabrication technology, synthesized solid-state membranes are promising candidate substrates in respect of their exceptional robustness and controllable size and shape. Here, a 30-60 (tip-base) nm conical nanopore fabricated in 100 nm thick silicon nitride (Si(3)N(4)) membrane by focused ion beam (FIB) has been employed for the analysis of λ-DNA translocations at different voltage biases from 200 to 450 mV. The distributions of translocation time and current blockage, as well as the events frequencies as a function of voltage are investigated. Similar to previously published work, the presence and configurations of λ-DNA molecules are characterized, also, we find that greater applied voltages markedly increase the events rate, and stretch the coiled λ-DNA molecules into linear form. However, compared to 6-30 nm ultrathin solid-state nanopores, a threshold voltage of 181 mV is found to be necessary to drive DNA molecules through the nanopore due to conical shape and length of the pore. The speed is slowed down ∼5 times, while the capture radius is ∼2 fold larger. The results show that the large nanopore in thick membrane with an improved stability and throughput also has the ability to detect the molecules at a single molecular level, as well as slows down the velocity of molecules passing through the pore. This work will provide more motivations for the development of nanopores as a Multi-functional sensor for a wide range of biopolymers and nano materials.
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Affiliation(s)
- Quanjun Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China.
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37
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Cressiot B, Oukhaled A, Patriarche G, Pastoriza-Gallego M, Betton JM, Auvray L, Muthukumar M, Bacri L, Pelta J. Protein transport through a narrow solid-state nanopore at high voltage: experiments and theory. ACS NANO 2012; 6:6236-6243. [PMID: 22670559 DOI: 10.1021/nn301672g] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report experimentally the transport of an unfolded protein through a narrow solid-state nanopore of 3 nm diameter as a function of applied voltage. The random coil polypeptide chain is larger than the nanopore. The event frequency dependency of current blockades from 200 to 750 mV follows a van't Hoff-Arrhenius law due to the confinement of the unfolded chain. The protein is an extended conformation inside the pore at high voltage. We observe that the protein dwell time decreases exponentially at medium voltage and is inversely proportional to voltage for higher values. This is consistent with the translocation mechanism where the protein is confined in the pore, creating an entropic barrier, followed by electrophoretic transport. We compare these results to our previous work with a larger pore of 20 nm diameter. Our data suggest that electro-osmotic flow and protein adsorption on the narrowest nanopore wall are minimized. We discuss the experimental data obtained as compared with recent theory for the polyelectrolyte translocation process. This theory reproduces clearly the experimental crossover between the entropic barrier regime with medium voltage and the electrophoretic regime with higher voltage.
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38
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Nikoofard N, Fazli H. Electric-field-driven polymer entry into asymmetric nanoscale channels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:021804. [PMID: 22463233 DOI: 10.1103/physreve.85.021804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 12/19/2011] [Indexed: 05/31/2023]
Abstract
The electric-field-driven entry process of flexible charged polymers such as single-stranded DNA (ssDNA) into asymmetric nanoscale channels such as the α-hemolysin protein channel is studied theoretically and using molecular dynamics simulations. Dependence of the height of the free-energy barrier on the polymer length, the strength of the applied electric field, and the channel entrance geometry is investigated. It is shown that the squeezing effect of the driving field on the polymer and the lateral confinement of the polymer before its entry to the channel crucially affect the barrier height and its dependence on the system parameters. The attempt frequency of the polymer for passing the channel is also discussed. Our theoretical and simulation results support each other and describe related data sets of polymer translocation experiments through the α-hemolysin protein channel reasonably well.
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Affiliation(s)
- Narges Nikoofard
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
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39
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Nanopores: Single-Molecule Sensors of Nucleic Acid-Based Complexes. ADVANCES IN CHEMICAL PHYSICS 2012. [DOI: 10.1002/9781118180396.ch6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
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40
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Schink S, Renner S, Alim K, Arnaut V, Simmel FC, Gerland U. Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides. Biophys J 2012; 102:85-95. [PMID: 22225801 DOI: 10.1016/j.bpj.2011.11.4011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 11/02/2011] [Accepted: 11/21/2011] [Indexed: 10/14/2022] Open
Abstract
Nanopore translocation experiments are increasingly applied to probe the secondary structures of RNA and DNA molecules. Here, we report two vital steps toward establishing nanopore translocation as a tool for the systematic and quantitative analysis of polynucleotide folding: 1), Using α-hemolysin pores and a diverse set of different DNA hairpins, we demonstrate that backward nanopore force spectroscopy is particularly well suited for quantitative analysis. In contrast to forward translocation from the vestibule side of the pore, backward translocation times do not appear to be significantly affected by pore-DNA interactions. 2), We develop and verify experimentally a versatile mesoscopic theoretical framework for the quantitative analysis of translocation experiments with structured polynucleotides. The underlying model is based on sequence-dependent free energy landscapes constructed using the known thermodynamic parameters for polynucleotide basepairing. This approach limits the adjustable parameters to a small set of sequence-independent parameters. After parameter calibration, the theoretical model predicts the translocation dynamics of new sequences. These predictions can be leveraged to generate a baseline expectation even for more complicated structures where the assumptions underlying the one-dimensional free energy landscape may no longer be satisfied. Taken together, backward translocation through α-hemolysin pores combined with mesoscopic theoretical modeling is a promising approach for label-free single-molecule analysis of DNA and RNA folding.
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Affiliation(s)
- Severin Schink
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
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41
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He Y, Tsutsui M, Taniguchi M, Kawai T. DNA capture in nanopores for genome sequencing: challenges and opportunities. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm31495a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Oukhaled A, Cressiot B, Bacri L, Pastoriza-Gallego M, Betton JM, Bourhis E, Jede R, Gierak J, Auvray L, Pelta J. Dynamics of completely unfolded and native proteins through solid-state nanopores as a function of electric driving force. ACS NANO 2011; 5:3628-38. [PMID: 21476590 DOI: 10.1021/nn1034795] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We report experimentally the dynamic properties of the entry and transport of unfolded and native proteins through a solid-state nanopore as a function of applied voltage, and we discuss the experimental data obtained as compared to theory. We show an exponential increase in the event frequency of current blockades and an exponential decrease in transport times as a function of the electric driving force. The normalized current blockage ratio remains constant or decreases for folded or unfolded proteins, respectively, as a function of the transmembrane potential. The unfolded protein is stretched under the electric driving force. The dwell time of native compact proteins in the pore is almost 1 order of magnitude longer than that of unfolded proteins, and the event frequency for both protein conformations is low. We discuss the possible phenomena hindering the transport of proteins through the pores, which could explain these anomalous dynamics, in particular, electro-osmotic counterflow and protein adsorption on the nanopore wall.
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Pastoriza-Gallego M, Rabah L, Gibrat G, Thiebot B, van der Goot FG, Auvray L, Betton JM, Pelta J. Dynamics of Unfolded Protein Transport through an Aerolysin Pore. J Am Chem Soc 2011; 133:2923-31. [DOI: 10.1021/ja1073245] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuela Pastoriza-Gallego
- Equipe Matériaux Polymères aux Interfaces, CNRS-UMR 8587, LAMBE, Université d’Évry, Bd F. Mitterrand, 91025 Évry France
- Equipe Matériaux Polymeres aux Interfaces, CNRS-UMR 8587, LAMBE, Université de Cergy-Pontoise, 2 avenue A. Chauvin, 95302 Cergy-Pontoise Cedex France
- Unité de Biochimie Structurale, CNRS-URA 2185, Institut Pasteur, 28, rue du Docteur Roux, 75724 Paris cedex 15 France
| | - Leila Rabah
- Equipe Matériaux Polymères aux Interfaces, CNRS-UMR 8587, LAMBE, Université d’Évry, Bd F. Mitterrand, 91025 Évry France
| | - Gabriel Gibrat
- Equipe Matériaux Polymères aux Interfaces, CNRS-UMR 8587, LAMBE, Université d’Évry, Bd F. Mitterrand, 91025 Évry France
| | - Bénédicte Thiebot
- Equipe Matériaux Polymeres aux Interfaces, CNRS-UMR 8587, LAMBE, Université de Cergy-Pontoise, 2 avenue A. Chauvin, 95302 Cergy-Pontoise Cedex France
| | | | - Loïc Auvray
- Matière et Systèmes Complexes, CNRS-UMR 7057, Université Paris-Diderot, 10 rue Alice Domont et Léonie Duquet, 75205 Paris cedex 13, France
| | - Jean-Michel Betton
- Unité de Biochimie Structurale, CNRS-URA 2185, Institut Pasteur, 28, rue du Docteur Roux, 75724 Paris cedex 15 France
| | - Juan Pelta
- Equipe Matériaux Polymères aux Interfaces, CNRS-UMR 8587, LAMBE, Université d’Évry, Bd F. Mitterrand, 91025 Évry France
- Equipe Matériaux Polymeres aux Interfaces, CNRS-UMR 8587, LAMBE, Université de Cergy-Pontoise, 2 avenue A. Chauvin, 95302 Cergy-Pontoise Cedex France
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44
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Grosberg AY, Rabin Y. DNA capture into a nanopore: Interplay of diffusion and electrohydrodynamics. J Chem Phys 2010; 133:165102. [DOI: 10.1063/1.3495481] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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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.
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Affiliation(s)
- Aleksei Aksimentiev
- Department of Physics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.
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46
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Lathrop DK, Ervin EN, Barrall GA, Keehan MG, Kawano R, Krupka MA, White HS, Hibbs AH. Monitoring the escape of DNA from a nanopore using an alternating current signal. J Am Chem Soc 2010; 132:1878-85. [PMID: 20099878 PMCID: PMC2913974 DOI: 10.1021/ja906951g] [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: 12/28/2022]
Abstract
We present the use of an alternating current (AC) signal as a means to monitor the conductance of an alpha-hemolysin (alphaHL) pore as a DNA hairpin with a polydeoxyadenosine tail is driven into and released from the pore. Specifically, a 12 base pair DNA hairpin attached to a 50-nucleotide poly-A tail (HP-A(50)) is threaded into an alphaHL channel using a DC driving voltage. Once the HP-A(50) molecule is trapped within the alphaHL channel, the DC driving voltage is turned off and the conductance of the channel is monitored using an AC voltage. The escape time, defined as the time it takes the HP-A(50) molecule to transport out of the alphaHL channel, is then measured. This escape time has been monitored as a function of AC amplitude (20 to 250 mV(ac)), AC frequency (60-200 kHz), DC drive voltage (0 to 100 mV(dc)), and temperature (-10 to 20 degrees C), in order to determine their effect on the predominantly diffusive motion of the DNA through the nanopore. The applied AC voltage used to monitor the conductance of the nanopore has been found to play a significant role in the DNA/nanopore interaction. The experimental results are described by a one-dimensional asymmetric periodic potential model that includes the influence of the AC voltage. An activation enthalpy barrier of 1.74 x 10(-19) J and a periodic potential asymmetry parameter of 0.575 are obtained for the diffusion at zero electrical bias of a single nucleotide through alphaHL.
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Affiliation(s)
- Daniel K Lathrop
- Electronic Bio Sciences, 5754 Pacific Center Boulevard, Suite 204, San Diego, California 92121, USA
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47
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Postma HWC. Rapid sequencing of individual DNA molecules in graphene nanogaps. NANO LETTERS 2010; 10:420-5. [PMID: 20044842 DOI: 10.1021/nl9029237] [Citation(s) in RCA: 194] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
I propose a technique for reading the base sequence of a single DNA molecule using a graphene nanogap to read the DNA's transverse conductance. Because graphene is a single atom thick, single-base resolution of the conductance is readily obtained. The nonlinear current-voltage characteristic is used to determine the base type independent of nanogap-width variations that cause the current to change by 5 orders of magnitude. The expected sequencing error rate is 0% up to a nanogap width of 1.6 nm.
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Affiliation(s)
- Henk W Ch Postma
- Department of Physics, California State University Northridge, 18111 Nordhoff Street, Northridge, California 91330-8268, USA.
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48
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Wanunu M, Morrison W, Rabin Y, Grosberg AY, Meller A. Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient. NATURE NANOTECHNOLOGY 2010; 5:160-5. [PMID: 20023645 PMCID: PMC2849735 DOI: 10.1038/nnano.2009.379] [Citation(s) in RCA: 504] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 11/12/2009] [Indexed: 04/14/2023]
Abstract
Solid-state nanopores are sensors capable of analysing individual unlabelled DNA molecules in solution. Although the critical information obtained from nanopores (for example, DNA sequence) comes from the signal collected during DNA translocation, the throughput of the method is determined by the rate at which molecules arrive and thread into the pores. Here, we study the process of DNA capture into nanofabricated SiN pores of molecular dimensions. For fixed analyte concentrations we find an increase in capture rate as the DNA length increases from 800 to 8,000 base pairs, a length-independent capture rate for longer molecules, and increasing capture rates when ionic gradients are established across the pore. Furthermore, we show that application of a 20-fold salt gradient allows the detection of picomolar DNA concentrations at high throughput. The salt gradients enhance the electric field, focusing more molecules into the pore, thereby advancing the possibility of analysing unamplified DNA samples using nanopores.
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Affiliation(s)
- Meni Wanunu
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
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49
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Leveritt JM, Dibaya C, Tesar S, Shrestha R, Burin AL. One-dimensional confinement of electric field and humidity dependent DNA conductivity. J Chem Phys 2009; 131:245102. [DOI: 10.1063/1.3273211] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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de Zoysa RSS, Jayawardhana DA, Zhao Q, Wang D, Armstrong DW, Guan X. Slowing DNA translocation through nanopores using a solution containing organic salts. J Phys Chem B 2009; 113:13332-6. [PMID: 19736966 DOI: 10.1021/jp9040293] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the key challenges to nanopore DNA sequencing is to slow down DNA translocation. Here, we report that the translocation velocities of various DNA homo- and copolymers through protein pores could be significantly decreased by using electrolyte solutions containing organic salts. Using a butylmethylimidazolium chloride (BMIM-Cl) solution instead of the commonly used KCl solution, DNA translocation rates on the order of hundreds of microseconds per nucleotide base were achieved. The much enhanced resolution of the nanopore coupled with different event blockage amplitudes produced by different nucleotides permits the convenient differentiation between various DNA molecules.
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Affiliation(s)
- Ranulu Samanthi S de Zoysa
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019-0065, USA
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