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Cui Y, Ying C, Huang XY, Ye Q, Tian J, Liu Z. Electrical Transport and Dynamics of Confined DNA through Highly Conductive 2D Graphene Nanochannels. NANO LETTERS 2024; 24:4485-4492. [PMID: 38578031 DOI: 10.1021/acs.nanolett.4c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Confining DNA in nanochannels is an important approach to studying its structure and transportation dynamics. Graphene nanochannels are particularly attractive for studying DNA confinement due to their atomic flatness, precise height control, and excellent mechanical strength. Here, using femtosecond laser etching and wetting transfer, we fabricate graphene nanochannels down to less than 4.3 nm in height, with the length-to-height ratios up to 103. These channels exhibit high stability, low noise, and self-cleaning ability during the long-term ionic current recording. We report a clear linear relationship between DNA length and the residence time in the channel and further utilize this relationship to differentiate DNA fragments based on their lengths, ranging widely from 200 bps to 48.5 kbps. The graphene nanochannel presented here provides a potential platform for label-free analyses and reveals fundamental insights into the conformational dynamics of DNA and proteins in confined space.
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Affiliation(s)
- Yangjun Cui
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Cuifeng Ying
- Advanced Optics & Photonics Laboratory, Department of Engineering, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, U.K
| | - Xiao-Yu Huang
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Qing Ye
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Jianguo Tian
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
| | - Zhibo Liu
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
- The Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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2
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Affiliation(s)
- Peter Cifra
- Polymer Institute Slovak Academy of Sciences Bratislava 84541 Slovakia
| | - Tomáš Bleha
- Polymer Institute Slovak Academy of Sciences Bratislava 84541 Slovakia
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3
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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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4
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Yeh JW, Taloni A, Sriram KK, Shen JP, Kao DY, Chou CF. Nanoconfinement-Induced DNA Reptating Motion and Analogy to Fluctuating Interfaces. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jia-Wei Yeh
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Alessandro Taloni
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- CNR-Consiglio Nazionale delle Ricerche, ISC, Via dei Taurini 19, 00185 Roma, Italy
| | - K. K. Sriram
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Jie-Pan Shen
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Der-You Kao
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Fu Chou
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- Research Centre for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
- Genomics Research Centre, Academia Sinica, Taipei 11529, Taiwan
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5
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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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Bleha T, Cifra P. Force-displacement relations at compression of dsDNA macromolecules. J Chem Phys 2019; 151:014901. [PMID: 31272182 DOI: 10.1063/1.5099522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The elasticity of dsDNA molecules is investigated by Monte Carlo simulations based on a coarse-grained model of DNA. The force-displacement (f-r) curves are computed under the constraints of the constant force (Gibbs) or the constant length (Helmholtz) ensemble. Particular attention was paid to the compressional (negative) and weak tensile forces. It was confirmed that simulations using the vector Gibbs ensemble fail to represent the compression behavior of polymers. Simulations using the scalar Gibbs protocol resulted in a qualitatively correct compressional response of DNA provided that the quadratic averages of displacements were employed. Furthermore, a well-known shortcoming of the popular Marko-Siggia relation for DNA elasticity at weak tensile forces is elucidated. Conversely, the function f-r from the simulation at the constant length constraint, as well as the new closed-form expressions, provides a realistic depiction of the DNA elasticity over the wide range of negative and positive forces. Merely a qualitative resemblance of the compression functions f-r predicted by the employed approaches supports the notion that the elastic response of DNA molecules may be greatly affected by the specifics of the experimental setups and the kind of averaging of the measured variable.
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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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Bleha T, Cifra P. Correlation anisotropy and stiffness of DNA molecules confined in nanochannels. J Chem Phys 2018; 149:054903. [PMID: 30089382 DOI: 10.1063/1.5034219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The anisotropy of orientational correlations in DNA molecules confined in cylindrical channels is explored by Monte Carlo simulations using a coarse-grained model of double-stranded (ds) DNA. We find that the correlation function ⟨C(s)⟩⊥ in the transverse (confined) dimension exhibits a region of negative values in the whole range of channel sizes. Such a clear-cut sign of the opposite orientation of chain segments represents a microscopic validation of the Odijk deflection mechanism in narrow channels. At moderate-to-weak confinement, the negative ⟨C(s)⟩⊥ correlations imply a preference of DNA segments for transverse looping. The inclination for looping can explain a reduction of stiffness as well as the enhanced knotting of confined DNA relative to that detected earlier in bulk at some channel sizes. Furthermore, it is shown that the orientational persistence length Por fails to convey the apparent stiffness of DNA molecules in channels. Instead, correlation lengths P∥ and P⊥ in the axial and transverse directions, respectively, encompass the channel-induced modifications of DNA stiffness.
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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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Bleha T, Cifra P. Stretching and compression of DNA by external forces under nanochannel confinement. SOFT MATTER 2018; 14:1247-1259. [PMID: 29363709 DOI: 10.1039/c7sm02413d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mechanical deformation of dsDNA molecules inside square nanochannels is investigated using simulations based on a coarse-grained model of DNA. The combined action of confinement and weak external forces is explored in a variety of confinement regimes, including the transition zone relevant to nanofluidic experiments. The computed free energy and force profiles are markedly affected by the channel size. Effective elastic softening of confined DNA molecules relative to the bulk DNA is observed in the channels of intermediate widths. The extension of DNA from its bulk equilibrium length in nanofluidic devices is resolved into contributions from the passive extension due to confinement and from the active stretching induced by force. Potential implications of the very different energy costs computed for the two extension modes (extension by confinement takes much more free energy than stretching by force) for behavior of DNA in nanofluidic chips are indicated.
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Affiliation(s)
- Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia.
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VandeSande MC, Pasut DJ, de Haan HW. Sorting polymers by size via an array of viscous posts. Electrophoresis 2017; 38:2488-2497. [PMID: 28975695 DOI: 10.1002/elps.201700136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 11/07/2022]
Abstract
DNA fragments can be sorted according to size by forcing them through an array of nanoposts. Whereas previous studies have explored solid nanoposts, this work examines nanoposts constructed out of viscous inclusions. Langevin dynamics simulations are used to study the dynamics of polymers driven through arrays of these viscous nanoposts for a range of post viscosities. The results are compared to the solid post case. Increasing post viscosity causes a decrease in the mobility of polymers traversing the array. In the limit of high post viscosity, the mobility becomes lower than in the solid post arrays, rather than converging to it. Analysis of the distributions of event times also shows that the viscous case is fundamentally different from the solid post case. The decrease in mobility in the viscous case arises from slowing down the polymer as it interacts with or even moves through the nanoposts, whereas the solid post case exhibits wrapping and unwrapping dynamics, yielding escape-like statistics. This work suggests that it may be possible to use viscous inclusions within nanofluidic and microfluidic devices to sort biomolecules with high resolution.
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Affiliation(s)
- Matthew C VandeSande
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | - Daniel J Pasut
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | - Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
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10
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Saadat A, Khomami B. A new bead-spring model for simulation of semi-flexible macromolecules. J Chem Phys 2016; 145:204902. [DOI: 10.1063/1.4968020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Amir Saadat
- Material Research and Innovation Laboratory, Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996-2200, USA
| | - Bamin Khomami
- Material Research and Innovation Laboratory, Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996-2200, USA
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11
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Vollmer SC, de Haan HW. Translocation is a nonequilibrium process at all stages: Simulating the capture and translocation of a polymer by a nanopore. J Chem Phys 2016; 145:154902. [DOI: 10.1063/1.4964630] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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12
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Abstract
External forces and confinement are two fundamental and complementary approaches for biopolymer stretching. By employing micro- and nanofluidics, we study the force-extension dynamics by simultaneously applying external forces and confinement to single-DNA molecules. In particular, we apply external electric fields to stretch single DNA molecules that are attached to microspheres anchored at a nanoslit entrance. Using this method, we measure the force-extension relation of tethered DNA and describe this relation with modified wormlike chain models. This allowed experimental validations of several theoretical predictions, including the increase in the global persistence length of confined DNA with increasing degree of confinement and the "confined Pincus" regime in slit confinement.
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Affiliation(s)
- Jia-Wei Yeh
- School
of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
- Department
of Physics, University of California, San Diego, La Jolla, California 92122, United States
| | - Kylan Szeto
- School
of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
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13
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Pedersen JN, Marie R, Kristensen A, Flyvbjerg H. How to determine local stretching and tension in a flow-stretched DNA molecule. Phys Rev E 2016; 93:042405. [PMID: 27176327 DOI: 10.1103/physreve.93.042405] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Indexed: 11/07/2022]
Abstract
We determine the nonuniform stretching of and tension in a mega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA-e.g., native DNA extracted from human cells or bacteria-must be stretched with ease for inspection, this method applies.
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Affiliation(s)
- Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
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14
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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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Klepinger AC, Greenier MK, Levy SL. Stretching DNA Molecules in Strongly Confining Nanofluidic Slits. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01712] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Madeline K. Greenier
- Department
of Physics, Binghamton University, Binghamton, New York 13902, United States
| | - Stephen L. Levy
- Department
of Physics, Binghamton University, Binghamton, New York 13902, United States
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16
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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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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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