101
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Jain A, Dorfman KD. Evaluation of the Kirkwood approximation for the diffusivity of channel-confined DNA chains in the de Gennes regime. BIOMICROFLUIDICS 2015; 9:024112. [PMID: 25945138 PMCID: PMC4393413 DOI: 10.1063/1.4917269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 03/30/2015] [Indexed: 05/30/2023]
Abstract
We use Brownian dynamics with hydrodynamic interactions to calculate both the Kirkwood (short-time) diffusivity and the long-time diffusivity of DNA chains from free solution down to channel confinement in the de Gennes regime. The Kirkwood diffusivity in confinement is always higher than the diffusivity obtained from the mean-squared displacement of the center-of-mass, as is the case in free solution. Moreover, the divergence of the local diffusion tensor, which is non-zero in confinement, makes a negligible contribution to the latter diffusivity in confinement. The maximum error in the Kirkwood approximation in our simulations is about 2% for experimentally relevant simulation times. The error decreases with increasing confinement, consistent with arguments from blob theory and the molecular-weight dependence of the error in free solution. In light of the typical experimental errors in measuring the properties of channel-confined DNA, our results suggest that the Kirkwood approximation is sufficiently accurate to model experimental data.
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Affiliation(s)
- Aashish Jain
- Department of Chemical Engineering and Material Science, University of Minnesota-Twin Cities , 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Material Science, University of Minnesota-Twin Cities , 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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102
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Kurganov AA, Svec F, Kanateva AY. Flow induced conformational transitions of macromolecules and their effect on chromatographic separations. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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103
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Reinhart WF, Reifenberger JG, Gupta D, Muralidhar A, Sheats J, Cao H, Dorfman KD. Distribution of distances between DNA barcode labels in nanochannels close to the persistence length. J Chem Phys 2015; 142:064902. [PMID: 25681938 PMCID: PMC4327924 DOI: 10.1063/1.4907552] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 01/25/2015] [Indexed: 11/14/2022] Open
Abstract
We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension.
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Affiliation(s)
- Wesley F Reinhart
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeff G Reifenberger
- BioNano Genomics, 9640 Towne Centre Dr., Ste. 100, San Diego, California 92121, USA
| | - Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- 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 Dr., Ste. 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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104
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de Haan HW, Sean D, Slater GW. Using a Péclet number for the translocation of a polymer through a nanopore to tune coarse-grained simulations to experimental conditions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022601. [PMID: 25768522 DOI: 10.1103/physreve.91.022601] [Citation(s) in RCA: 14] [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
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavor to match any particular set of experimental conditions. In this manuscript, we use the concept of a Péclet number for translocation, P(t), to compare the drift-diffusion balance in a typical experiment vs a typical simulation. We find that the standard coarse-grained approach overestimates diffusion effects by anywhere from a factor of 5 to 50 compared to experimental conditions using double stranded DNA (dsDNA). By defining a Péclet control parameter, λ, we are able to correct this and tune the simulations to replicate the experimental P(t) (for dsDNA and other scenarios). To show the effect that a particular P(t) can have on the dynamics of translocation, we perform simulations across a wide range of P(t) values for two different types of driving forces: a force applied in the pore and a pulling force applied to the end of the polymer. As P(t) brings the system from a diffusion dominated to a drift dominated regime, a variety of effects are observed including a non-monotonic dependence of the translocation time τ on P(t) and a steep rise in the probability of translocating. Comparing the two force cases illustrates the impact of the crowding effects that occur on the trans side: a non-monotonic dependence of the width of the τ distributions is obtained for the in-pore force but not for the pulling force.
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Affiliation(s)
- Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario L1H 7K4, Canada
| | - David Sean
- Physics Department, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Gary W Slater
- Physics Department, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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105
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Alizadehheidari M, Werner E, Noble C, Reiter-Schad M, Nyberg LK, Fritzsche J, Mehlig B, Tegenfeldt JO, Ambjörnsson T, Persson F, Westerlund F. Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics. Macromolecules 2015. [DOI: 10.1021/ma5022067] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Erik Werner
- Department
of Physics, Gothenburg University, Gothenburg, Sweden
| | | | | | | | | | - Bernhard Mehlig
- Department
of Physics, Gothenburg University, Gothenburg, Sweden
| | | | | | - Fredrik Persson
- Department of Cell and
Molecular Biology, Uppsala University, Uppsala, Sweden
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106
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Welling RC, Knotts TA. The effects of multiple probes on the hybridization of target DNA on surfaces. J Chem Phys 2015; 142:015102. [DOI: 10.1063/1.4904929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Ryan C. Welling
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA
| | - Thomas A. Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA
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107
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Khorshid A, Zimny P, Tétreault-La Roche D, Massarelli G, Sakaue T, Reisner W. Dynamic compression of single nanochannel confined DNA via a nanodozer assay. PHYSICAL REVIEW LETTERS 2014; 113:268104. [PMID: 25615391 DOI: 10.1103/physrevlett.113.268104] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 06/04/2023]
Abstract
We show that a single DNA molecule confined and extended in a nanochannel can be dynamically compressed by sliding a permeable gasket at a fixed velocity relative to the stationary polymer. The gasket is realized experimentally by optically trapping a nanosphere inside a nanochannel. The trapped bead acts like a "nanodozer," directly applying compressive forces to the molecule without requirement of chemical attachment. Remarkably, these strongly nonequilibrium measurements can be quantified via a simple nonlinear convective-diffusion formalism and yield insights into the local blob statistics, allowing us to conclude that the compressed nanochannel-confined chain exhibits mean-field behavior.
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Affiliation(s)
- Ahmed Khorshid
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Philip Zimny
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | | | - Geremia Massarelli
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Takahiro Sakaue
- Department of Physics, Kyushu University 33, Fukuoka 812-8581, Japan
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
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108
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Werner E, Mehlig B. Confined polymers in the extended de Gennes regime. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:062602. [PMID: 25615121 DOI: 10.1103/physreve.90.062602] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Indexed: 05/27/2023]
Abstract
We show that the problem of describing the conformations of a semiflexible polymer confined to a channel can be mapped onto an exactly solvable model in the so-called extended de Gennes regime. This regime (where the polymer is neither weakly nor strongly confined) has recently been intensively studied experimentally and by means of computer simulations. The exact solution predicts precisely how the conformational fluctuations depend upon the channel width and upon the microscopic parameters characterizing the physical properties of the polymer.
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Affiliation(s)
- E Werner
- Department of Physics, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - B Mehlig
- Department of Physics, University of Gothenburg, SE-40530 Gothenburg, Sweden
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109
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Muralidhar A, Tree DR, Dorfman KD. Backfolding of Wormlike Chains Confined in Nanochannels. Macromolecules 2014. [DOI: 10.1021/ma501687k] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Abhiram Muralidhar
- Department
of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, United States
| | - Douglas R. Tree
- Department
of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, United States
- Materials
Research Laboratory, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Kevin D. Dorfman
- Department
of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, United States
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110
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van der Maarel JRC, Zhang C, van Kan JA. A Nanochannel Platform for Single DNA Studies: From Crowding, Protein DNA Interaction, to Sequencing of Genomic Information. Isr J Chem 2014. [DOI: 10.1002/ijch.201400091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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111
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Micheletti C, Orlandini E. Knotting and Unknotting Dynamics of DNA Strands in Nanochannels. ACS Macro Lett 2014; 3:876-880. [PMID: 35596352 DOI: 10.1021/mz500402s] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The self-knotting dynamics of DNA strands confined in nanochannels is studied with Brownian simulations. The model DNA chains are several microns long and placed inside channels that are 50-300 nm wide. This width range covers the transition between different metric scaling regimes and the concomitant drop of DNA knotting probability for channel widths below ∼75 nm. We find that knots typically originate from deep looping and backfoldings of the chain ends. Upon lowering the channel width, backfoldings become shallower and rarer and the lifetime of knots decreases while that of unknots increases. This lifetimes interplay causes the dramatic reduction of knots incidence for increasing confinement. The results can aid the design of nanochannels capable of harnessing the self-knotting dynamics to quench or relax the DNA topological state as desired.
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Affiliation(s)
- Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
| | - Enzo Orlandini
- Dipartimento
di Fisica, Sezione CNISM, and Università di Padova, via Marzolo 8, I-35131 Padova, Italy
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112
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Kurganov AA, Kanateva AY, Orekhov VA. Conformational transitions of macromolecules in an eluent flow and their manifestation in the chromatography of polymers. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n07abeh004433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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113
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Gao J, Tang P, Yang Y, Chen JZY. Free energy of a long semiflexible polymer confined in a spherical cavity. SOFT MATTER 2014; 10:4674-4685. [PMID: 24839199 DOI: 10.1039/c4sm00605d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The free energy and conformational properties of a wormlike chain confined inside a spherical surface are investigated. We show that in the weak-confinement limit, the wormlike chain model exactly reproduces the confinement properties of a Gaussian chain; in such a case the confinement entropy dominates the free energy; in the strong-confinement limit, the free energy is dominated by the bending energy of the chain, which is forced to wrap around the confining surface. We also present a numerical solution within the crossover region between the two limits, solving the differential equation that the probability distribution function satisfies.
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Affiliation(s)
- Jie Gao
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
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114
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Gupta D, Sheats J, Muralidhar A, Miller JJ, Huang DE, Mahshid S, Dorfman KD, Reisner W. Mixed confinement regimes during equilibrium confinement spectroscopy of DNA. J Chem Phys 2014; 140:214901. [PMID: 24908035 PMCID: PMC4048444 DOI: 10.1063/1.4879515] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/12/2014] [Indexed: 11/14/2022] Open
Abstract
We have used a combination of fluorescence microscopy experiments and Pruned Enriched Rosenbluth Method simulations of a discrete wormlike chain model to measure the mean extension and the variance in the mean extension of λ-DNA in 100 nm deep nanochannels with widths ranging from 100 nm to 1000 nm in discrete 100 nm steps. The mean extension is only weakly affected by the channel aspect ratio. In contrast, the fluctuations of the chain extension qualitatively differ between rectangular channels and square channels with the same cross-sectional area, owing to the "mixing" of different confinement regimes in the rectangular channels. The agreement between experiment and simulation is very good, using the extension due to intercalation as the only adjustable parameter.
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Affiliation(s)
- Damini Gupta
- 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
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeremy J Miller
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Derek E Huang
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Sara Mahshid
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Walter Reisner
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
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115
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Patra TK, Singh JK. Localization and stretching of polymer chains at the junction of two surfaces. J Chem Phys 2014; 140:204909. [PMID: 24880327 DOI: 10.1063/1.4878499] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a molecular dynamics study on the stretching of a linear polymer chain that is adsorbed at the junction of two intersecting flat surfaces of varying alignments. We observe a transition from a two-dimensional to one-dimensional (1D) structure of the adsorbed polymer when the alignment, i.e., the angle between the two surfaces that form a groove, θ, is below 135°. We show that the radius of gyration of the polymer chain Rg scales as Rg ∼ N(3/4) with the degree of polymerization N for θ = 180° (planer substrate), and the scaling changes to Rg ∼ N(1.0) for θ < 135° in good solvents. At the crossover point, θ = 135°, the exponent becomes 1.15. The 1D stretching of the polymer chain is found to be 84% of its contour length for θ ⩽ 90°. The center of mass diffusion coefficient D decreases sharply with θ. However, the diffusion coefficient scales with N as D ∼ N(-1), and is independent of θ. The relaxation time τ, for the diffusive motion, scales as τ ∼ N(2.5) for θ = 180° (planar substrate), which changes to τ ∼ N(3.0) for θ ⩽ 90°. At the crossover point, the exponent is 3.4, which is slightly higher than the 1D value of 3.0. Further, a signature of reptation-like dynamics of the polymer chain is observed at the junction for θ ⩽ 90° due to its strong 1D localization and stretching.
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Affiliation(s)
- Tarak K Patra
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jayant K Singh
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
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116
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Affiliation(s)
- Douglas R. Tree
- Department
of Chemical Engineering
and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Wesley F. Reinhart
- Department
of Chemical Engineering
and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kevin D. Dorfman
- Department
of Chemical Engineering
and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
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117
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Roushan M, Kaur P, Karpusenko A, Countryman PJ, Ortiz CP, Fang Lim S, Wang H, Riehn R. Probing transient protein-mediated DNA linkages using nanoconfinement. BIOMICROFLUIDICS 2014; 8:034113. [PMID: 25379073 PMCID: PMC4162420 DOI: 10.1063/1.4882775] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 05/30/2014] [Indexed: 05/16/2023]
Abstract
We present an analytic technique for probing protein-catalyzed transient DNA loops that is based on nanofluidic channels. In these nanochannels, DNA is forced in a linear configuration that makes loops appear as folds whose size can easily be quantified. Using this technique, we study the interaction between T4 DNA ligase and DNA. We find that T4 DNA ligase binding changes the physical characteristics of the DNApolymer, in particular persistence length and effective width. We find that the rate of DNA fold unrolling is significantly reduced when T4 DNA ligase and ATP are applied to bare DNA. Together with evidence of T4 DNA ligase bridging two different segments of DNA based on AFM imaging, we thus conclude that ligase can transiently stabilize folded DNA configurations by coordinating genetically distant DNA stretches.
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Affiliation(s)
- Maedeh Roushan
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Parminder Kaur
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Alena Karpusenko
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | | | - Carlos P Ortiz
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Shuang Fang Lim
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Hong Wang
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Robert Riehn
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
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118
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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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119
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Gupta C, Liao WC, Gallego-Perez D, Castro CE, Lee LJ. DNA translocation through short nanofluidic channels under asymmetric pulsed electric field. BIOMICROFLUIDICS 2014; 8:024114. [PMID: 24803963 PMCID: PMC4000398 DOI: 10.1063/1.4871595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/07/2014] [Indexed: 05/08/2023]
Abstract
Investigation of single molecule DNA dynamics in confined environments has led to important applications in DNA analysis, separation, and sequencing. Here, we studied the electrophoretic transport of DNA molecules through nanochannels shorter than the DNA contour length and calculated the associated translocation time curves. We found that the longer T4 DNA molecules required a longer time to traverse a fixed length nanochannel than shorter λ DNA molecules and that the translocation time decreased with increasing electric field which agreed with theoretical predictions. We applied this knowledge to design an asymmetric electric pulse and demonstrate the different responses of λ and T4 DNA to the pulses. We used Brownian dynamics simulations to corroborate our experimental results on DNA translocation behaviour. This work contributes to the fundamental understanding of polymer transport through nanochannels and may help in designing better separation techniques in the future.
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Affiliation(s)
- C Gupta
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, USA ; Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA
| | - W-C Liao
- Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA
| | - D Gallego-Perez
- Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA
| | - C E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, USA ; Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA
| | - L J Lee
- Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA ; William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
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120
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Muralidhar A, Tree DR, Wang Y, Dorfman KD. Interplay between chain stiffness and excluded volume of semiflexible polymers confined in nanochannels. J Chem Phys 2014; 140:084905. [PMID: 24588196 PMCID: PMC3977884 DOI: 10.1063/1.4865965] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/05/2014] [Indexed: 11/14/2022] Open
Abstract
The properties of channel-confined semiflexible polymers are determined by a complicated interplay of chain stiffness and excluded volume effects. Using Pruned-Enriched Rosenbluth Method (PERM) simulations, we study the equilibrium properties of channel-confined polymers by systematically controlling chain stiffness and excluded volume. Our calculations of chain extension and confinement free energy for freely jointed chains with and without excluded volume show excellent agreement with theoretical predictions. For ideal wormlike chains, the extension is seen to crossover from Odijk behavior in strong confinement to zero-stretching, bulk-like behavior in weak confinement. In contrast, for self-avoiding wormlike chains, we always observe that the linear scaling of the extension with the contour length is valid in the long-chain limit irrespective of the regime of confinement, owing to the coexistence of stiffness and excluded volume effects. We further propose that the long-chain limit for the extension corresponds to chain lengths wherein the projection of the end-to-end distance along the axis of the channel is nearly equal to the mean span parallel to the axis. For DNA in nanochannels, this limit was identified using PERM simulations out to molecular weights of more than 1 megabase pairs; the molecular weight of λ-DNA is found to exhibit nearly asymptotic fractional extension for channels sizes used commonly in experiments.
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Affiliation(s)
- Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Douglas R Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Yanwei Wang
- Department of Polymer Science and Engineering, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren-ai Road, Suzhou 215123, People's Republic of China
| | - 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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121
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Chen YL, Lin YH, Chang JF, Lin PK. Dynamics and Conformation of Semiflexible Polymers in Strong Quasi-1D and -2D Confinement. Macromolecules 2014. [DOI: 10.1021/ma401923t] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Yeng-Long Chen
- Institute
of Physics, Academia Sinica, Taipei, Taiwan
- Department
of Physics, National Taiwan University, Taipei, Taiwan
- Department
of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
| | - Yu-Hui Lin
- Institute
of Physics, Academia Sinica, Taipei, Taiwan
| | | | - Po-keng Lin
- Institute
of Physics, Academia Sinica, Taipei, Taiwan
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122
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Affiliation(s)
- Jeff Z. Y. Chen
- Department
of Physics and
Astronomy, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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123
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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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124
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Tree DR, Muralidhar A, Doyle PS, Dorfman KD. Is DNA a Good Model Polymer? Macromolecules 2013; 46:10.1021/ma401507f. [PMID: 24347685 PMCID: PMC3859536 DOI: 10.1021/ma401507f] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48,500 base pairs) does not exhibit "ideal" scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior.
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Affiliation(s)
- Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota
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125
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Kounovsky-Shafer KL, Hernández-Ortiz JP, Jo K, Odijk T, de Pablo JJ, Schwartz DC. Presentation of large DNA molecules for analysis as nanoconfined dumbbells. Macromolecules 2013; 46:8356-8368. [PMID: 24683272 PMCID: PMC3964590 DOI: 10.1021/ma400926h] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multi-pronged approach that marshaled molecular confinement, ionic environment, and DNA elastic properties-but tressed by molecular simulations-we have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green's function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the "Odijk regime" does indeed start when the confinement dimensions size are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics.
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Affiliation(s)
- Kristy L. Kounovsky-Shafer
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and UW-Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706-1580
| | - Juan P. Hernández-Ortiz
- Departamento de Materiales, Universidad Nacional de Colombia, Sede Medellín, Kra 80 # 65-223
| | - Kyubong Jo
- Bloque M3-050, Medellín Colombia, Department of Chemistry, Sogang University, Seoul, Korea
| | - Theo Odijk
- Lorentz Institute for Theoretical Physics, University of Leiden, The Netherlands
| | - Juan J. de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and UW-Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706-1580
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126
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Affiliation(s)
| | - Jia-Wei Yeh
- Institute
of Physics, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Chia-Fu Chou
- Institute
of Physics, Academia Sinica, Nangang, Taipei 11529, Taiwan
- Research Center for Applied Sciences, Nangang, Taipei 11529, Taiwan
- Genomics
Research Center, Academia Sinica, Nangang, Taipei 11529, Taiwan
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127
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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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128
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Viktorova EN, Korolev AA, Orekhov VA, Kanat’eva AY, Kurganov AA. Conformational transitions in ultrahigh-molecular-mass polymers and their manifestation in chromatography on monolithic columns. POLYMER SCIENCE SERIES A 2013. [DOI: 10.1134/s0965545x13070079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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129
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Tree DR, Wang Y, Dorfman KD. Extension of DNA in a nanochannel as a rod-to-coil transition. PHYSICAL REVIEW LETTERS 2013; 110:208103. [PMID: 25167455 PMCID: PMC4156158 DOI: 10.1103/physrevlett.110.208103] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Indexed: 05/14/2023]
Abstract
DNA confinement in nanochannels is emerging as an important tool for genomics and an excellent platform for testing the theories of confined wormlike polymers. Using cutting-edge, large scale Monte Carlo simulations of asymptotically long wormlike chains, we show that, in analogy to the rod-to-coil transition for free wormlike polymers, there exists a universal, Gauss-de Gennes regime that connects the classic Odijk and de Gennes regimes of channel-confined chains. For DNA in a nanochannel, this Gauss-de Gennes regime spans practically the entire experimentally relevant range of channel sizes, including the nanochannels used in an incipient genome mapping technology.
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Affiliation(s)
- Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota ― Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455
| | - Yanwei Wang
- Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren-ai Road, Suzhou, 215123, P.R. China
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota ― Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455
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130
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Račko D, Cifra P. Segregation of semiflexible macromolecules in nanochannel. J Chem Phys 2013; 138:184904. [DOI: 10.1063/1.4803674] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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131
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Manneschi C, Angeli E, Ala-Nissila T, Repetto L, Firpo G, Valbusa U. Conformations of DNA in Triangular Nanochannels. Macromolecules 2013. [DOI: 10.1021/ma4000545] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chiara Manneschi
- Nanomed Laboratories, Dipartimento
di Fisica, Università di Genova,
via Dodecaneso 33, 16146 Genova, Italy
| | - Elena Angeli
- Nanomed Laboratories, Dipartimento
di Fisica, Università di Genova,
via Dodecaneso 33, 16146 Genova, Italy
| | - Tapio Ala-Nissila
- COMP Centre of Excellence, Department
of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland
| | - Luca Repetto
- Nanomed Laboratories, Dipartimento
di Fisica, Università di Genova,
via Dodecaneso 33, 16146 Genova, Italy
| | - Giuseppe Firpo
- Nanomed Laboratories, Dipartimento
di Fisica, Università di Genova,
via Dodecaneso 33, 16146 Genova, Italy
| | - Ugo Valbusa
- Nanomed Laboratories, Dipartimento
di Fisica, Università di Genova,
via Dodecaneso 33, 16146 Genova, Italy
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132
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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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133
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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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134
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Comparison of linear and ring DNA macromolecules moderately and strongly confined in nanochannels. Biochem Soc Trans 2013; 41:625-9. [DOI: 10.1042/bst20120279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Understanding the mechanism of DNA extension in nanochannels is necessary for interpretation of experiments in nanofluidic channel devices that have been conducted recently with both linear and ring chains. The present article reviews the situation with linear chains and analyses the experimental results and simulations for channel-induced extension (linearization) of ring chains. Results for confined rings indicate a transition between moderate and strong confinement similar to that of linear chains. Owing to stronger self-avoidance in confined rings, the transition and chain extension is shifted relative to linear DNA. We suggest that a relationship similar to that used for the extension of linear chains may also be used for circular DNA.
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135
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Affiliation(s)
- Kevin D. Dorfman
- Dept. of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Ave. SE; Minneapolis; MN 55455
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136
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Schmitt TJ, Rogers JB, Knotts TA. Exploring the mechanisms of DNA hybridization on a surface. J Chem Phys 2013; 138:035102. [DOI: 10.1063/1.4775480] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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137
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Chen YL. Electro-entropic excluded volume effects on DNA looping and relaxation in nanochannels. BIOMICROFLUIDICS 2013; 7:54119. [PMID: 24255695 PMCID: PMC3820673 DOI: 10.1063/1.4826157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/07/2013] [Indexed: 05/14/2023]
Abstract
We investigate the fluctuation-relaxation dynamics of entropically restricted DNA molecules in square nanochannels ranging from 0.09 to 19.9 times the persistence length. In nanochannels smaller than the persistence length, the chain relaxation time is found to have cubic dependence on the channel size. It is found that the effective polymer width significantly alter the chain conformation and relaxation time in strong confinement. For thinner chains, looped chain configurations are found in channels with height comparable to the persistence length, with very slow relaxation compared to un-looped chains. Larger effective chain widths inhibit the formation of hairpin loops.
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Affiliation(s)
- Yeng-Long Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan ; Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan ; Department of Physics, National Taiwan University, Taipei, Taiwan
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138
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Østergaard PF, Matteucci M, Reisner W, Taboryski R. DNA barcoding via counterstaining with AT/GC sensitive ligands in injection-molded all-polymer nanochannel devices. Analyst 2013; 138:1249-55. [DOI: 10.1039/c2an36522g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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139
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Reinhart WF, Tree DR, Dorfman KD. Entropic depletion of DNA in triangular nanochannels. BIOMICROFLUIDICS 2013; 7:24102. [PMID: 24309518 PMCID: PMC3598824 DOI: 10.1063/1.4794371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 02/14/2013] [Indexed: 05/14/2023]
Abstract
Using Monte Carlo simulations of a touching-bead model of double-stranded DNA, we show that DNA extension is enhanced in isosceles triangular nanochannels (relative to a circular nanochannel of the same effective size) due to entropic depletion in the channel corners. The extent of the enhanced extension depends non-monotonically on both the accessible area of the nanochannel and the apex angle of the triangle. We also develop a metric to quantify the extent of entropic depletion, thereby collapsing the extension data for circular, square, and various triangular nanochannels onto a single master curve for channel sizes in the transition between the Odijk and de Gennes regimes.
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Affiliation(s)
- Wesley F Reinhart
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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140
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Menard LD, Ramsey JM. Electrokinetically-driven transport of DNA through focused ion beam milled nanofluidic channels. Anal Chem 2012; 85:1146-53. [PMID: 23234458 DOI: 10.1021/ac303074f] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The electrophoretically driven transport of double-stranded λ-phage DNA through focused ion beam (FIB) milled nanochannels is described. Nanochannels were fabricated having critical dimensions (width and depth) corresponding to 0.5×, 1×, and 2× the DNA persistence length, or 25 nm, 50 nm, and 100 nm, respectively. The threshold field strength required to drive transport, the threading mobility, and the transport mobility were measured as a function of nanochannel size. As the nanochannel dimensions decreased, the entropic barrier to translocation increased and transport became more constrained. Equilibrium models of confinement provide a framework in which to understand the observed trends, although the dynamic nature of the experiments resulted in significant deviations from theory. It was also demonstrated that the use of dynamic wall coatings for the purpose of electroosmotic flow suppression can have a significant impact on transport dynamics that may obfuscate entropic contributions. The nonintermittent DNA transport through the FIB milled nanochannels demonstrates that they are well suited for use in nanofluidic devices. We expect that an understanding of the dynamic transport properties reported here will facilitate the incorporation of FIB-milled nanochannels in devices for single molecule and ensemble analyses.
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Affiliation(s)
- Laurent D Menard
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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141
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Werner E, Persson F, Westerlund F, Tegenfeldt JO, Mehlig B. Orientational correlations in confined DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:041802. [PMID: 23214605 DOI: 10.1103/physreve.86.041802] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Indexed: 05/14/2023]
Abstract
We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where the Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.
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Affiliation(s)
- E Werner
- Department of Physics, University of Gothenburg, Sweden
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142
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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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143
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Chang R, Jo K. DNA conformation in nanochannels: Monte Carlo simulation studies using a primitive DNA model. J Chem Phys 2012; 136:095101. [PMID: 22401472 DOI: 10.1063/1.3682984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We have performed canonical ensemble Monte Carlo simulations of a primitive DNA model to study the conformation of 2.56 ~ 21.8 μm long DNA molecules confined in nanochannels at various ionic concentrations with the comparison of our previous experimental findings. In the model, the DNA molecule is represented as a chain of charged hard spheres connected by fixed bond length and the nanochannels as planar hard walls. System potentials consist of explicit electrostatic potential along with short-ranged hard-sphere and angle potentials. Our primitive model system provides valuable insight into the DNA conformation, which cannot be easily obtained from experiments or theories. First, the visualization and statistical analysis of DNA molecules in various channel dimensions and ionic strengths verified the formation of locally coiled structures such as backfolding or hairpin and their significance even in highly stretched states. Although the folding events mostly occur within the region of ~0.5 μm from both chain ends, significant portion of the events still take place in the middle region. Second, our study also showed that two controlling factors such as channel dimension and ionic strength widely used in stretching DNA molecules have different influence on the local DNA structure. Ionic strength changes local correlation between neighboring monomers by controlling the strength of electrostatic interaction (and thus the persistence length of DNA), which leads to more coiled local conformation. On the other hand, channel dimension controls the overall stretch by applying the geometric constraint to the non-local DNA conformation instead of directly affecting local correlation. Third, the molecular weight dependence of DNA stretch was observed especially in low stretch regime, which is mainly due to the fact that low stretch modes observed in short DNA molecules are not readily accessible to much longer DNA molecules, resulting in the increase in the stretch of longer DNA molecules.
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Affiliation(s)
- Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 139-701, South Korea.
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144
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Dai L, Ng SY, Doyle PS, van der Maarel JRC. Conformation Model of Back-Folding and Looping of a Single DNA Molecule Confined Inside a Nanochannel. ACS Macro Lett 2012; 1:1046-1050. [PMID: 35607035 DOI: 10.1021/mz300323a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Currently, no theory is available to describe the conformation of DNA confined in a channel when the nanochannel diameter is around the persistence length. Back-folded hairpins in the undulating wormlike chain conformation result in the formation of loops, which reduces the stretch of the molecule in the longitudinal direction of the channel. A cooperativity model is used to quantify the frequency and size of the loop domains. The predictions agree with results from the Monte Carlo simulation.
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics, Singapore−MIT Alliance for Research and Technology, Singapore
| | - Siow Yee Ng
- Department of Physics, National University of Singapore, Singapore 117542
| | - Patrick S. Doyle
- BioSystems and Micromechanics, Singapore−MIT Alliance for Research and Technology, Singapore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Johan R. C. van der Maarel
- BioSystems and Micromechanics, Singapore−MIT Alliance for Research and Technology, Singapore
- Department of Physics, National University of Singapore, Singapore 117542
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145
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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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146
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Tree DR, Wang Y, Dorfman KD. Mobility of a semiflexible chain confined in a nanochannel. PHYSICAL REVIEW LETTERS 2012; 108:228105. [PMID: 23003659 PMCID: PMC3503239 DOI: 10.1103/physrevlett.108.228105] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Indexed: 05/14/2023]
Abstract
The classic results of de Gennes and Odijk describe the mobility of a semiflexible chain confined in a nanochannel only in the limits of very weak and very strong confinement, respectively. Using Monte Carlo sampling of the Kirkwood diffusivity with full hydrodynamic interactions, we show that the mobility of a semiflexible chain exhibits a broad plateau as a function of extension before transitioning to an Odijk regime, and that the width of the plateau depends on the anisotropy of the monomers. For the particular case of DNA in a high ionic strength buffer, which has highly anisotropic monomers, we predict that this Rouse-like behavior will be observed over most of the measurable chain extensions seen in experiments.
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Affiliation(s)
- Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455
| | - Yanwei Wang
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren-ai Road, Suzhou, 215123, P.R. China
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455
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147
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Jung Y, Kim J, Jun S, Ha BY. Intrachain Ordering and Segregation of Polymers under Confinement. Macromolecules 2012. [DOI: 10.1021/ma2025732] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Youngkyun Jung
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon
305-806, Korea
| | - Juin Kim
- Department
of Physics, Korea Advanced Institute of Science and Technology,
Daejeon 305-701, Korea
| | - Suckjoon Jun
- FAS
Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138,
United States
| | - Bae-Yeun Ha
- Department
of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada N2L
3G1
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148
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Wang Y, Reinhart WF, Tree DR, Dorfman KD. Resolution limit for DNA barcodes in the Odijk regime. BIOMICROFLUIDICS 2012; 6:14101-141019. [PMID: 22299023 PMCID: PMC3269310 DOI: 10.1063/1.3672691] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 12/06/2011] [Indexed: 05/21/2023]
Abstract
We develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective width). The theoretical predictions agree well with equivalent data produced by Monte Carlo simulations of a touching wormlike bead model of DNA in a high ionic strength buffer. Although the theory is only strictly valid in the limit where the effective width of the nanochannel is small compared with the persistence length of the DNA, simulations indicate that the theoretical predictions are reasonably accurate for channel widths up to two-thirds of the persistence length. Our results quantify the conjecture that DNA barcoding has kilobase pair resolution-provided the nanochannel lies in the Odijk regime.
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149
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Benková Z, Cifra P. Simulation of Semiflexible Cyclic and Linear Chains Moderately and Strongly Confined in Nanochannels. Macromolecules 2012. [DOI: 10.1021/ma202730c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská
cesta 9, 845 41 Bratislava, Slovakia
- REQUIMTE, Chemistry Department, University of Porto, Rua do Campo Alegre 687, 4169-007
Porto, Portugal
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská
cesta 9, 845 41 Bratislava, Slovakia
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150
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Nöding B, Köster S. Intermediate filaments in small configuration spaces. PHYSICAL REVIEW LETTERS 2012; 108:088101. [PMID: 22463576 DOI: 10.1103/physrevlett.108.088101] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Indexed: 05/17/2023]
Abstract
Intermediate filaments play a key role in cell mechanics. Apart from their great importance from a biomedical point of view, they also act as a very suitable micrometer-sized model system for semiflexible polymers. We perform a statistical analysis of the thermal fluctuations of individual filaments confined in microchannels. The small channel width and the resulting deflections at the walls give rise to a reduction of the configuration space by about 2 orders of magnitude. This circumstance enables us to precisely measure the intrinsic persistence length of vimentin intermediate filaments and to show that they behave as ideal wormlike chains; we observe that small fluctuations in perpendicular planes decouple. Furthermore, the inclusion of results for confined actin filaments demonstrates that the Odijk confinement regime is valid over at least 1 order of magnitude in persistence length.
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Affiliation(s)
- Bernd Nöding
- Institute for X-Ray Physics and Courant Research Centre Nano-Spectroscopy and X-Ray Imaging, Georg-August-Universität Göttingen, Göttingen, Germany
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