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Kumar A, Bakli C, Chakraborty S. Ion-Solvent Interactions under Confinement Hold the Key to Tuning the DNA Translocation Speeds in Polyelectrolyte-Functionalized Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7300-7309. [PMID: 38536237 DOI: 10.1021/acs.langmuir.3c02816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
DNA sequencing and sensing using nanopore technology delves critically into the alterations in the measurable electrical signal as single-stranded DNA is drawn through a tiny passage. To make such precise measurements, however, slowing down the DNA in the tightly confined passage is a key requirement, which may be achieved by grafting the nanopore walls with a polyelectrolyte layer (PEL). This soft functional layer at the wall, under an off-design condition, however, may block the DNA passage completely, leading to the complete loss of output signal from the nanobio sensor. Whereas theoretical postulates have previously been put forward to explain the essential physics of DNA translocation in nanopores, these have turned out to be somewhat inadequate when confronted with the experimental findings on functionalized nanopores, including the prediction of the events of complete signal losses. Circumventing these constraints, herein we bring out a possible decisive role of the interplay between the inevitable variabilities in the ionic distribution along the nanopore axis due to its finite length as opposed to its idealized "infinite" limit as well as the differential permittivity of PEL and bulk solution that cannot be captured by the commonly used one-dimensional variant of the electrical double layer theory. Our analysis, for the first time, captures variations in the ionic concentration distribution across multidimensional physical space and delineates its impact on the DNA translocation characteristics that have hitherto remained unaddressed. Our results reveal possible complete blockages of DNA translocation as influenced by less-than-threshold permittivity values or greater-than-threshold grafting densities of the PEL. In addition, electrohydrodynamic blocking is witnessed due to the ion-selective nature of the nanopore at low ionic concentrations. Hence, our study establishes a functionally active regime over which the PEL layer in a finite-length nanopore facilitates controllable DNA translocation, enabling successful sequencing and sensing through the explicit modulation of translocation speed.
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Affiliation(s)
- Avinash Kumar
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Chirodeep Bakli
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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2
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Vahid H, Scacchi A, Sammalkorpi M, Ala-Nissila T. Nonmonotonic electrophoretic mobility of rodlike polyelectrolytes by multivalent coions in added salt. Phys Rev E 2024; 109:014501. [PMID: 38366448 DOI: 10.1103/physreve.109.014501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/30/2023] [Indexed: 02/18/2024]
Abstract
It is well established that when multivalent counterions or salts are added to a solution of highly charged polyelectrolytes (PEs), correlation effects can cause charge inversion of the PE, leading to electrophoretic mobility (EM) reversal. In this work, we use coarse-grained molecular-dynamics simulations to unravel the less understood effect of coion valency on EM reversal for rigid DNA-like PEs. We find that EM reversal induced by multivalent counterions is suppressed with increasing coion valency in the salt added and eventually vanishes. Further, we find that EM is enhanced at fixed low salt concentrations for salts with monovalent counterions when multivalent coions with increasing valency are introduced. However, increasing the salt concentration causes a crossover that leads to EM reversal which is enhanced by increasing coion valency at high salt concentration. Remarkably, this multivalent coion-induced EM reversal persists even for low values of PE linear charge densities where multivalent counterions alone cannot induce EM reversal. These results facilitate tuning PE-PE interactions and self-assembly with both coion and counterion valencies.
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Affiliation(s)
- Hossein Vahid
- Department of Applied Physics, Aalto University, P.O. Box 11000, 00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Alberto Scacchi
- Department of Applied Physics, Aalto University, P.O. Box 11000, 00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Tapio Ala-Nissila
- Department of Applied Physics, Aalto University, P.O. Box 11000, 00076 Aalto, Finland
- Quantum Technology Finland Center of Excellence, Department of Applied Physics, Aalto University, P.O. Box 11000, 00076 Aalto, Finland
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
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3
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Ahmadi E, Sadeghi A, Chakraborty S. Slip-Coupled Electroosmosis and Electrophoresis Dictate DNA Translocation Speed in Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:12292-12301. [PMID: 37603825 DOI: 10.1021/acs.langmuir.3c01230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Controlling the DNA translocation speed is critical in nanopore sequencing, but remains rather challenging in practice, as attributable to a complex coupling between nanoscale fluidics and electrically mediated migration of DNA in a dynamically evolving manner. One important factor influencing the translocation speed is the DNA-liquid slippage stemming from the hydrophobic nature of the oligonucleotide, an aspect that has been widely ignored in the reported literature. In an effort to circumvent this conceptual deficit, here we first develop an analytical model to bring out the slip-mediated coupling between the electroosmosis and DNA-electrophoresis in a solid-state nanopore at low surface charge limits, ignoring the end effects. Subsequently, we compare these results with the numerical simulation data on electrokinetically modulated DNA translocation in such a nanopore, albeit of finite length with due accommodation of the end effects, connecting two end reservoirs by deploying a fully coupled Poisson-Nernst-Plank-Stokes flow model. Both the numerical and analytical results indicate that the DNA translocation speed is a linearly increasing function of the slip length, with more than four-fold increase being observed for a slip length as minimal as 0.5 nm as compared to the no-slip scenario. Considering specific strategies on demand for arresting high translocation speeds for accurate DNA sequencing, the above results establish a theoretical proposition for the same, premised on an analytical expression of the DNA-hydrophobicity modulated enhancement in the translocation speed for designing a nanopore-based sequencing platform─a paradigm that remained to be underemphasized thus far.
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Affiliation(s)
- Elham Ahmadi
- Department of Mechanical Engineering, University of Kurdistan, Sanandaj 66177-15175, Iran
| | - Arman Sadeghi
- Department of Mechanical Engineering, University of Kurdistan, Sanandaj 66177-15175, Iran
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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4
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Mayer DB, Braun D, Franosch T. Thermophoretic motion of a charged single colloidal particle. Phys Rev E 2023; 107:044602. [PMID: 37198806 DOI: 10.1103/physreve.107.044602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 03/13/2023] [Indexed: 05/19/2023]
Abstract
We calculate the thermophoretic drift of a charged single colloidal particle with hydrodynamically slipping surface immersed in an electrolyte solution in response to a small temperature gradient. Here we rely on a linearized hydrodynamic approach for the fluid flow and the motion of the electrolyte ions while keeping the full nonlinearity of the Poisson-Boltzmann equation of the unperturbed system to account for possible large surface charging. The partial differential equations are transformed into a coupled set of ordinary differential equations in linear response. Numerical solutions are elaborated for parameter regimes of small and large Debye shielding and different hydrodynamic boundary conditions encoded in a varying slip length. Our results are in good agreement with predictions from recent theoretical work and successfully describe experimental observations on thermophoresis of DNA. We also compare our numerical results with experimental data on polystyrene beads.
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Affiliation(s)
- Daniel B Mayer
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Dieter Braun
- Systems Biophysics, Physics Department, Nanosystems Initiative Munich and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, D-80799 München, Germany
| | - Thomas Franosch
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
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5
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Yang X, Buyukdagli S, Scacchi A, Sammalkorpi M, Ala-Nissila T. Theoretical and computational analysis of the electrophoretic polymer mobility inversion induced by charge correlations. Phys Rev E 2023; 107:034503. [PMID: 37073074 DOI: 10.1103/physreve.107.034503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/14/2023] [Indexed: 04/20/2023]
Abstract
Electrophoretic (EP) mobility reversal is commonly observed for strongly charged macromolecules in multivalent salt solutions. This curious effect takes place, e.g., when a charged polymer, such as DNA, adsorbs excess counterions so that the counterion-dressed surface charge reverses its sign, leading to the inversion of the polymer drift driven by an external electric field. In order to characterize this seemingly counterintuitive phenomenon that cannot be captured by electrostatic mean-field theories, we adapt here a previously developed strong-coupling-dressed Poisson-Boltzmann approach to the cylindrical geometry of the polyelectrolyte-salt system. Within the framework of this formalism, we derive an analytical polymer mobility formula dressed by charge correlations. In qualitative agreement with polymer transport experiments, this mobility formula predicts that the increment of the monovalent salt, the decrease of the multivalent counterion valency, and the increase of the dielectric permittivity of the background solvent suppress charge correlations and increase the multivalent bulk counterion concentration required for EP mobility reversal. These results are corroborated by coarse-grained molecular dynamics simulations showing how multivalent counterions induce mobility inversion at dilute concentrations and suppress the inversion effect at large concentrations. This re-entrant behavior, previously observed in the aggregation of like-charged polymer solutions, calls for verification by polymer transport experiments.
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Affiliation(s)
- Xiang Yang
- Department of Applied Physics, Aalto University, P. O. Box 11000, FI-00076 Aalto, Finland
| | | | - Alberto Scacchi
- Department of Applied Physics, Aalto University, P. O. Box 11000, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland
- Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland
| | - Tapio Ala-Nissila
- Department of Applied Physics, Aalto University, P. O. Box 11000, FI-00076 Aalto, Finland
- Quantum Technology Finland Center of Excellence, Department of Applied Physics, Aalto University, P. O. Box 11000, FI-00076 Aalto, Finland
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
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6
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Chantipmanee N, Xu Y. Nanofluidics for chemical and biological dynamics in solution at the single molecular level. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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Yang L, Hu J, Li MC, Xu M, Gu ZY. Solid-state nanopore: chemical modifications, interactions, and functionalities. Chem Asian J 2022; 17:e202200775. [PMID: 36071031 DOI: 10.1002/asia.202200775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/06/2022] [Indexed: 11/08/2022]
Abstract
Nanopore technology is a burgeoning detection technology for single-molecular sensing and ion rectification. Solid-state nanopores have attracted more and more attention because of their higher stability and tunability than biological nanopores. However, solid-state nanopores still suffer the drawbacks of low signal-to-noise ratio and low resolution, which hinders their practical applications. Thus, developing operatical and useful methods to overcome the shortages of solid-state nanopores is urgently needed. Here, we summarize the recent research on nanopore modification to achieve this goal. Modifying solid-state nanopores with different coating molecules can improve the selectivity, sensitivity, and stability of nanopores. The modified molecules can introduce different functions into the nanopores, greatly expanding the applications of this novel detection technology. We hope that this review of nanopore modification will provide new ideas for this field.
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Affiliation(s)
- Lei Yang
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Jun Hu
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Min-Chao Li
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Ming Xu
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Zhi-Yuan Gu
- Nanjing Normal University, College of Chemistry and Materials Science, 1 Wenyuan Rd, 210023, Nanjing, CHINA
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8
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Yang J, Xu Y. Nanofluidics for sub-single cellular studies: Nascent progress, critical technologies, and future perspectives. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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9
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Ying C, Houghtaling J, Mayer M. Effects of off-axis translocation through nanopores on the determination of shape and volume estimates for individual particles. NANOTECHNOLOGY 2022; 33:275501. [PMID: 35320779 DOI: 10.1088/1361-6528/ac6087] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Resistive pulses generated by nanoparticles that translocate through a nanopore contain multi-parametric information about the physical properties of those particles. For example, non-spherical particles sample several different orientations during translocation, producing fluctuations in blockade current that relate to their shape. Due to the heterogenous distribution of electric field from the center to the wall of a nanopore while a particle travels through the pore, its radial position influences the blockade current, thereby affecting the quantification of parameters related to the particle's characteristics. Here, we investigate the influence of these off-axis effects on parameters estimated by performing finite element simulations of dielectric particles transiting a cylindrical nanopore. We varied the size, ellipsoidal shape, and radial position of individual particles, as well as the size of the nanopore. As expected, nanoparticles translocating near the nanopore wall produce increase current blockades, resulting in overestimates of particle volume. We demonstrated that off-axis effects also influence estimates of shape determined from resistive pulse analyses, sometimes producing a multiple-fold deviation in ellipsoidal length-to-diameter ratio between estimates and reference values. By using a nanopore with the minimum possible diameter that still allows the particle to rotate while translocating, off-axis effects on the determination of both volume and shape can be minimized. In addition, tethering the nanoparticles to a fluid coating on the nanopore wall makes it possible to determine an accurate particle shape with an overestimated volume. This work provides a framework to select optimal ratios of nanopore to nanoparticle size for experiments targeting free translocations.
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Affiliation(s)
- Cuifeng Ying
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Jared Houghtaling
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
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10
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Corti HR, Appignanesi GA, Barbosa MC, Bordin JR, Calero C, Camisasca G, Elola MD, Franzese G, Gallo P, Hassanali A, Huang K, Laria D, Menéndez CA, de Oca JMM, Longinotti MP, Rodriguez J, Rovere M, Scherlis D, Szleifer I. Structure and dynamics of nanoconfined water and aqueous solutions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:136. [PMID: 34779954 DOI: 10.1140/epje/s10189-021-00136-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.
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Affiliation(s)
- Horacio R Corti
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina.
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, 8000, Bahía Blanca, Argentina
| | - Marcia C Barbosa
- Institute of Physics, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, Brazil
| | - J Rafael Bordin
- Department of Physics, Institute of Physics and Mathematics, 96050-500, Pelotas, RS, Brazil
| | - Carles Calero
- Secció de Física Estadística i Interdisciplinària - Departament de Física de la Matèria Condensada, Universitat de Barcelona & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, 00146, Roma, Italy
| | - M Dolores Elola
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària - Departament de Física de la Matèria Condensada, Universitat de Barcelona & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, 00146, Roma, Italy
| | - Ali Hassanali
- Condensed Matter and Statistical Physics Section (CMSP), The International Center for Theoretical Physics (ICTP), Trieste, Italy
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Daniel Laria
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cintia A Menéndez
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, 8000, Bahía Blanca, Argentina
| | - Joan M Montes de Oca
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, 8000, Bahía Blanca, Argentina
| | - M Paula Longinotti
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Javier Rodriguez
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de General San Martín, San Martín, Buenos Aires, Argentina
| | - Mauro Rovere
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, 00146, Roma, Italy
| | - Damián Scherlis
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Igal Szleifer
- Biomedical Engineering Department, Northwestern University, Evanston, USA
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11
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Das N, Ropmay GD, Joseph AM, RoyChaudhuri C. Modeling the Effective Conductance Drop Due to a Particle in a Solid State Nanopore Towards Optimized Design. IEEE Trans Nanobioscience 2020; 19:598-608. [PMID: 32780701 DOI: 10.1109/tnb.2020.3015592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An understanding of the current change in a solid state nanopore due to particle movement or capture is crucial for improvement of nanopore based sensing technologies. For lower aspect ratio pores, which are gaining importance due to their high sensitivity, there is interplay between access and pore resistance and the existing theories for computation of access resistance cannot explain most of the experimental observations. Hence, there is a need to develop a comprehensive model for calculating the effective conductance drop in presence of particles in a solid state nanopore. In this paper, we develop analytical models to calculate both the access and pore resistance in presence of particle at different positions during translocation and also when captured by receptors in functionalized nanopores. A wide range of pore geometry and molar strength has been investigated. Taking into consideration the positional uncertainty during particle translocation, the effective resistance sensitivity has been found to agree very well with the experimental observations in low aspect ratio pore. Additionally, we observe that in functionalized nanopores, a pore of higher diameter results in around 50% increase in sensitivity compared to a pore with half its diameter, which indicates the scope of design optimization in such systems.
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12
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Kazoe Y, Mawatari K, Li L, Emon H, Miyawaki N, Chinen H, Morikawa K, Yoshizaki A, Dittrich PS, Kitamori T. Lipid Bilayer-Modified Nanofluidic Channels of Sizes with Hundreds of Nanometers for Characterization of Confined Water and Molecular/Ion Transport. J Phys Chem Lett 2020; 11:5756-5762. [PMID: 32633535 DOI: 10.1021/acs.jpclett.0c01084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Water inside and between cells with dimensions on the order of 101-103 nm such as synaptic clefts and mitochondria is thought to be important to biological functions, such as signal transmissions and energy production. However, the characterization of water in such spaces has been difficult owing to the small size and complexity of cellular environments. To this end, we proposed and fabricated a biomimetic nanospace exploiting nanofluidic channels with defined dimensions of hundreds of nanometers and controlled environments. A method of modifying a glass nanochannel with a unilamellar lipid bilayer was developed. We revealed that 2.1-5.6 times higher viscosity of water arises in a 200 nm sized biomimetic nanospace by interactions between water molecules and the lipid bilayer surface and significantly affects the molecular/ion transport that is required for the biological functions. The proposed method provides both a technical breakthrough and new findings to the fields of physical chemistry and biology.
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Affiliation(s)
- Yutaka Kazoe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Kazuma Mawatari
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Lixiao Li
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Hisaki Emon
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Naoya Miyawaki
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Hiroyuki Chinen
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Kyojiro Morikawa
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Ayumi Yoshizaki
- Department of Dermatology, School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Takehiko Kitamori
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
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13
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Eggenberger OM, Ying C, Mayer M. Surface coatings for solid-state nanopores. NANOSCALE 2019; 11:19636-19657. [PMID: 31603455 DOI: 10.1039/c9nr05367k] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.
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Affiliation(s)
- Olivia M Eggenberger
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Cuifeng Ying
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Michael Mayer
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
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14
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Houghtaling J, Ying C, Eggenberger OM, Fennouri A, Nandivada S, Acharjee M, Li J, Hall AR, Mayer M. Estimation of Shape, Volume, and Dipole Moment of Individual Proteins Freely Transiting a Synthetic Nanopore. ACS NANO 2019; 13:5231-5242. [PMID: 30995394 DOI: 10.1021/acsnano.8b09555] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This paper demonstrates that high-bandwidth current recordings in combination with low-noise silicon nitride nanopores make it possible to determine the molecular volume, approximate shape, and dipole moment of single native proteins in solution without the need for labeling, tethering, or other chemical modifications of these proteins. The analysis is based on current modulations caused by the translation and rotation of single proteins through a uniform electric field inside of a nanopore. We applied this technique to nine proteins and show that the measured protein parameters agree well with reference values but only if the nanopore walls were coated with a nonstick fluid lipid bilayer. One potential challenge with this approach is that an untethered protein is able to diffuse laterally while transiting a nanopore, which generates increasingly asymmetric disruptions in the electric field as it approaches the nanopore walls. These "off-axis" effects add an additional noise-like element to the electrical recordings, which can be exacerbated by nonspecific interactions with pore walls that are not coated by a fluid lipid bilayer. We performed finite element simulations to quantify the influence of these effects on subsequent analyses. Examining the size, approximate shape, and dipole moment of unperturbed, native proteins in aqueous solution on a single-molecule level in real time while they translocate through a nanopore may enable applications such as identifying or characterizing proteins in a mixture, or monitoring the assembly or disassembly of transient protein complexes based on their shape, volume, or dipole moment.
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Affiliation(s)
- Jared Houghtaling
- Department of Biomedical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Cuifeng Ying
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Olivia M Eggenberger
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Aziz Fennouri
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Santoshi Nandivada
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Mitu Acharjee
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Jiali Li
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Adam R Hall
- Wake Forest University School of Medicine , Winston Salem , North Carolina 27157 , United States
| | - Michael Mayer
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
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15
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Burelbach J, Stark H. Determining phoretic mobilities with Onsager's reciprocal relations: Electro- and thermophoresis revisited. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:4. [PMID: 30643995 DOI: 10.1140/epje/i2019-11769-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
We use a hydrodynamic reciprocal approach to phoretic motion to derive general expressions for the electrophoretic and thermophoretic mobility of weakly charged colloids in aqueous electrolyte solutions. Our approach shows that phoretic motion can be understood in terms of the interfacial transport of thermodynamic excess quantities that arises when a colloid is kept stationary inside a bulk fluid flow. The obtained expressions for the mobilities are extensions of previously known results as they can account for different hydrodynamic boundary conditions at the colloidal surface, irrespective of how the colloid-fluid interaction range compares to the colloidal radius.
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Affiliation(s)
- Jérôme Burelbach
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623, Berlin, Germany.
| | - Holger Stark
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623, Berlin, Germany
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16
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Töws T, Reimann P. Lateral trapping of DNA inside a voltage gated nanopore. Phys Rev E 2017; 95:062413. [PMID: 28709268 DOI: 10.1103/physreve.95.062413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 11/07/2022]
Abstract
The translocation of a short DNA fragment through a nanopore is addressed when the perforated membrane contains an embedded electrode. Accurate numerical solutions of the coupled Poisson, Nernst-Planck, and Stokes equations for a realistic, fully three-dimensional setup as well as analytical approximations for a simplified model are worked out. By applying a suitable voltage to the membrane electrode, the DNA can be forced to preferably traverse the pore either along the pore axis or at a small but finite distance from the pore wall.
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Affiliation(s)
- Thomas Töws
- Fakultät für Physik, Universität Bielefeld, 33615 Bielefeld, Germany
| | - Peter Reimann
- Fakultät für Physik, Universität Bielefeld, 33615 Bielefeld, Germany
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17
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18
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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19
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Adur J, Barbosa G, Pelegati V, Baratti M, Cesar C, Casco V, Carvalho H. Multimodal and non-linear optical microscopy applications in reproductive biology. Microsc Res Tech 2016; 79:567-82. [DOI: 10.1002/jemt.22684] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/18/2016] [Accepted: 05/04/2016] [Indexed: 01/11/2023]
Affiliation(s)
- J. Adur
- Biophotonic Group. Optics and Photonics Research Center (CEPOF); Institute of Physics “Gleb Wataghin,” State University of Campinas; Brazil
- Biofotónica y Procesamiento de Información Biológica (ByPIB); CITER - Centro de Investigación y Transferencia de Entre Ríos, CONICET-UNER; Argentina
- Microscopy Laboratory Applied to Molecular and Cellular Studies, School of Bioengineering; National University of Entre Ríos; Argentina
| | - G.O. Barbosa
- Department of Structural and Functional Biology; Biology Institute, State University of Campinas; Brazil
| | - V.B. Pelegati
- Biophotonic Group. Optics and Photonics Research Center (CEPOF); Institute of Physics “Gleb Wataghin,” State University of Campinas; Brazil
- INFABiC - National Institute of Science and Technology on Photonics Applied to Cell Biology, Campinas; Brazil
| | - M.O. Baratti
- INFABiC - National Institute of Science and Technology on Photonics Applied to Cell Biology, Campinas; Brazil
| | - C.L. Cesar
- Biophotonic Group. Optics and Photonics Research Center (CEPOF); Institute of Physics “Gleb Wataghin,” State University of Campinas; Brazil
- INFABiC - National Institute of Science and Technology on Photonics Applied to Cell Biology, Campinas; Brazil
- Department of Physics of Federal University of Ceara (UFC); Brazil
| | - V.H. Casco
- Biofotónica y Procesamiento de Información Biológica (ByPIB); CITER - Centro de Investigación y Transferencia de Entre Ríos, CONICET-UNER; Argentina
- Microscopy Laboratory Applied to Molecular and Cellular Studies, School of Bioengineering; National University of Entre Ríos; Argentina
| | - H.F. Carvalho
- Department of Structural and Functional Biology; Biology Institute, State University of Campinas; Brazil
- INFABiC - National Institute of Science and Technology on Photonics Applied to Cell Biology, Campinas; Brazil
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20
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Zhai S, Zhao H. Influence of concentration polarization on DNA translocation through a nanopore. Phys Rev E 2016; 93:052409. [PMID: 27300926 PMCID: PMC4910644 DOI: 10.1103/physreve.93.052409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 11/07/2022]
Abstract
Concentration polarization can be induced by the unique ion-perm selectivity of small nanopores, leading to a salt concentration gradient across nanopores. This concentration gradient can create diffusio-osmosis and induce an electric field, affecting ionic currents on DNA that translocates through a nanopore. Here this influence is theoretically investigated by solving the continuum Poisson-Nernst-Planck model for different salt concentrations, DNA surface charge densities, and pore properties. By implementing the perturbation method, we can explicitly compute the contribution of concentration polarization to the ionic current. The induced electric field by concentration polarization is opposite to the imposed electric field and decreases the migration current, and the induced diffusio-osmosis can decrease the convection current as well. Our studies suggest that the importance of the concentration polarization can be determined by the parameter λ/G where λ is the double-layer thickness and G is the gap size. When λ/G is larger than a critical value, the influence of concentration polarization becomes more prominent. This conclusion is supported by the studies on the dependence of the ionic current on salt concentration and pore properties, showing that the difference between two models with and without accounting for concentration polarization is larger for low salts and small pores, which correspond to larger λ/G.
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Affiliation(s)
- Shengjie Zhai
- Department of Mechanical Engineering, University of Nevada, Las Vegas, NV, 89154
| | - Hui Zhao
- Department of Mechanical Engineering, University of Nevada, Las Vegas, NV, 89154
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21
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Zahid OK, Hall AR. Helium Ion Microscope Fabrication of Solid-State Nanopore Devices for Biomolecule Analysis. HELIUM ION MICROSCOPY 2016. [DOI: 10.1007/978-3-319-41990-9_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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22
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Henley RY, Carson S, Wanunu M. Studies of RNA Sequence and Structure Using Nanopores. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 139:73-99. [PMID: 26970191 DOI: 10.1016/bs.pmbts.2015.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nanopores are powerful single-molecule sensors with nanometer scale dimensions suitable for detection, quantification, and characterization of nucleic acids and proteins. Beyond sequencing applications, both biological and solid-state nanopores hold great promise as tools for studying the biophysical properties of RNA. In this review, we highlight selected landmark nanopore studies with regards to RNA sequencing, microRNA detection, RNA/ligand interactions, and RNA structural/conformational analysis.
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Affiliation(s)
- Robert Y Henley
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts, USA; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA.
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23
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Bulushev RD, Marion S, Radenovic A. Relevance of the Drag Force during Controlled Translocation of a DNA-Protein Complex through a Glass Nanocapillary. NANO LETTERS 2015; 15:7118-25. [PMID: 26393370 DOI: 10.1021/acs.nanolett.5b03264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Combination of glass nanocapillaries with optical tweezers allowed us to detect DNA-protein complexes in physiological conditions. In this system, a protein bound to DNA is characterized by a simultaneous change of the force and ionic current signals from the level observed for the bare DNA. Controlled displacement of the protein away from the nanocapillary opening revealed decay in the values of the force and ionic current. Negatively charged proteins EcoRI, RecA, and RNA polymerase formed complexes with DNA that experienced electrophoretic force lower than the bare DNA inside nanocapillaries. Force profiles obtained for DNA-RecA in our system were different than those in the system with nanopores in membranes and optical tweezers. We suggest that such behavior is due to the dominant impact of the drag force comparing to the electrostatic force acting on a DNA-protein complex inside nanocapillaries. We explained our results using a stochastic model taking into account the conical shape of glass nanocapillaries.
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Affiliation(s)
- Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sanjin Marion
- Institute of Physics , Bijenicka cesta 46, HR-10000 Zagreb, Croatia
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
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24
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Li J, Yu D, Zhao Q. Solid-state nanopore-based DNA single molecule detection and sequencing. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1542-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Lepoitevin M, Coulon PE, Bechelany M, Cambedouzou J, Janot JM, Balme S. Influence of nanopore surface charge and magnesium ion on polyadenosine translocation. NANOTECHNOLOGY 2015; 26:144001. [PMID: 25785663 DOI: 10.1088/0957-4484/26/14/144001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We investigate the influence of a nanopore surface state and the addition of Mg(2+) on poly-adenosine translocation. To do so, two kinds of nanopores with a low aspect ratio (diameter ∼3-5 nm, length 30 nm) were tailored: the first one with a negative charge surface and the second one uncharged. It was shown that the velocity and the energy barrier strongly depend on the nanopore surface. Typically if the nanopore and polyA exhibit a similar charge, the macromolecule velocity increases and its global energy barrier of entrance in the nanopore decreases, as opposed to the non-charged nanopore. Moreover, the addition of a divalent chelating cation induces an increase of energy barrier of entrance, as expected. However, for a negative nanopore, this effect is counterbalanced by the inversion of the surface charge induced by the adsorption of divalent cations.
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Affiliation(s)
- Mathilde Lepoitevin
- Institut Européen des Membranes, UMR5635 CNRS-UM2-ENSCM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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26
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Sischka A, Galla L, Meyer AJ, Spiering A, Knust S, Mayer M, Hall AR, Beyer A, Reimann P, Gölzhäuser A, Anselmetti D. Controlled translocation of DNA through nanopores in carbon nano-, silicon-nitride- and lipid-coated membranes. Analyst 2015; 140:4843-7. [DOI: 10.1039/c4an02319f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The DNA threading forces through nanopores in novel carbon nano membranes and other membrane materials and their theory are presented.
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27
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Freedman KJ, Haq SR, Fletcher MR, Foley JP, Jemth P, Edel JB, Kim MJ. Nonequilibrium capture rates induce protein accumulation and enhanced adsorption to solid-state nanopores. ACS NANO 2014; 8:12238-49. [PMID: 25426798 DOI: 10.1021/nn5062645] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Single molecule capturing of analytes using an electrically biased nanopore is the fundamental mechanism in which nearly all nanopore experiments are conducted. With pore dimensions being on the order of a single molecule, the spatial zone of sensing only contains approximately a zeptoliter of volume. As a result, nanopores offer high precision sensing within the pore but provide little to no information about the analytes outside the pore. In this study, we use capture frequency and rate balance theory to predict and study the accumulation of proteins at the entrance to the pore. Protein accumulation is found to have positive attributes such as capture rate enhancement over time but can additionally lead to negative effects such as long-term blockages typically attributed to protein adsorption on the surface of the pore. Working with the folded and unfolded states of the protein domain PDZ2 from SAP97, we show that applying short (e.g., 3-25 s in duration) positive voltage pulses, rather than a constant voltage, can prevent long-term current blockades (i.e., adsorption events). By showing that the concentration of proteins around the pore can be controlled in real time using modified voltage protocols, new experiments can be explored which study the role of concentration on single molecular kinetics including protein aggregation, folding, and protein binding.
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Affiliation(s)
- Kevin J Freedman
- Department of Chemistry, Imperial College London , South Kensington, SW7 2AZ London, United Kingdom
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28
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Palyulin VV, Ala-Nissila T, Metzler R. Polymer translocation: the first two decades and the recent diversification. SOFT MATTER 2014; 10:9016-37. [PMID: 25301107 DOI: 10.1039/c4sm01819b] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Probably no other field of statistical physics at the borderline of soft matter and biological physics has caused such a flurry of papers as polymer translocation since the 1994 landmark paper by Bezrukov, Vodyanoy, and Parsegian and the study of Kasianowicz in 1996. Experiments, simulations, and theoretical approaches are still contributing novel insights to date, while no universal consensus on the statistical understanding of polymer translocation has been reached. We here collect the published results, in particular, the famous-infamous debate on the scaling exponents governing the translocation process. We put these results into perspective and discuss where the field is going. In particular, we argue that the phenomenon of polymer translocation is non-universal and highly sensitive to the exact specifications of the models and experiments used towards its analysis.
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Affiliation(s)
- Vladimir V Palyulin
- Institute for Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany.
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29
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Bulushev RD, Steinbock LJ, Khlybov S, Steinbock JF, Keyser UF, Radenovic A. Measurement of the position-dependent electrophoretic force on DNA in a glass nanocapillary. NANO LETTERS 2014; 14:6606-13. [PMID: 25343616 DOI: 10.1021/nl503272r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling forces and mapped the position-dependent force profiles acting on DNA inside nanocapillaries of different sizes. We showed that the stalling force is higher in nanocapillaries of smaller diameters. The position-dependent force profiles strongly depend on the size of the nanocapillary opening, and for openings smaller than 20 nm, the profiles resemble the behavior observed in solid-state nanopores. To characterize the position-dependent force profiles in nanocapillaries of different sizes, we used a model that combines information from both analytical approximations and numerical calculations.
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Affiliation(s)
- Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
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30
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Drücker P, Gerke V, Galla HJ. Importance of phospholipid bilayer integrity in the analysis of protein-lipid interactions. Biochem Biophys Res Commun 2014; 453:143-7. [PMID: 25264195 DOI: 10.1016/j.bbrc.2014.09.079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 09/18/2014] [Indexed: 11/29/2022]
Abstract
The integrity of supported phospholipid bilayer membranes is of crucial importance for the investigation of lipid-protein interactions. Therefore we recorded the formation of supported membranes on SiO2 and mica by quartz crystal microbalance and controlled the integrity by atomic force microscopy. This study aims to analyze how membrane defects affect protein-lipid interactions. The experiments focused on a lipid mixture of POPC/DOPC/Chol/POPS/PI(4,5)P2 (37:20:20:20:3) and the binding of the peripheral membrane associated protein annexin A2. We found that formation of a continuous undisturbed bilayer is an indispensable precondition for a reliable determination and quantification of lipid-protein-interactions. If membrane defects were present, protein adsorption causes membrane disruption and lipid detachment on a support thus leading to false determination of binding constants. Our results obtained for PI(4,5)P2 and cholesterol containing supported membranes yield new knowledge to construct functional surfaces that may cover nanoporous substrates, form free standing membranes or may be used for lab-on-a-chip applications.
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Affiliation(s)
- Patrick Drücker
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, D-48149 Münster, Germany
| | - Volker Gerke
- Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Hans-Joachim Galla
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, D-48149 Münster, Germany.
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