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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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Buyukdagli S. Dielectric Manipulation of Polymer Translocation Dynamics in Engineered Membrane Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:122-131. [PMID: 34958582 DOI: 10.1021/acs.langmuir.1c02174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The alteration of the dielectric membrane properties by membrane engineering techniques such as carbon nanotube (CNT) coating opens the way to novel molecular transport strategies for biosensing purposes. In this article, we predict a macromolecular transport mechanism enabling the dielectric manipulation of the polymer translocation dynamics in dielectric membrane pores confining mixed electrolytes. In the giant permittivity regime of these engineered membranes governed by attractive polarization forces, multivalent ions adsorbed by the membrane nanopore trigger a monovalent ion separation and set an electroosmotic counterion flow. The drag force exerted by this flow is sufficiently strong to suppress and invert the electrophoretic velocity of anionic polymers and also to generate the mobility of neutral polymers whose speed and direction can be solely adjusted by the charge and concentration of the added multivalent ions. These features identify the dielectrically generated transport mechanism as an efficient means to drive overall neutral or weakly charged analytes that cannot be controlled by an external voltage. We also reveal that, in anionic polymer translocation, multivalent cation addition into the monovalent salt solution amplifies the electric current signal by several factors. The signal amplification is caused by the electrostatic many-body interactions replacing the monovalent polymer counterions by the multivalent cations of higher electric mobility. The strength of this electrokinetic charge discrimination points out the potential of multivalent ions as current amplifiers capable of providing boosted resolution in nanopore-based biosensing techniques.
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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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Bearden S, Wang F, Hall AR. Simple and Efficient Room-Temperature Release of Biotinylated Nucleic Acids from Streptavidin and Its Application to Selective Molecular Detection. Anal Chem 2019; 91:7996-8001. [PMID: 31144812 PMCID: PMC6854530 DOI: 10.1021/acs.analchem.9b01873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biotin-streptavidin bond is the strongest noncovalent bond in nature and is thus used extensively in biotechnology applications. However, the difficulty of releasing the bond without high temperatures or corrosive solutions can be a barrier to applications involving nucleic acids and other delicate substrates. Here, room-temperature phenol is employed to release biotin-tagged DNA constructs from streptavidin rapidly and efficiently. It is demonstrated that synthetic biotinylated DNA can be recovered at yields approaching 100% from both solution-phase and bead-bound streptavidin with as little as 12% (v/v) phenol, leaving the biotin tag active and reusable after extraction. As an application of this recovery method, biotinylated DNA fragments are isolated from a mixed solution to provide selectivity for solid-state nanopore detection.
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Affiliation(s)
- Samuel Bearden
- Virginia Tech–Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Fanny Wang
- Virginia Tech–Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Adam R. Hall
- Virginia Tech–Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, United States
- Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
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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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Polymer translocation through a hairy channel mimicking the inner plug of a nuclear pore complex. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:317-327. [PMID: 30927020 DOI: 10.1007/s00249-019-01356-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/23/2019] [Accepted: 03/08/2019] [Indexed: 10/27/2022]
Abstract
A microscopic transport model of a polymer translocating through a nuclear pore complex (NPC) is presented based on self-consistent field theory (SCFT), with the NPC and its nucleoporins mimicked by a hairy channel. Multiple cell environment effects (electrolyte effect, excluded volume effect, NPC drag effect, and hydrophobic effect) are all considered in this hairy channel model. The influence of various parameters (polymer chain length, length of NPC, strength of hydrophobic effect, and excluded volume effect) on translocation time is studied through theoretical analysis and numerical calculation. Numerical simulation results show that an area of low nucleoporin number density exists in the NPC, which facilitates the translocation of the polymer. The results also show that the translocation time curves with increasing NPC length and polymer charge number are concave. In addition, there are critical values for NPC length and polymer charge number for which the translocation time has a minimal value. The translocation time decreases with the increasing strength of the hydrophobic effect and excluded volume effect.
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Bioinspired, nanoscale approaches in contemporary bioanalytics (Review). Biointerphases 2018; 13:040801. [DOI: 10.1116/1.5037582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Song Y, Zhang J, Li D. Microfluidic and Nanofluidic Resistive Pulse Sensing: A Review. MICROMACHINES 2017; 8:E204. [PMID: 30400393 PMCID: PMC6190343 DOI: 10.3390/mi8070204] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/11/2017] [Accepted: 06/21/2017] [Indexed: 12/31/2022]
Abstract
The resistive pulse sensing (RPS) method based on the Coulter principle is a powerful method for particle counting and sizing in electrolyte solutions. With the advancement of micro- and nano-fabrication technologies, microfluidic and nanofluidic resistive pulse sensing technologies and devices have been developed. Due to the unique advantages of microfluidics and nanofluidics, RPS sensors are enabled with more functions with greatly improved sensitivity and throughput and thus have wide applications in fields of biomedical research, clinical diagnosis, and so on. Firstly, this paper reviews some basic theories of particle sizing and counting. Emphasis is then given to the latest development of microfuidic and nanofluidic RPS technologies within the last 6 years, ranging from some new phenomena, methods of improving the sensitivity and throughput, and their applications, to some popular nanopore or nanochannel fabrication techniques. The future research directions and challenges on microfluidic and nanofluidic RPS are also outlined.
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Affiliation(s)
- Yongxin Song
- Department of Marine Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Junyan Zhang
- Department of Marine Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Dongqing Li
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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10
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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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Knust S, Kreft D, Hillmann R, Meyer A, Viefhues M, Reimann P, Anselmetti D. Measuring DNA Translocation Forces through MoS 2 -Nanopores with Optical Tweezers. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.matpr.2017.09.182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Fabrication of Low Noise Borosilicate Glass Nanopores for Single Molecule Sensing. PLoS One 2016; 11:e0157399. [PMID: 27285088 PMCID: PMC4902259 DOI: 10.1371/journal.pone.0157399] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 05/27/2016] [Indexed: 11/19/2022] Open
Abstract
We show low-cost fabrication and characterization of borosilicate glass nanopores for single molecule sensing. Nanopores with diameters of ~100 nm were fabricated in borosilicate glass capillaries using laser assisted glass puller. We further achieve controlled reduction and nanometer-size control in pore diameter by sculpting them under constant electron beam exposure. We successfully fabricate pore diameters down to 6 nm. We next show electrical characterization and low-noise behavior of these borosilicate nanopores and compare their taper geometries. We show, for the first time, a comprehensive characterization of glass nanopore conductance across six-orders of magnitude (1M-1μM) of salt conditions, highlighting the role of buffer conditions. Finally, we demonstrate single molecule sensing capabilities of these devices with real-time translocation experiments of individual λ-DNA molecules. We observe distinct current blockage signatures of linear as well as folded DNA molecules as they undergo voltage-driven translocation through the glass nanopores. We find increased signal to noise for single molecule detection for higher trans-nanopore driving voltages. We propose these nanopores will expand the realm of applications for nanopore platform.
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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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