1
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Bucci G, Gadelrab K, Spakowitz AJ. Free Energy and Dynamics of Annihilation of Topological Defects in Nanoconfined DNA. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giovanna Bucci
- Robert Bosch LLC, 384 Santa Trinita Ave, Sunnyvale, California 94085, United States
| | - Karim Gadelrab
- Robert Bosch LLC, 1 Kendall Square, Suite 7-101, Cambridge, Massachusetts 02139, United States
| | - Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Applied Physics, Stanford University, Stanford, California 94305, United States
- Biophysics Program, Stanford University, Stanford, California 94305, United States
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2
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Nguyen T, Chidambara VA, Andreasen SZ, Golabi M, Huynh VN, Linh QT, Bang DD, Wolff A. Point-of-care devices for pathogen detections: The three most important factors to realise towards commercialization. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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3
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Bucci G, Spakowitz AJ. Systematic Approach toward Accurate and Efficient DNA Sequencing via Nanoconfinement. ACS Macro Lett 2020; 9:1184-1191. [PMID: 35653210 DOI: 10.1021/acsmacrolett.0c00423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Coarse-grained modeling tools are employed to simulate the mechanics of DNA loading within a nanoscale confinement and predict semiflexible polymer conformations within the confinement, providing design recommendations for DNA-sequencing devices. A workflow is developed to quantify competing requirements of efficiency and accuracy and extract metrics that guide design optimization. The mean first-passage time for DNA loading is calculated as a function of the nanochannel geometry and the applied electric field. We analyze the interplay between the free energy of confinement and the electric potential energy in achieving high-throughput, base-pair detection. The single-read probability is investigated as informative metrics for sequencing accuracy and for sensing-strategy design. High cost, low throughput, and low accuracy have so far limited the adoption of nanochannel analysis and other long-read technologies. Our work directly addresses these limitations with a systematic approach that is scalable to long molecules and complex geometries.
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Affiliation(s)
- Giovanna Bucci
- Robert Bosch LLC, 384 Santa Trinita Avenue, Sunnyvale, California 94085, United States
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4
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Bleha T, Cifra P. Compression and Stretching of Single DNA Molecules under Channel Confinement. J Phys Chem B 2020; 124:1691-1702. [PMID: 32045238 DOI: 10.1021/acs.jpcb.9b11602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We study the compression and extension response of single dsDNA (double-stranded DNA) molecules confined in cylindrical channels by means of Monte Carlo simulations. The elastic response of micrometer-sized DNA to the external force acting through the chain ends or through the piston is markedly affected by the size of the channel. The interpretation of the force (f)-displacement (R) functions under quasi-one-dimensional confinement is facilitated by resolving the overall change of displacement ΔR into the confinement contribution ΔRD and the force contribution ΔRf. The external stretching of confined DNA results in a characteristic pattern of f-R functions involving their shift to the larger extensions due to the channel-induced pre-stretching ΔRD. A smooth end-chain compression into loop-like conformations observed in moderately confined DNA can be accounted for by the relationship valid for a Gaussian chain in bulk. In narrow channels, the considerably pre-stretched DNA molecules abruptly buckle on compression by the backfolding into hairpins. On the contrary, the piston compression of DNA is characterized by a gradual reduction of the chain span S and by smooth f-S functions in the whole spatial range from the 3d near to 1d limits. The observed discrepancy between the shape of the f-R and f-S functions from two compression methods can be important for designing nanopiston experiments of compaction and knotting of single DNA in nanochannels.
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Affiliation(s)
- Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
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5
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Rišpanová L, Benková Z, Cifra P. Block Copolymer of Flexible and Semi-Flexible Block Confined in Nanopost Array. Polymers (Basel) 2018; 10:E1301. [PMID: 30961226 PMCID: PMC6401765 DOI: 10.3390/polym10121301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022] Open
Abstract
Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the two blocks of the confined diblock chain were investigated through a comparison of their size, structure, and penetration among nanoposts with the corresponding separate chains. The geometry of a nanopost array was varied at constant post separation or at constant width of the passage between nanoposts. The size of a single interstitial volume was comparable to or smaller than the size of the diblock chain. A comparison of the blocks with their separate analogous chains revealed that the mutual interactions between the blocks were shielded by the nanoposts and, thus, the blocks behaved independently. At constant passage width, competitive effects of the axial chain extension in interstitial volumes and the lateral chain expansion among interstitial volumes led to a nonmonotonic behavior of the axial span. The position of the maximum in the span plotted against the filling fraction for a diblock chain was dictated by the semi-flexible block. The semi-flexible block penetrates among the nanoposts more readily and the expansion of the whole diblock copolymer is governed by the semiflexible block. The main findings were explained using the free energy arguments when an interstitial volume was approximated by a channel geometry and a passage aperture by a slit geometry. Detail knowledge of controlled conformational behavior in a compartmentalized environment can contribute to new processes in the storage and retrieval of information.
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Affiliation(s)
- Lucia Rišpanová
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
| | - Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
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6
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Ruggeri F, Krishnan M. Entropic Trapping of a Singly Charged Molecule in Solution. NANO LETTERS 2018; 18:3773-3779. [PMID: 29688720 DOI: 10.1021/acs.nanolett.8b01011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We demonstrate the ability to confine a single molecule in solution by spatial modulation of its local configurational entropy. Previously we established electrostatic trapping of a charged macromolecule by geometric tailoring of a repulsive electrical interaction potential in a parallel plate system. However, since the lifetime of the trapped state depends exponentially on the electrical charge of the molecule, the electrostatic interaction alone is often insufficient in magnitude to stably confine molecules carrying a net charge of magnitude ≤5 e. Here we show that the configurational entropy of a thermally fluctuating molecule in a geometrically modulated system can be exploited to spatially confine weakly charged molecules in solution. Measurement of the configurational entropy contribution reveals good agreement with theoretical expectations. This additional translational contribution to the total free energy facilitates direct optical imaging and measurement of the effective charge of molecules on the size scale of ∼1 nm and a charge as low as 1 e, physical properties comparable with those of a monovalent ion in solution.
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Affiliation(s)
- Francesca Ruggeri
- Department of Chemistry , University of Zürich , Winterthurerstrasse 190 , CH 8057 Zürich , Switzerland
| | - Madhavi Krishnan
- Department of Chemistry , University of Zürich , Winterthurerstrasse 190 , CH 8057 Zürich , Switzerland
- Department of Physics , University of Zürich , Winterthurerstrasse 190 , CH 8057 Zürich , Switzerland
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7
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Transverse dielectrophoretic-based DNA nanoscale confinement. Sci Rep 2018; 8:5981. [PMID: 29654238 PMCID: PMC5899125 DOI: 10.1038/s41598-018-24132-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/26/2018] [Indexed: 11/19/2022] Open
Abstract
Confinement of single molecules within nanoscale environments is crucial in a range of fields, including biomedicine, genomics, and biophysics. Here, we present a method that can concentrate, confine, and linearly stretch DNA molecules within a single optical field of view using dielectrophoretic (DEP) force. The method can convert an open surface into one confining DNA molecules without a requirement for bonding, hydrodynamic or mechanical components. We use a transverse DEP field between a top coverslip and a bottom substrate, both of which are coated with a transparent conductive material. Both layers are attached using double-sided tape, defining the chamber. The nanofeatures lie at the “floor” and do not require any bonding. With the application of an alternating (AC) electric field (2 Vp-p) between the top and bottom electrodes, a DEP field gradient is established and used to concentrate, confine and linearly extend DNA in nanogrooves as small as 100-nm in width. We also demonstrate reversible loading/unloading of DNA molecules into nanogrooves and nanopits by switching frequency (between 10 kHz to 100 kHz). The technology presented in this paper provides a new method for single-molecule trapping and analysis.
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8
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Ven K, Vanspauwen B, Pérez-Ruiz E, Leirs K, Decrop D, Gerstmans H, Spasic D, Lammertyn J. Target Confinement in Small Reaction Volumes Using Microfluidic Technologies: A Smart Approach for Single-Entity Detection and Analysis. ACS Sens 2018; 3:264-284. [PMID: 29363316 DOI: 10.1021/acssensors.7b00873] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the last decades, the study of cells, nucleic acid molecules, and proteins has evolved from ensemble measurements to so-called single-entity studies. The latter offers huge benefits, not only as biological research tools to examine heterogeneities among individual entities within a population, but also as biosensing tools for medical diagnostics, which can reach the ultimate sensitivity by detecting single targets. Whereas various techniques for single-entity detection have been reported, this review focuses on microfluidic systems that physically confine single targets in small reaction volumes. We categorize these techniques as droplet-, microchamber-, and nanostructure-based and provide an overview of their implementation for studying single cells, nucleic acids, and proteins. We furthermore reflect on the advantages and limitations of these techniques and highlight future opportunities in the field.
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Affiliation(s)
- Karen Ven
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Bram Vanspauwen
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Elena Pérez-Ruiz
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Karen Leirs
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Deborah Decrop
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Hans Gerstmans
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Department
of Applied biosciences, Ghent University, Valentyn Vaerwyckweg 1 - building
C, 9000 Gent, Belgium
- Department
of Biosystems, KU Leuven - University of Leuven, Kasteelpark Arenberg
21, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
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9
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Marie R, Pedersen JN, Mir KU, Bilenberg B, Kristensen A. Concentrating and labeling genomic DNA in a nanofluidic array. NANOSCALE 2018; 10:1376-1382. [PMID: 29300409 DOI: 10.1039/c7nr06016e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nucleotide incorporation by DNA polymerase forms the basis of DNA sequencing-by-synthesis. In current platforms, either the single-stranded DNA or the enzyme is immobilized on a solid surface to locate the incorporation of individual nucleotides in space and/or time. Solid-phase reactions may, however, hinder the polymerase activity. We demonstrate a device and a protocol for the enzymatic labeling of genomic DNA arranged in a dense array of single molecules without attaching the enzyme or the DNA to a surface. DNA molecules accumulate in a dense array of pits embedded within a nanoslit due to entropic trapping. We then perform ϕ29 polymerase extension from single-strand nicks created on the trapped molecules to incorporate fluorescent nucleotides into the DNA. The array of entropic traps can be loaded with λ-DNA molecules to more than 90% of capacity at a flow rate of 10 pL min-1. The final concentration can reach up to 100 μg mL-1, and the DNA is eluted from the array by increasing the flow rate. The device may be an important preparative module for carrying out enzymatic processing on DNA extracted from single-cells in a microfluidic chip.
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Affiliation(s)
- Rodolphe Marie
- Department of Micro and Nanotechnology, Technical University of Denmark, Kongens Lyngby, Denmark.
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10
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Qi Y, Zeng L, Khorshid A, Hill RJ, Reisner WW. Compression of Nanoslit Confined Polymer Solutions. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b01894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yue Qi
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| | - Lili Zeng
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| | - Ahmed Khorshid
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| | - Reghan J. Hill
- Department
of Chemical Engineering, McGill University, 3610 University Street, Montreal, Quebec H3A 0C5, Canada
| | - Walter W. Reisner
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
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11
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Benková Z, Rišpanová L, Cifra P. Effect of chain stiffness for semiflexible macromolecules in array of cylindrical nanoposts. J Chem Phys 2017; 147:134907. [DOI: 10.1063/1.4991649] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
| | - Lucia Rišpanová
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
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12
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Dai L, Jones JJ, Klotz AR, Levy S, Doyle PS. Nanoconfinement greatly speeds up the nucleation and the annealing in single-DNA collapse. SOFT MATTER 2017; 13:6363-6371. [PMID: 28868564 DOI: 10.1039/c7sm01249g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Manipulating and measuring single-molecule dynamics and reactions in nanofluidics is a rapidly growing field with broad applications in developing new biotechnologies, understanding nanoconfinement effects in vivo, and exploring new phenomena in confinement. In this work, we investigate the kinetics of DNA collapse in nanoslits using single T4-DNA (165.6 kbp) and λ-DNA (48.5 kbp), with particular focus on the measurement of the nucleation and annealing times. Fixing the ethanol concentration at 35% and varying the slit height from 2000 to 31 nm, the nucleation time dramatically decreases from more than 1 hour to a few minutes or less. The increased collapsed rate results from the larger free energy experienced by coiled DNA in confinement relative to compacted DNA. Our results also shed light on other conformational transitions in confinement, such as protein folding.
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore 117543, Singapore.
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13
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Duan L, Yobas L. On-chip hydrodynamic chromatography of DNA through centimeters-long glass nanocapillaries. Analyst 2017; 142:2191-2198. [PMID: 28536716 DOI: 10.1039/c7an00499k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study demonstrates hydrodynamic chromatography of DNA fragments in a microchip. The microchip contains a highly regular array of nanofluidic channels (nanocapillaries) that are essential for resolving DNA in this chromatography mode. The nanocapillaries are self-enclosed robust structures built inside a doped glass layer on silicon using low-resolution photolithography and standard semiconductor processing techniques. Additionally, the unique nanocapillaries feature a cylindrical inner radius of 600 nm maintained over a length scale of 5 cm. The microchip with bare open nanocapillaries is shown to rapidly separate a digest of lambda DNA in free solution (<5 min under the elution pressure of 60 to 120 psi), relying entirely on pressure-driven flows and, in doing so, avoiding the field-induced DNA aggregations encountered in gel-free electrophoresis. The nanocapillaries, despite their relatively short length, are observed to fractionate DNA fragments reasonably well with a minimum resolvable size difference below 5 kbp. In the chromatograms obtained, the number of theoretical plates exceeds 105 plates per m for 3.5 and 21 kbp long DNA fragments. The relative mobility of fragments in relation to their size is found to be in excellent agreement with the simple quadratic model of hydrodynamic chromatography. The model is shown to estimate greater effective hydrodynamic radii than those of respective fragments being unconfined in bulk solution, implying increased drag forces and reduced diffusion coefficients, which is also a noticeable trend among diffusion coefficient estimates derived from the experimentally obtained plate heights. This robust mass-producible microchip can be further developed into a fully integrated bioanalytic microsystem.
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Affiliation(s)
- Lian Duan
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China.
| | - Levent Yobas
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China. and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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14
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Smith CLC, Thilsted AH, Pedersen JN, Youngman TH, Dyrnum JC, Michaelsen NA, Marie R, Kristensen A. Photothermal Transport of DNA in Entropy-Landscape Plasmonic Waveguides. ACS NANO 2017; 11:4553-4563. [PMID: 28453288 DOI: 10.1021/acsnano.6b08563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The ability to handle single, free molecules in lab-on-a-chip systems is key to the development of advanced biotechnologies. Entropic confinement offers passive control of polymers in nanofluidic systems by locally asserting a molecule's number of available conformation states through structured landscapes. Separately, a range of plasmonic configurations have demonstrated active manipulation of nano-objects by harnessing concentrated electric fields. The integration of these two independent techniques promises a range of sophisticated and complementary functions to handle, for example, DNA, but numerous difficulties, in particular, conflicting requirements of channel size, have prevented progress. Here, we show that metallic V-groove waveguides, embedded in fluidic nanoslits, form entropic potentials that trap and guide DNA molecules over well-defined routes while simultaneously promoting photothermal transport of DNA through the losses of plasmonic modes. The propulsive forces, assisted by in-coupling to propagating channel plasmon polaritons, extend along the V-grooves with a directed motion up to ≈0.5 μm·mW-1 away from the input beam and λ-DNA velocities reaching ≈0.2 μm·s-1·mW-1. The entropic trapping enables the V-grooves to be flexibly loaded and unloaded with DNA by variation of transverse fluid flow, a process that is selective to biopolymers versus fixed-shape objects and also allows the technique to address the challenges of nanoscale interaction volumes. Our self-aligning, light-driven actuator provides a convenient platform to filter, route, and manipulate individual molecules and may be realized wholly by wafer-scale fabrication suitable for parallelized investigation.
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Affiliation(s)
- Cameron L C Smith
- Department of Micro- and Nanotechnology, Technical University of Denmark , DK-2800 Kongens Lyngby, Denmark
| | - Anil H Thilsted
- Department of Micro- and Nanotechnology, Technical University of Denmark , DK-2800 Kongens Lyngby, Denmark
| | - Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark , DK-2800 Kongens Lyngby, Denmark
| | - Tomas H Youngman
- Department of Micro- and Nanotechnology, Technical University of Denmark , DK-2800 Kongens Lyngby, Denmark
| | - Julia C Dyrnum
- Department of Micro- and Nanotechnology, Technical University of Denmark , DK-2800 Kongens Lyngby, Denmark
| | - Nicolai A Michaelsen
- Department of Micro- and Nanotechnology, Technical University of Denmark , DK-2800 Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department of Micro- and Nanotechnology, Technical University of Denmark , DK-2800 Kongens Lyngby, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of Denmark , DK-2800 Kongens Lyngby, Denmark
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15
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Joo H, Kim JS. Confinement-driven organization of a histone-complexed DNA molecule in a dense array of nanoposts. NANOSCALE 2017; 9:6391-6398. [PMID: 28453018 DOI: 10.1039/c7nr00859g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The first step in the controlled storage of lengthy DNA molecules is to keep DNA molecules separated while integrated in micrometer-sized space. Herein, we present hybrid Monte Carlo simulations of a histone-complexed DNA (hcDNA) molecule confined in a dense array of nanoposts. Depending on the nanopost dimension, a single, 8.7 kilobase pair hcDNA molecule was either localized and elongated in a single inter-post space surrounded by four nanoposts or spread over several inter-post spaces through passages between two neighboring nanoposts. The conformational change of a hcDNA molecule is interpreted in terms of competitive effects of confinements in the inter-post and passage spaces. We propose that, by elaborately designing nanopost arrays, the competitive confinement effects can be adjusted such that each hcDNA molecule is localized in a single inter-post space, and thereby multiple hcDNA molecules can be physically separated from each other while stored together in the nanopost array.
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Affiliation(s)
- Heesun Joo
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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16
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Kim D, Bowman C, Del Bonis-O'Donnell JT, Matzavinos A, Stein D. Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers. PHYSICAL REVIEW LETTERS 2017; 118:048002. [PMID: 28186790 DOI: 10.1103/physrevlett.118.048002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Indexed: 06/06/2023]
Abstract
We investigate with experiments and computer simulations the nonequilibrium dynamics of DNA polymers crossing arrays of entropic barriers in nanofluidic devices in a pressure-driven flow. With increasing driving pressure, the effective diffusivity of DNA rises and then peaks at a value that is many times higher than the equilibrium diffusivity. This is an entropic manifestation of "giant acceleration of diffusion." The phenomenon is sensitive to the effective energy landscape; thus, it offers a unique probe of entropic barriers in a system driven away from equilibrium.
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Affiliation(s)
- Daniel Kim
- Department of Physics, Brown University, Providence, Rhode Island 02912, USA
| | - Clark Bowman
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
| | | | - Anastasios Matzavinos
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
- Computational Science and Engineering Laboratory, Department of Mechanical and Process Engineering, CH-8092 ETH Zürich, Switzerland
| | - Derek Stein
- Department of Physics, Brown University, Providence, Rhode Island 02912, USA
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17
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Klotz AR, de Haan HW, Reisner WW. Waves of DNA: Propagating excitations in extended nanoconfined polymers. Phys Rev E 2016; 94:042603. [PMID: 27841510 DOI: 10.1103/physreve.94.042603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 12/30/2022]
Abstract
We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain occupies multiple cavities. Fluorescent video-microscopy data shows fluctuations in intensity between cavities, including waves of excess fluorescence that propagate across the cavity-straddling molecule, corresponding to propagating fluctuations of contour overdensity in the cavities. The transfer of DNA between neighboring pits is quantified by examining the correlation in intensity fluctuations between neighboring cavities. Correlations grow from an anticorrelated minimum to a correlated maximum before decaying, corresponding to a transfer of contour between neighboring cavities at a fixed transfer time scale. The observed dynamics can be modeled using Langevin dynamics simulations and a minimal lattice model of coupled diffusion. This study shows how confinement-based sculpting of the polymer equilibrium configuration, by renormalizing the physical system into a series of discrete cavity states, can lead to new types of dynamic collective phenomena.
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Affiliation(s)
- Alexander R Klotz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada L1H 7K4
| | - Walter W Reisner
- Department of Physics, McGill University, Montreal, QC Canada, H3A 2T8
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18
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Huang HZ, Chen YH, Yu WC, Luo KF. Superselective Adsorption of Multivalent Polymer Chains to a Surface with Receptors. CHINESE J CHEM PHYS 2016. [DOI: 10.1063/1674-0068/29/cjcp1603060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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Rems L, Kawale D, Lee LJ, Boukany PE. Flow of DNA in micro/nanofluidics: From fundamentals to applications. BIOMICROFLUIDICS 2016; 10:043403. [PMID: 27493701 PMCID: PMC4958106 DOI: 10.1063/1.4958719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/29/2016] [Indexed: 05/26/2023]
Abstract
Thanks to direct observation and manipulation of DNA in micro/nanofluidic devices, we are now able to elucidate the relationship between the polymer microstructure and its rheological properties, as well as to design new single-molecule platforms for biophysics and biomedicine. This allows exploration of many new mechanisms and phenomena, which were previously unachievable with conventional methods such as bulk rheometry tests. For instance, the field of polymer rheology is at a turning point to relate the complex molecular conformations to the nonlinear viscoelasticity of polymeric fluids (such as coil-stretch transition, shear thinning, and stress overshoot in startup shear). In addition, nanofluidic devices provided a starting point for manipulating single DNA molecules by applying basic principles of polymer physics, which is highly relevant to numerous processes in biosciences. In this article, we review recent progress regarding the flow and deformation of DNA in micro/nanofluidic systems from both fundamental and application perspectives. We particularly focus on advances in the understanding of polymer rheology and identify the emerging research trends and challenges, especially with respect to future applications of nanofluidics in the biomedical field.
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Affiliation(s)
- Lea Rems
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - Durgesh Kawale
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - L James Lee
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University , Columbus, Ohio 43210, USA
| | - Pouyan E Boukany
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
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20
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Dai L, Renner CB, Doyle PS. The polymer physics of single DNA confined in nanochannels. Adv Colloid Interface Sci 2016; 232:80-100. [PMID: 26782150 DOI: 10.1016/j.cis.2015.12.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 11/17/2022]
Abstract
In recent years, applications and experimental studies of DNA in nanochannels have stimulated the investigation of the polymer physics of DNA in confinement. Recent advances in the physics of confined polymers, using DNA as a model polymer, have moved beyond the classic Odijk theory for the strong confinement, and the classic blob theory for the weak confinement. In this review, we present the current understanding of the behaviors of confined polymers while briefly reviewing classic theories. Three aspects of confined DNA are presented: static, dynamic, and topological properties. The relevant simulation methods are also summarized. In addition, comparisons of confined DNA with DNA under tension and DNA in semidilute solution are made to emphasize universal behaviors. Finally, an outlook of the possible future research for confined DNA is given.
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 138602, Singapore
| | - C Benjamin Renner
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, United States
| | - Patrick S Doyle
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 138602, Singapore; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, United States.
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21
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Ahamed MJ, Mahshid S, Berard DJ, Michaud F, Sladek R, Reisner WW, Leslie SR. Continuous Confinement Fluidics: Getting Lots of Molecules into Small Spaces with High Fidelity. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b02617] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | - Sara Mahshid
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Daniel J. Berard
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - François Michaud
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Rob Sladek
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Walter W. Reisner
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Sabrina R. Leslie
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
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22
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Li X, Dorfman KD. Effect of excluded volume on the force-extension of wormlike chains in slit confinement. J Chem Phys 2016; 144:104902. [PMID: 26979704 DOI: 10.1063/1.4943195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use pruned-enriched Rosenbluth method simulations to develop a quantitative phase diagram for the stretching of a real wormlike chain confined in a slit. Our simulations confirm the existence of a "confined Pincus" regime in slit confinement, analogous to the Pincus regime in free solution, where excluded volume effects are sensible. The lower bound for the confined Pincus regime in the force-molecular weight plane, as well as the scaling of the extension with force and slit size, agree with an existing scaling theory for this regime. The upper bound of the confined Pincus regime depends on the strength of the confinement. For strong confinement, the confined Pincus regime ends when the contour length in the Pincus blob is too short to have intrablob excluded volume. As a result, the chain statistics become ideal and the confined Pincus regime at low forces is connected directly to ideal chain stretching at large forces. In contrast, for weak confinement, the confined Pincus regime ends when the Pincus blobs no longer fit inside the slit, even though there is sufficient contour length to have excluded volume inside the Pincus blob. As a result, weak confinement leads to a free-solution Pincus regime intervening between the confined Pincus regime for weak forces and ideal chain stretching at strong forces. Our results highlight shortcomings in existing models for the stretching of wormlike chains in slits.
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Affiliation(s)
- Xiaolan Li
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
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23
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Joo H, Kim JS. Confinement and partitioning of a single polymer chain in a dense array of nanoposts. SOFT MATTER 2015; 11:8262-8272. [PMID: 26350540 DOI: 10.1039/c5sm01585e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a Brownian dynamics simulation study on the confinement and partitioning of a single, flexible polymer chain in a dense array of nanoposts with different sizes and separations, especially, when the volume of an interstitial space formed among four nanoposts is less than the volume of the polymer chain. As the interstitial volume decreases by either increasing the nanopost diameter or decreasing the separation between nanoposts, the chain conformation becomes elongated in the direction parallel to the nanoposts. Interestingly, however, the degree of chain elongation varies in a non-monotonic fashion as the interstitial volume decreases while keeping the passage width between two nanoposts constant at a small value. We calculate the free energy of chain partitioning over several interstitial spaces from the partitioning probability, and find that the non-monotonic dependence of the chain elongation results from an interplay between the confinement-driven chain elongation along the direction parallel to the nanoposts and the chain spreading perpendicular to the nanoposts by partitioning chain segments over several interstitial spaces. These results present the possibility of utilizing a dense array of nanoposts as a template to control polymer conformations.
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Affiliation(s)
- Heesun Joo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - Jun Soo Kim
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Republic of Korea.
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24
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Zhang Y, Reisner W. Fabrication and characterization of nanopore-interfaced nanochannel devices. NANOTECHNOLOGY 2015; 26:455301. [PMID: 26472174 DOI: 10.1088/0957-4484/26/45/455301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanofluidic devices combining nanochannels and nanopores may enable a range of novel applications in the field of single-molecule biosensing and manipulation. Here we combine classic lithographically based fabrication and electron beam milling to construct a device that integrates sealed transverse features, such as nanocavities and nanochannels, with embedded pores vertically intersecting the nanochannels. Using fluorescent microscopy, we demonstrate that DNA molecules can be introduced into the nanochannels and translated transversely across the embedded pore in an extended-conformation without undergoing cross-pore translocation. Upon application of a trans-pore voltage drop, the molecules will undergo cross-pore translocation into an adjoining macroscopic reservoir.
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Affiliation(s)
- Yuning Zhang
- Dept. of Physics, McGill University, 3600 Rue University, Montreal QC H3A 2T8, Canada
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25
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Mahshid S, Ahamed MJ, Berard D, Amin S, Sladek R, Leslie SR, Reisner W. Development of a platform for single cell genomics using convex lens-induced confinement. LAB ON A CHIP 2015; 15:3013-20. [PMID: 26062011 DOI: 10.1039/c5lc00492f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We demonstrate a lab-on-a-chip that combines micro/nano-fabricated features with a Convex Lens-Induced Confinement (CLIC) device for the in situ analysis of single cells. A complete cycle of single cell analysis was achieved that includes: cell trapping, cell isolation, lysis, protein digestion, genomic DNA extraction and on-chip genomic DNA linearization. The ability to dynamically alter the flow-cell dimensions using the CLIC method was coupled with a flow-control mechanism for achieving efficient cell trapping, buffer exchange, and loading of long DNA molecules into nanofluidic arrays. Finite element simulation of fluid flow gives rise to optimized design parameters for overcoming the high hydraulic resistance present in the micro/nano-confinement region. By tuning design parameters such as the pressure gradient and CLIC confinement, an efficient on-chip single cell analysis protocol can be obtained. We demonstrate that we can extract Mbp long genomic DNA molecules from a single human lybphoblastoid cell and stretch these molecules in the nanochannels for optical interrogation.
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Affiliation(s)
- Sara Mahshid
- Department of Physics, McGill University, 3600 rue University, Montreal, Canada.
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26
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Klotz AR, Duong L, Mamaev M, de Haan HW, Chen JZY, Reisner WW. Measuring the Confinement Free Energy and Effective Width of Single Polymer Chains via Single-Molecule Tetris. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00977] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Lyndon Duong
- Department
of Physics, McGill University, Montreal, QC, Canada H3A 2T8
| | - Mikhail Mamaev
- Department
of Physics, McGill University, Montreal, QC, Canada H3A 2T8
| | - Hendrick W. de Haan
- Faculty
of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada L1H 7K4
| | - Jeff Z. Y. Chen
- Department
of Physics and Astronomy, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Walter W. Reisner
- Department
of Physics, McGill University, Montreal, QC, Canada H3A 2T8
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27
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Klotz AR, Mamaev M, Duong L, de Haan HW, Reisner WW. Correlated Fluctuations of DNA between Nanofluidic Entropic Traps. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00961] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Mikhail Mamaev
- Department
of Physics, McGill University, Montreal, QC H3A 0G4, Canada
| | - Lyndon Duong
- Department
of Physics, McGill University, Montreal, QC H3A 0G4, Canada
| | - Hendrick W. de Haan
- Faculty
of Science, University of Ontario Institute of Technology, Oshawa, ON L1H 7K4, Canada
| | - Walter W. Reisner
- Department
of Physics, McGill University, Montreal, QC H3A 0G4, Canada
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28
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de Haan HW, Shendruk TN. Force-Extension for DNA in a Nanoslit: Mapping between the 3D and 2D Limits. ACS Macro Lett 2015; 4:632-635. [PMID: 35596406 DOI: 10.1021/acsmacrolett.5b00138] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The force-extension relation for a semiflexible polymer confined in a nanoslit is investigated. Both the effective correlation length and force-extension relation change as the chain goes from 3D (large slit heights) to 2D (tight confinement). At low forces, correlations along the polymer give an effective dimensionality. The strong force limit can be interpolated with the weak force limit for two regimes: when confinement dominates over extensile force and vice versa. These interpolations give good agreement with simulations for all slit heights and forces. We thus generalize the Marko-Siggia force-extension relation for DNA and other semiflexible biopolymers in nanoconfinement.
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Affiliation(s)
- Hendrick W. de Haan
- University of Ontario Institute of Technology, Faculty
of Science, 2000 Simcoe
Street North, Oshawa, Ontario L1H 7K4, Canada
| | - Tyler N. Shendruk
- The
Rudolf Peierls Centre for Theoretical Physics, Department of Physics,
Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, United Kingdom
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29
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Leïchlé T, Chou CF. Biofunctionalized nanoslits for wash-free and spatially resolved real-time sensing with full target capture. BIOMICROFLUIDICS 2015; 9:034103. [PMID: 26015840 PMCID: PMC4433482 DOI: 10.1063/1.4921252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/06/2015] [Indexed: 05/05/2023]
Abstract
We propose biofunctionalized nanofluidic slits (nanoslits) as an effective platform for real-time fluorescence-based biosensing in a reaction-limited regime with optimized target capture efficiency. This is achieved by the drastic reduction of the diffusion length, thereby a boosted collision frequency between the target analytes and the sensor, and the size reduction of the sensing element down to the channel height comparable to the depletion layer caused by the reaction. Hybridization experiments conducted in DNA-functionalized nanoslits demonstrate the analyte depletion and the wash-free detection ∼10 times faster compared to the best microfluidic sensing platforms. The signal to background fluorescence ratio is drastically increased at lower target concentrations, in favor of low-copy number analyte analysis. Experimental and simulation results further show that biofunctionalized nanoslits provide a simple means to study reaction kinetics at the single-pixel level using conventional fluorescence microscopy with reduced optical depth.
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30
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Pedersen JN, Lüscher CJ, Marie R, Thamdrup LH, Kristensen A, Flyvbjerg H. Thermophoretic forces on DNA measured with a single-molecule spring balance. PHYSICAL REVIEW LETTERS 2014; 113:268301. [PMID: 25615393 DOI: 10.1103/physrevlett.113.268301] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 06/04/2023]
Abstract
We stretch a single DNA molecule with thermophoretic forces and measure these forces with a spring balance: the DNA molecule itself. It is an entropic spring which we calibrate, using as a benchmark its Brownian motion in the nanochannel that contains and prestretches it. This direct measurement of the thermophoretic force in a static configuration finds forces up to 130 fN. This is eleven times stronger than the force experienced by the same molecule in the same thermal gradient in bulk, where the molecule shields itself. Our stronger forces stretch the middle of the molecule up to 80% of its contour length. We find the Soret coefficient per unit length of DNA at various ionic strengths. It agrees, with novel precision, with results obtained in bulk for DNA too short to shield itself and with the thermodynamic model of thermophoresis.
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Affiliation(s)
- Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Christopher J Lüscher
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Rodolphe Marie
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Lasse H Thamdrup
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
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31
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Berard DJ, Michaud F, Mahshid S, Ahamed MJ, McFaul CMJ, Leith JS, Bérubé P, Sladek R, Reisner W, Leslie SR. Convex lens-induced nanoscale templating. Proc Natl Acad Sci U S A 2014; 111:13295-300. [PMID: 25092333 PMCID: PMC4169971 DOI: 10.1073/pnas.1321089111] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We demonstrate a new platform, convex lens-induced nanoscale templating (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of transforming a macroscale flow cell into a nanofluidic device without the need for permanent direct bonding, thus simplifying sample loading, providing greater accessibility of the surface for functionalization, and enabling dynamic manipulation of confinement during device operation. Moreover, as DNA molecules present in the gap are driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields required to load DNA into direct-bonded nanofluidic devices. To demonstrate the versatility of CLINT, we confine DNA to nanogroove and nanopit structures, demonstrating DNA nanochannel-based stretching, denaturation mapping, and partitioning/trapping of single molecules in multiple embedded cavities. In particular, using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub-30-nm nanochannels, achieving high stretching (90%) that is in good agreement with Odijk deflection theory, and we have mapped genomic features using denaturation analysis.
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Affiliation(s)
- Daniel J Berard
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - François Michaud
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - Sara Mahshid
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1
| | | | | | - Jason S Leith
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - Pierre Bérubé
- Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1
| | - Rob Sladek
- Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1
| | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - Sabrina R Leslie
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
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32
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33
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Dai L, van der Maarel J, Doyle PS. Extended de Gennes Regime of DNA Confined in a Nanochannel. Macromolecules 2014. [DOI: 10.1021/ma500326w] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Liang Dai
- BioSystems
and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Republic of Singapore 138602
| | - Johan van der Maarel
- BioSystems
and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Republic of Singapore 138602
- Department
of Physics, National University of Singapore, 2 Science Drive 3, Republic of Singapore 117551
| | - Patrick S. Doyle
- BioSystems
and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Republic of Singapore 138602
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
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34
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Levy-Sakin M, Grunwald A, Kim S, Gassman NR, Gottfried A, Antelman J, Kim Y, Ho S, Samuel R, Michalet X, Lin RR, Dertinger T, Kim AS, Chung S, Colyer RA, Weinhold E, Weiss S, Ebenstein Y. Toward single-molecule optical mapping of the epigenome. ACS NANO 2014; 8:14-26. [PMID: 24328256 PMCID: PMC4022788 DOI: 10.1021/nn4050694] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The past decade has seen an explosive growth in the utilization of single-molecule techniques for the study of complex systems. The ability to resolve phenomena otherwise masked by ensemble averaging has made these approaches especially attractive for the study of biological systems, where stochastic events lead to inherent inhomogeneity at the population level. The complex composition of the genome has made it an ideal system to study at the single-molecule level, and methods aimed at resolving genetic information from long, individual, genomic DNA molecules have been in use for the last 30 years. These methods, and particularly optical-based mapping of DNA, have been instrumental in highlighting genomic variation and contributed significantly to the assembly of many genomes including the human genome. Nanotechnology and nanoscopy have been a strong driving force for advancing genomic mapping approaches, allowing both better manipulation of DNA on the nanoscale and enhanced optical resolving power for analysis of genomic information. During the past few years, these developments have been adopted also for epigenetic studies. The common principle for these studies is the use of advanced optical microscopy for the detection of fluorescently labeled epigenetic marks on long, extended DNA molecules. Here we will discuss recent single-molecule studies for the mapping of chromatin composition and epigenetic DNA modifications, such as DNA methylation.
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Affiliation(s)
- Michal Levy-Sakin
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel
| | - Assaf Grunwald
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel
| | - Soohong Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Natalie R. Gassman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Anna Gottfried
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Josh Antelman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Younggyu Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Sam Ho
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Robin Samuel
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Ron R. Lin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Thomas Dertinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Andrew S. Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Sangyoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Ryan A. Colyer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
- Corresponding authors: (Y. Ebenstein), (S. Weiss)
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel
- Corresponding authors: (Y. Ebenstein), (S. Weiss)
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35
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Iliev GK, Whittington SG. Pulling alternating copolymers adsorbed on a striped surface. Phys Rev E 2013; 88:052105. [PMID: 24329212 DOI: 10.1103/physreve.88.052105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Indexed: 11/07/2022]
Abstract
We consider a partially directed walk model of a strictly alternating copolymer adsorbing on a striped surface where the energy is associated with the numbers of the two types of monomers adsorbed on the two types of surface sites. A force is applied to the last monomer and the polymer responds to this force, sometimes by desorbing. The force can be applied at various angles, with the surface component parallel or perpendicular (or at some other angle) to the stripe direction. The desorption behavior is strongly dependent on the force direction and the response gives information about the shape and direction of the polymer adsorbed on the surface, especially at low temperatures. In some cases the ground state is degenerate and this also has an important effect on the temperature dependence of the critical force needed for desorption. We give a complete solution of the problem using generating function techniques and an approximate treatment that is especially useful at low temperatures and helps in our physical understanding of the situation.
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Affiliation(s)
- G K Iliev
- Department of Mathematics and Statistics, York University, Toronto, Canada
| | - S G Whittington
- Department of Chemistry, University of Toronto, Toronto, Canada
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36
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Werner E, Westerlund F, Tegenfeldt JO, Mehlig B. Monomer Distributions and Intrachain Collisions of a Polymer Confined to a Channel. Macromolecules 2013. [DOI: 10.1021/ma400464c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- E. Werner
- Department of Physics, University of Gothenburg, Göteborg, Sweden
| | - F. Westerlund
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - J. O. Tegenfeldt
- Department of Physics, Division
of Solid State Physics, Lund University, Lund, Sweden
| | - B. Mehlig
- Department of Physics, University of Gothenburg, Göteborg, Sweden
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37
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics
(BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 3 Science Drive 2, Republic
of Singapore 117543
| | - Patrick S. Doyle
- BioSystems and Micromechanics
(BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 3 Science Drive 2, Republic
of Singapore 117543
- Department
of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge,
Massachusetts 02139, United States
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38
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Dai L, Tree DR, van der Maarel JRC, Dorfman KD, Doyle PS. Revisiting blob theory for DNA diffusivity in slitlike confinement. PHYSICAL REVIEW LETTERS 2013; 110:168105. [PMID: 23679643 PMCID: PMC3670611 DOI: 10.1103/physrevlett.110.168105] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Indexed: 05/25/2023]
Abstract
Blob theory has been widely applied to describe polymer conformations and dynamics in nanoconfinement. In slit confinement, blob theory predicts a scaling exponent of 2/3 for polymer diffusivity as a function of slit height, yet a large body of experimental studies using DNA produce a scaling exponent significantly less than 2/3. In this work, we develop a theory that predicts that this discrepancy occurs because the segment correlation function for a semiflexible chain such as DNA does not follow the Flory exponent for length scales smaller than the persistence length. We show that these short length scale effects contribute significantly to the scaling for the DNA diffusivity, but do not appreciably affect the scalings for static properties. Our theory is fully supported by Monte Carlo simulations, quantitative agreement with DNA experiments, and the results reconcile this outstanding problem for confined polymers.
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore 117543
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Johan R. C. van der Maarel
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore 117543
- Department of Physics, National University of Singapore, Singapore 117551
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Patrick S. Doyle
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore 117543
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
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39
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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40
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Krishnan M. Electrostatic free energy for a confined nanoscale object in a fluid. J Chem Phys 2013; 138:114906. [DOI: 10.1063/1.4795087] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Yasui T, Motoyama K, Kaji N, Tokeshi M, Baba Y. Enzyme-catalysed reaction for long-term fluorescent observation of single DNA molecules. RSC Adv 2013. [DOI: 10.1039/c3ra22999h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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42
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Reisner W, Pedersen JN, Austin RH. DNA confinement in nanochannels: physics and biological applications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:106601. [PMID: 22975868 DOI: 10.1088/0034-4885/75/10/106601] [Citation(s) in RCA: 246] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement--including the effect of varying ionic strength--and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range.
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Affiliation(s)
- Walter Reisner
- Physics Department, McGill University, Montreal QC, Canada.
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43
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Marie R, Kristensen A. Nanofluidic devices towards single DNA molecule sequence mapping. JOURNAL OF BIOPHOTONICS 2012; 5:673-686. [PMID: 22815200 DOI: 10.1002/jbio.201200050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 06/18/2012] [Accepted: 06/18/2012] [Indexed: 06/01/2023]
Abstract
Nanofluidics enables the imaging of stretched single molecules with potential applications for single molecule sequence mapping. Lab-on-a-chip devices for single cell trapping and lyzing, genomic DNA extraction from single cells, and optical mapping of genomic length DNA has been demonstrated separately. Yet the pursuit for applying DNA optical mapping to solve real genomics challenges is still to come. We review lab-on-a-chip devices from literature that could be part of a complete system for the sequence mapping of single DNA molecules.
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Affiliation(s)
- Rodolphe Marie
- Department of micro- and nanotechnology, Technical University of Denmark, Oersteds plads Building 345east, 2800 Kongens Lyngby, Denmark.
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44
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Dai L, van der Maarel JRC, Doyle PS. Effect of Nanoslit Confinement on the Knotting Probability of Circular DNA. ACS Macro Lett 2012; 1:732-736. [PMID: 35607094 DOI: 10.1021/mz3001622] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Monte Carlo simulations are used to study the knotting probability of circular DNA confined in a slit. We systematically vary the slit height, the width, and the contour length of the DNA molecule. We find that the trend in knotting probability with respect to slit height can be monotonic or nonmonotonic, depending on the width and contour length. The nonmonotonic trend is caused by two competing factors: the increase of the effective persistence length and the increase of segment density by slit confinement. These factors are antagonistic, in the sense that the increase in effective persistence length disfavors knot formation, whereas the increase in segment density favors the knotting probability. Our simulation results bring to light the importance of both chain length and width for slit-confined circular DNA and can be used to guide future experiments which aim to produce populations of knotted DNA through cyclization or catalyzed double-strand passage reactions in confinement.
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics
(BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 3 Science Drive 2, Republic
of Singapore 117543
| | - Johan R. C. van der Maarel
- BioSystems and Micromechanics
(BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 3 Science Drive 2, Republic
of Singapore 117543
- Department
of Physics, National University of Singapore, 2 Science Drive 3,
Republic of Singapore 117551
| | - Patrick S. Doyle
- BioSystems and Micromechanics
(BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 3 Science Drive 2, Republic
of Singapore 117543
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge,
Massachusetts 02139, United States
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45
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Shendruk T, Hickey O, Slater G, Harden J. Electrophoresis: When hydrodynamics matter. Curr Opin Colloid Interface Sci 2012. [DOI: 10.1016/j.cocis.2011.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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46
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Stavis SM, Geist J, Gaitan M, Locascio LE, Strychalski EA. DNA molecules descending a nanofluidic staircase by entropophoresis. LAB ON A CHIP 2012; 12:1174-1182. [PMID: 22278088 DOI: 10.1039/c2lc21152a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A complex entropy gradient for confined DNA molecules was engineered for the first time. Following the second law of thermodynamics, this enabled the directed self-transport and self-concentration of DNA molecules. This new nanofluidic method is termed entropophoresis. As implemented in experiments, long DNA molecules were dyed with cyanine dimers, dispersed in a high ionic strength buffer, and confined by a nanofluidic channel with a depth profile approximated by a staircase function. The staircase step depths spanned the transition from strong to moderate confinement. The diffusion of DNA molecules across slitlike steps was ratcheted by entropic forces applied at step edges, so that DNA molecules descended and collected at the bottom of the staircase, as observed by fluorescence microscopy. Different DNA morphologies, lengths, and stoichiometric base pair to dye molecule ratios were tested and determined to influence the rate of transport by entropophoresis. A model of ratcheted diffusion was used to interpret a shifting balance of forces applied to linear DNA molecules of standard length in a complex free energy landscape. Related metrics for the overall and optimum performance of entropophoresis were developed. The device and method reported here transcend current limitations in nanofluidics and present new possibilities in polymer physics, biophysics, separation science, and lab-on-a-chip technology.
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Affiliation(s)
- Samuel M Stavis
- Semiconductor and Dimensional Metrology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
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47
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Yeh JW, Taloni A, Chen YL, Chou CF. Entropy-driven single molecule tug-of-war of DNA at micro-nanofluidic interfaces. NANO LETTERS 2012; 12:1597-602. [PMID: 22329347 DOI: 10.1021/nl2045292] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Entropy-driven polymer dynamics at the nanoscale is fundamentally important in biological systems but the dependence of the entropic force on the nanoconfinement remains elusive. Here, we established an entropy-driven single molecule tug-of-war (TOW) at two micro-nanofluidic interfaces bridged by a nanoslit, performed the force analysis from a modified wormlike chain in the TOW scenario and the entropic recoiling process, and determined the associated scalings on the nanoconfinement. Our results provide a direct experimental evidence that the entropic forces in these two regimes, though unequal, are essentially constant at defined slit heights, irrespective of the slit lengths and the DNA segments within. Our findings have the implications to polymer transport at the nanoscale, device design for single molecule analysis, and biotechnological applications.
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Affiliation(s)
- Jia-Wei Yeh
- Department of Physics, National Taiwan University, Taipei, Taiwan
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48
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Affiliation(s)
- Alexander R. Klotz
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Hugo B. Brandão
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Walter W. Reisner
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
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49
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Liu C, Qu Y, Luo Y, Fang N. Recent advances in single-molecule detection on micro- and nano-fluidic devices. Electrophoresis 2012; 32:3308-18. [PMID: 22134976 DOI: 10.1002/elps.201100159] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule detection (SMD) allows static and dynamic heterogeneities from seemingly equal molecules to be revealed in the studies of molecular structures and intra- and inter-molecular interactions. Micro- and nanometer-sized structures, including channels, chambers, droplets, etc., in microfluidic and nanofluidic devices allow diffusion-controlled reactions to be accelerated and provide high signal-to-noise ratio for optical signals. These two active research frontiers have been combined to provide unprecedented capabilities for chemical and biological studies. This review summarizes the advances of SMD performed on microfluidic and nanofluidic devices published in the past five years. The latest developments on optical SMD methods, microfluidic SMD platforms, and on-chip SMD applications are discussed herein and future development directions are also envisioned.
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Affiliation(s)
- Chang Liu
- Ames Laboratory, US Department of Energy, Ames, Iowa, USA
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50
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Zhang Y, de Pablo JJ, Graham MD. An immersed boundary method for Brownian dynamics simulation of polymers in complex geometries: Application to DNA flowing through a nanoslit with embedded nanopits. J Chem Phys 2012; 136:014901. [DOI: 10.1063/1.3672103] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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