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Chen J, Sun L, Wang S, Tian F, Zhu H, Zhang R, Dai L. Crowding-induced polymer trapping in a channel. Phys Rev E 2021; 104:054502. [PMID: 34942690 DOI: 10.1103/physreve.104.054502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/20/2021] [Indexed: 11/07/2022]
Abstract
In this work, we report an intriguing phenomenon: crowding-induced polymer trapping in a channel. Using Langevin dynamics simulations and analytical calculations, we find that for a polymer confined in a channel, crowding particles can push a polymer into the channel corner through inducing an effective polymer-corner attraction due to the depletion effect. This phenomenon is referred to as polymer trapping. The occurrence of polymer trapping requires a minimum volume fraction of crowders, ϕ^{*}, which scales as ϕ^{*}∼(a_{c}/L_{p})^{1/3} for a_{c}≫a_{m} and ϕ^{*}∼(a_{c}/L_{p})^{1/3}(a_{c}/a_{m})^{1/2} for a_{c}≪a_{m}, where a_{c} is the crowder diameter, a_{m} is the monomer diameter, and L_{p} is the polymer persistence length. For DNA, ϕ^{*} is estimated to be around 0.25 for crowders with a_{c}=2nm. We find that ϕ^{*} also strongly depends on the shape of the channel cross section, and ϕ^{*} is much smaller for a triangle channel than a square channel. The polymer trapping leads to a nearly fully stretched polymer conformation along a channel corner, which may have practical applications, such as full stretching of DNA for the nanochannel-based genome mapping technology.
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Affiliation(s)
- Jialu Chen
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Ruiqin Zhang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong, China
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2
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Li M, Wang J. Stretching Wormlike Chains in Narrow Tubes of Arbitrary Cross-Sections. Polymers (Basel) 2019; 11:E2050. [PMID: 31835594 PMCID: PMC6960511 DOI: 10.3390/polym11122050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 12/06/2019] [Indexed: 12/03/2022] Open
Abstract
We considered the stretching of semiflexible polymer chains confined in narrow tubes with arbitrary cross-sections. Based on the wormlike chain model and technique of normal mode decomposition in statistical physics, we derived a compact analytical expression on the force-confinement-extension relation of the chains. This single formula was generalized to be valid for tube confinements with arbitrary cross-sections. In addition, we extended the generalized bead-rod model for Brownian dynamics simulations of confined polymer chains subjected to force stretching, so that the confinement effects to the chains applied by the tubes with arbitrary cross-sections can be quantitatively taken into account through numerical simulations. Extensive simulation examples on the wormlike chains confined in tubes of various shapes quantitatively justified the theoretically derived generalized formula on the force-confinement-extension relation of the chains.
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Affiliation(s)
| | - Jizeng Wang
- Key Laboratory of Mechanics on Disaster and Environment in Western China, Ministry of Education, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou 730000, China;
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3
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Polson JM, Heckbert DR. Polymer translocation into cavities: Effects of confinement geometry, crowding, and bending rigidity on the free energy. Phys Rev E 2019; 100:012504. [PMID: 31499877 DOI: 10.1103/physreve.100.012504] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 06/10/2023]
Abstract
Monte Carlo simulations are used to study the translocation of a polymer into a cavity. Modeling the polymer as a hard-sphere chain with a length up to N=601 monomers, we use a multiple-histogram method to measure the variation of the conformational free energy of the polymer with respect to the number of translocated monomers. The resulting free-energy functions are then used to obtain the confinement free energy for the translocated portion of the polymer. We characterize the confinement free energy for a flexible polymer in cavities with constant cross-sectional area A for various cavity shapes (cylindrical, rectangular, and triangular) as well as for tapered cavities with pyramidal and conical shape. The scaling of the free energy with cavity volume and translocated polymer subchain length is generally consistent with predictions from simple scaling arguments, with small deviations in the scaling exponents likely due to finite-size effects. The confinement free energy depends strongly on cavity shape anisometry and is a minimum for an isometric cavity shape with a length-to-width ratio of unity. Entropic depletion at the edges or vertices of the confining cavity are evident in the results for constant-A and pyramidal cavities. For translocation into infinitely long cones, the scaling of the free energy with taper angle is consistent with a theoretical prediction employing the blob model. We also examine the effects of polymer bending rigidity on the translocation free energy for cylindrical cavities. For isometric cavities, the observed scaling behavior is in partial agreement with theoretical predictions, with discrepancies arising from finite-size effects that prevent the emergence of well-defined scaling regimes. In addition, translocation into highly anisometric cylindrical cavities leads to a multistage folding process for stiff polymers. Finally, we examine the effects of crowding agents inside the cavity. We find that the confinement free energy increases with crowder density. At constant packing fraction the magnitude of this effect lessens with increasing crowder size for a crowder-to-monomer size ratio ≥1.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island, Canada C1A 4P3
| | - David R Heckbert
- Department of Physics, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island, Canada C1A 4P3
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Polson JM. Free Energy of a Folded Semiflexible Polymer Confined to a Nanochannel of Various Geometries. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- James M. Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada
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Yu M, Hou Y, Song R, Xu X, Yao S. Tunable Confinement for Bridging Single-Cell Manipulation and Single-Molecule DNA Linearization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800229. [PMID: 29575689 DOI: 10.1002/smll.201800229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/07/2018] [Indexed: 06/08/2023]
Abstract
DNA linearization by nanoconfinement has offered a new avenue toward large-scale genome mapping. The ability to smoothly interface the widely different length scales from cell manipulation to DNA linearization is critical to the development of single-cell genomic mapping or sequencing technologies. Conventional nanochannel technologies for DNA analysis suffer from complex fabrication procedures, DNA stacking at the nanochannel entrance, and inefficient solution exchange. In this work, a dynamic and tunable confinement strategy is developed to manipulate and linearize genomic-length DNA molecules from a single cell. By leveraging pneumatic microvalve control and elastomeric collapse, an array of nanochannels with confining dimension down to 20 nm and length up to sub-millimeter is created and can be dynamically tuned in size. The curved edges of the microvalve form gradual transitions from microscale to nanoscale confinement, smoothly facilitating DNA entry into the nanochannels. A unified micro/nanofluidic device that integrates single-cell trapping and lysis, DNA extraction, purification, labeling, and linearization is developed based on dynamically controllable nanochannels. Mbp-long DNA molecules are extracted directly from a single cell and in situ linearized in the nanochannels. The device provides a facile and promising platform to achieve the ultimate goal of single-cell, single-genome analysis.
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Affiliation(s)
- Miao Yu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Youmin Hou
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Ruyuan Song
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Xiaonan Xu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
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6
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Japaridze A, Orlandini E, Smith KB, Gmür L, Valle F, Micheletti C, Dietler G. Spatial confinement induces hairpins in nicked circular DNA. Nucleic Acids Res 2017; 45:4905-4914. [PMID: 28201616 PMCID: PMC5605231 DOI: 10.1093/nar/gkx098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/25/2017] [Accepted: 02/06/2017] [Indexed: 01/05/2023] Open
Abstract
In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of spatial confinement on the local structure of the DNA. Here, we have used well characterized slits of different sizes to collect high resolution atomic force microscopy images of confined circular DNA with the aim of assessing the impact of the spatial confinement on global and local conformational properties of DNA. Our findings, supported by numerical simulations, indicate that confinement imposes a large mechanical stress on the DNA as evidenced by a pronounced anisotropy and tangent-tangent correlation function with respect to non-constrained DNA. For the strongest confinement we observed nanometer sized hairpins and interwound structures associated with the nicked sites in the DNA sequence. Based on these findings, we propose that spatial DNA confinement in vivo can promote the formation of localized defects at mechanically weak sites that could be co-opted for biological regulatory functions.
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Affiliation(s)
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universita di Padova, Via Marzolo 8, 35131 Padova, Italy
| | | | - Lucas Gmür
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Francesco Valle
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via P.Gobetti 101, Bologna 40129, Italy
| | - Cristian Micheletti
- SISSA - Scuola Internazionale Superiore di Studi Avanzati and CNR-IOM Democritos, Via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
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7
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Coil-helix-globule transition for self-attractive semiflexible ring chains. POLYMER 2017. [DOI: 10.1016/j.polymer.2016.12.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Han M, Kim BC, Matsuoka T, Thouless MD, Takayama S. Dynamic simulations show repeated narrowing maximizes DNA linearization in elastomeric nanochannels. BIOMICROFLUIDICS 2016; 10:064108. [PMID: 27965731 PMCID: PMC5123996 DOI: 10.1063/1.4967963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/03/2017] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
This paper uses computer simulations to reveal unprecedented details about linearization of deoxyribonucleic acid (DNA) inside dynamic nanochannels that can be repeatedly widened and narrowed. We first analyze the effect of rate of channel narrowing on DNA linearization dynamics. Quick (∼0.1 s) narrowing of nanoscale channels results in rapid overstretching of the semi-flexible chain followed by a slower (∼0.1-10 s) relaxation to an equilibrium extension. Two phenomena that induce linearization during channel narrowing, namely, elongational-flow and confinement, occur simultaneously, regardless of narrowing speed. Interestingly, although elongational flow is a minimum at the mid-point of the channel and increases towards the two ends, neither the linearization dynamics nor the degree of DNA extension varies significantly with the center-of-mass of the polymer projected on the channel axis. We also noticed that there was a significant difference in time to reach the equilibrium length, as well as the degree of DNA linearization at short times, depending on the initial conformation of the biopolymer. Based on these observations, we tested a novel linearization protocol where the channels are narrowed and widened repeatedly, allowing DNA to explore multiple conformations. Repeated narrowing and widening, something uniquely enabled by the elastomeric nanochannels, significantly decrease the time to reach the equilibrium-level of stretch when performed within periods comparable to the chain relaxation time and more effectively untangle chains into more linearized biopolymers.
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Affiliation(s)
- Minsub Han
- Department of Mechanical Engineering, College of Engineering, Incheon National University , Songdo-dong, Yeonsu-gu, Incheon 406-772, South Korea
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9
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Jain A, Sheats J, Reifenberger JG, Cao H, Dorfman KD. Modeling the relaxation of internal DNA segments during genome mapping in nanochannels. BIOMICROFLUIDICS 2016; 10:054117. [PMID: 27795749 PMCID: PMC5065570 DOI: 10.1063/1.4964927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/04/2016] [Indexed: 06/01/2023]
Abstract
We have developed a multi-scale model describing the dynamics of internal segments of DNA in nanochannels used for genome mapping. In addition to the channel geometry, the model takes as its inputs the DNA properties in free solution (persistence length, effective width, molecular weight, and segmental hydrodynamic radius) and buffer properties (temperature and viscosity). Using pruned-enriched Rosenbluth simulations of a discrete wormlike chain model with circa 10 base pair resolution and a numerical solution for the hydrodynamic interactions in confinement, we convert these experimentally available inputs into the necessary parameters for a one-dimensional, Rouse-like model of the confined chain. The resulting coarse-grained model resolves the DNA at a length scale of approximately 6 kilobase pairs in the absence of any global hairpin folds, and is readily studied using a normal-mode analysis or Brownian dynamics simulations. The Rouse-like model successfully reproduces both the trends and order of magnitude of the relaxation time of the distance between labeled segments of DNA obtained in experiments. The model also provides insights that are not readily accessible from experiments, such as the role of the molecular weight of the DNA and location of the labeled segments that impact the statistical models used to construct genome maps from data acquired in nanochannels. The multi-scale approach used here, while focused towards a technologically relevant scenario, is readily adapted to other channel sizes and polymers.
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Affiliation(s)
- Aashish Jain
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | | | - Han Cao
- BioNano Genomics , 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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10
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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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11
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de Carvalho SJ, Metzler R, Cherstvy AG. Inverted critical adsorption of polyelectrolytes in confinement. SOFT MATTER 2015; 11:4430-4443. [PMID: 25940939 DOI: 10.1039/c5sm00635j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
What are the fundamental laws for the adsorption of charged polymers onto oppositely charged surfaces, for convex, planar, and concave geometries? This question is at the heart of surface coating applications, various complex formation phenomena, as well as in the context of cellular and viral biophysics. It has been a long-standing challenge in theoretical polymer physics; for realistic systems the quantitative understanding is however often achievable only by computer simulations. In this study, we present the findings of such extensive Monte-Carlo in silico experiments for polymer-surface adsorption in confined domains. We study the inverted critical adsorption of finite-length polyelectrolytes in three fundamental geometries: planar slit, cylindrical pore, and spherical cavity. The scaling relations extracted from simulations for the critical surface charge density σc-defining the adsorption-desorption transition-are in excellent agreement with our analytical calculations based on the ground-state analysis of the Edwards equation. In particular, we confirm the magnitude and scaling of σc for the concave interfaces versus the Debye screening length 1/κ and the extent of confinement a for these three interfaces for small κa values. For large κa the critical adsorption condition approaches the known planar limit. The transition between the two regimes takes place when the radius of surface curvature or half of the slit thickness a is of the order of 1/κ. We also rationalize how σc(κ) dependence gets modified for semi-flexible versus flexible chains under external confinement. We examine the implications of the chain length for critical adsorption-the effect often hard to tackle theoretically-putting an emphasis on polymers inside attractive spherical cavities. The applications of our findings to some biological systems are discussed, for instance the adsorption of nucleic acids onto the inner surfaces of cylindrical and spherical viral capsids.
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Affiliation(s)
- Sidney J de Carvalho
- Institute of Biosciences, Letters and Exact Sciences, Sao Paulo State University, 15054-000 Sao Jose do Rio Preto, Brazil.
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12
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Japaridze A, Benke A, Renevey S, Benadiba C, Dietler G. Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy. Macromolecules 2015. [DOI: 10.1021/ma502537g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aleksandre Japaridze
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Alexander Benke
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Sylvain Renevey
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Carine Benadiba
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
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Dorfman KD, Gupta D, Jain A, Muralidhar A, Tree DR. Hydrodynamics of DNA confined in nanoslits and nanochannels. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2014; 223:3179-3200. [PMID: 25566349 PMCID: PMC4282777 DOI: 10.1140/epjst/e2014-02326-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Modeling the dynamics of a confined, semi exible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and "read" a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirk-wood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach.
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Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Aashish Jain
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
- Materials Research Laboratory, University of California – Santa Barbara, Santa Barbara, CA 93106 USA
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Manneschi C, Fanzio P, Ala-Nissila T, Angeli E, Repetto L, Firpo G, Valbusa U. Stretching of DNA confined in nanochannels with charged walls. BIOMICROFLUIDICS 2014; 8:064121. [PMID: 25553196 PMCID: PMC4265123 DOI: 10.1063/1.4904008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/01/2014] [Indexed: 05/04/2023]
Abstract
There is currently a growing interest in control of stretching of DNA inside nanoconfined regions due to the possibility to analyze and manipulate single biomolecules for applications such as DNA mapping and barcoding, which are based on stretching the DNA in a linear fashion. In the present work, we couple Finite Element Methods and Monte Carlo simulations in order to study the conformation of DNA molecules confined in nanofluidic channels with neutral and charged walls. We find that the electrostatic forces become more and more important when lowering the ionic strength of the solution. The influence of the nanochannel cross section geometry is also studied by evaluating the DNA elongation in square, rectangular, and triangular channels. We demonstrate that coupling electrostatically interacting walls with a triangular geometry is an efficient way to stretch DNA molecules at the scale of hundreds of nanometers. The paper reports experimental observations of λ-DNA molecules in poly(dimethylsiloxane) nanochannels filled with solutions of different ionic strength. The results are in good agreement with the theoretical predictions, confirming the crucial role of the electrostatic repulsion of the constraining walls on the molecule stretching.
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Affiliation(s)
| | - Paola Fanzio
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Tapio Ala-Nissila
- Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science , P.O. Box 11100, FIN-00076 Aalto, Espoo, Finland and Department of Physics, Brown University , Providence, Rhode Island 02912-1843, USA
| | - Elena Angeli
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Luca Repetto
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Giuseppe Firpo
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Ugo Valbusa
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
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15
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Ikonen T. Driven polymer transport through a periodically patterned channel. J Chem Phys 2014; 140:234906. [PMID: 24952567 DOI: 10.1063/1.4883055] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the driven transport of polymers in a periodically patterned channel using Langevin dynamics simulations in two dimensions. The channel walls are patterned with periodically alternating patches of attractive and non-attractive particles that act as trapping sites for the polymer. We find that the system shows rich dynamical behavior, observing giant diffusion, negative differential mobility, and several different transition mechanisms between the attractive patches. We also show that the channel can act as an efficient high-pass filter for polymers longer than a threshold length Nthr, which can be tuned by adjusting the length of the attractive patches and the driving force. Our findings suggest the possibility of fabricating polymer filtration devices based on patterned nanochannels.
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Affiliation(s)
- Timo Ikonen
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Finland and Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Finland
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16
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Tree DR, Wang Y, Dorfman KD. Modeling the relaxation time of DNA confined in a nanochannel. BIOMICROFLUIDICS 2013; 7:54118. [PMID: 24309551 PMCID: PMC3820670 DOI: 10.1063/1.4826156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/07/2013] [Indexed: 05/12/2023]
Abstract
Using a mapping between a Rouse dumbbell model and fine-grained Monte Carlo simulations, we have computed the relaxation time of λ-DNA in a high ionic strength buffer confined in a nanochannel. The relaxation time thus obtained agrees quantitatively with experimental data [Reisner et al., Phys. Rev. Lett. 94, 196101 (2005)] using only a single O(1) fitting parameter to account for the uncertainty in model parameters. In addition to validating our mapping, this agreement supports our previous estimates of the friction coefficient of DNA confined in a nanochannel [Tree et al., Phys. Rev. Lett. 108, 228105 (2012)], which have been difficult to validate due to the lack of direct experimental data. Furthermore, the model calculation shows that as the channel size passes below approximately 100 nm (or roughly the Kuhn length of DNA) there is a dramatic drop in the relaxation time. Inasmuch as the chain friction rises with decreasing channel size, the reduction in the relaxation time can be solely attributed to the sharp decline in the fluctuations of the chain extension. Practically, the low variance in the observed DNA extension in such small channels has important implications for genome mapping.
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Affiliation(s)
- Douglas R Tree
- Department of Chemical Engineering and Material Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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