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Gas Biosensor Arrays Based on Single-Stranded DNA-Functionalized Single-Walled Carbon Nanotubes for the Detection of Volatile Organic Compound Biomarkers Released by Huanglongbing Disease-Infected Citrus Trees. SENSORS 2019; 19:s19214795. [PMID: 31689974 PMCID: PMC6865013 DOI: 10.3390/s19214795] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 02/02/2023]
Abstract
Volatile organic compounds (VOCs) released by plants are closely associated with plant metabolism and can serve as biomarkers for disease diagnosis. Huanglongbing (HLB), also known as citrus greening or yellow shoot disease, is a lethal threat to the multi-billion-dollar citrus industry. Early detection of HLB is vital for removal of susceptible citrus trees and containment of the disease. Gas sensors are applied to monitor the air quality or toxic gases owing to their low-cost fabrication, smooth operation, and possible miniaturization. Here, we report on the development, characterization, and application of electrical biosensor arrays based on single-walled carbon nanotubes (SWNTs) decorated with single-stranded DNA (ssDNA) for the detection of four VOCs-ethylhexanol, linalool, tetradecene, and phenylacetaldehyde-that serve as secondary biomarkers for detection of infected citrus trees during the asymptomatic stage. SWNTs were noncovalently functionalized with ssDNA using π-π interaction between the nucleotide and sidewall of SWNTs. The resulting ssDNA-SWNT hybrid structure and device properties were investigated using Raman spectroscopy, ultraviolet (UV) spectroscopy, and electrical measurements. To monitor changes in the four VOCs, gas biosensor arrays consisting of bare SWNTs before and after being decorated with different ssDNA were employed to determine the different concentrations of the four VOCs. The data was processed using principal component analysis (PCA) and neural net fitting (NNF).
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Hartmann J, Roy T, Szuttor K, Smiatek J, Holm C, Hardt S. Relaxation of surface-tethered polymers under moderate confinement. SOFT MATTER 2018; 14:7926-7933. [PMID: 30238941 DOI: 10.1039/c8sm01246f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We study the relaxation of surface-tethered polymers in microchannels under moderate confinement (i.e. h ∼ Rg, where h is the channel height and Rg is the radius of gyration of the polymer) by experiments with fluorescence-marked DNA molecules and coupled lattice-Boltzmann/molecular dynamics simulations. The determined scaling exponent suggests that the relaxation is dominated by Zimm-dynamics with significant intra-chain hydrodynamic interactions. The relaxation of the DNA molecules is slower in shallower channels, indicating a pronounced effect of confinement on the longest relaxation time. An experimental correlation is obtained for the longest relaxation time as a function of the molecular contour length and the channel height. Good agreement between the experimental and the simulation results is found.
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Affiliation(s)
- Johannes Hartmann
- Institute for Nano- and Microfluidics, Technische Universität Darmstadt, Darmstadt, Germany.
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Huang A, Hsu HP, Bhattacharya A, Binder K. Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles. J Chem Phys 2016; 143:243102. [PMID: 26723587 DOI: 10.1063/1.4929600] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to self-avoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasi-one-dimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the Kratky-Porod model in the case of the bead-spring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓp is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes "string of blobs"-picture to the flexible rod picture when D decreases and/or the chain stiffness increases. Introducing a suitable further coarse-graining of the chain contours of the continuum model, direct estimates for the deflection length and its distribution could be obtained.
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Affiliation(s)
- Aiqun Huang
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Hsiao-Ping Hsu
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, D-55099 Mainz, Germany
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Kurt Binder
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, D-55099 Mainz, Germany
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Zinchenko A. DNA conformational behavior and compaction in biomimetic systems: Toward better understanding of DNA packaging in cell. Adv Colloid Interface Sci 2016; 232:70-79. [PMID: 26976700 DOI: 10.1016/j.cis.2016.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/05/2016] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
Abstract
In a living cell, long genomic DNA is strongly compacted and exists in the environment characterized by a dense macromolecular crowding, high concentrations of mono- and divalent cations, and confinement of ca. 10μm size surrounded by a phospholipid membrane. Experimental modelling of such complex biological system is challenging but important to understand spatiotemporal dynamics and functions of the DNA in cell. The accumulated knowledge about DNA condensation/compaction in conditions resembling those in the real cell can be eventually used to design and construct partly functional "artificial cells" having potential applications in drug delivery systems, gene therapy, and production of synthetic cells. In this review, I would like to overview the past progress in our understanding of the DNA conformational behavior and, in particular, DNA condensation/compaction phenomenon and its relation to the DNA biological activity. This understanding was gained by designing relevant experimental models mimicking DNA behavior in the environment of living cell. Starting with a brief summary of classic experimental systems to study DNA condensation/compaction, in later parts, I highlight recent experimental methodologies to address the effects of macromolecular crowding and nanoscale and microscale confinements on DNA conformation dynamics. All the studies are discussed in the light of their relevance to DNA behavior in living cells, and future prospects of the field are outlined.
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Dorfman KD, Gupta D, Jain A, Muralidhar A, Tree DR. Hydrodynamics of DNA confined in nanoslits and nanochannels. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2014; 223:3179-3200. [PMID: 25566349 PMCID: PMC4282777 DOI: 10.1140/epjst/e2014-02326-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Modeling the dynamics of a confined, semi exible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and "read" a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirk-wood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach.
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Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Aashish Jain
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
- Materials Research Laboratory, University of California – Santa Barbara, Santa Barbara, CA 93106 USA
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Nikoofard N, Hoseinpoor SM, Zahedifar M. Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:062603. [PMID: 25615122 DOI: 10.1103/physreve.90.062603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Indexed: 06/04/2023]
Abstract
The de Gennes' blob model is extensively used in different problems of polymer physics. This model is theoretically applicable when the number of monomers inside each blob is large enough. For confined flexible polymers, this requires the confining geometry to be much larger than the monomer size. In this paper, the opposite limit of polymer in nanoslits with one to several monomers width is studied, using molecular dynamics simulations. Extension of the polymer inside nanoslits, confinement force on the plates, and the effective spring constant of the confined polymer are investigated. Despite the theoretical limitations of the blob model, the simulation results are explained with the blob model very well. The agreement is observed for the static properties and the dynamic spring constant of the polymer. A theoretical description of the conditions under which the dynamic spring constant of the polymer is independent of the small number of monomers inside blobs is given. Our results on the limit of applicability of the blob model can be useful in the design of nanotechnology devices.
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Affiliation(s)
- Narges Nikoofard
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 51167-87317, Iran
| | - S Mohammad Hoseinpoor
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 51167-87317, Iran
| | - Mostafa Zahedifar
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 51167-87317, Iran
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Berard D, McFaul CMJ, Leith JS, Arsenault AKJ, Michaud F, Leslie SR. Precision platform for convex lens-induced confinement microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:103704. [PMID: 24182116 DOI: 10.1063/1.4822276] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We present the conception, fabrication, and demonstration of a versatile, computer-controlled microscopy device which transforms a standard inverted fluorescence microscope into a precision single-molecule imaging station. The device uses the principle of convex lens-induced confinement [S. R. Leslie, A. P. Fields, and A. E. Cohen, Anal. Chem. 82, 6224 (2010)], which employs a tunable imaging chamber to enhance background rejection and extend diffusion-limited observation periods. Using nanopositioning stages, this device achieves repeatable and dynamic control over the geometry of the sample chamber on scales as small as the size of individual molecules, enabling regulation of their configurations and dynamics. Using microfluidics, this device enables serial insertion as well as sample recovery, facilitating temporally controlled, high-throughput measurements of multiple reagents. We report on the simulation and experimental characterization of this tunable chamber geometry, and its influence upon the diffusion and conformations of DNA molecules over extended observation periods. This new microscopy platform has the potential to capture, probe, and influence the configurations of single molecules, with dramatically improved imaging conditions in comparison to existing technologies. These capabilities are of immediate interest to a wide range of research and industry sectors in biotechnology, biophysics, materials, and chemistry.
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Affiliation(s)
- Daniel Berard
- Department of Physics, McGill University, Montreal H3A 2T8, Canada
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Hsu HP, Binder K. Semiflexible Macromolecules with Discrete Bond Angles Confined in Nanoslits: A Monte Carlo Test of Scaling Concepts. Macromolecules 2013. [DOI: 10.1021/ma401374e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hsiao-Ping Hsu
- Institut
für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg
7, D-55099 Mainz, Germany
| | - Kurt Binder
- Institut
für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg
7, D-55099 Mainz, Germany
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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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10
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Fu CL, Sun ZY, An LJ. The properties of a single polymer chain in solvent confined in a slit: A molecular dynamics simulation. CHINESE JOURNAL OF POLYMER SCIENCE 2012. [DOI: 10.1007/s10118-013-1231-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Chaudhuri D, Mulder BM. Spontaneous helicity of a polymer with side loops confined to a cylinder. PHYSICAL REVIEW LETTERS 2012; 108:268305. [PMID: 23005022 DOI: 10.1103/physrevlett.108.268305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 05/03/2012] [Indexed: 06/01/2023]
Abstract
Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of "bottle-brush" polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model with an open linear backbone spontaneously adopts a helical structure with a well-defined pitch when confined to small cylindrical volume. This helicity persists over a range of sizes and aspect ratios of the cylinder, provided the packing fraction of the chain is suitably large. We analyze these results in terms of the interplay between the effective stiffness and actual intrachain packing effects caused by the side loops in response to the confinement.
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Affiliation(s)
- Debasish Chaudhuri
- FOM Institute AMOLF, Science Park 104, 1098XG Amsterdam, The Netherlands.
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12
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Strychalski EA, Geist J, Gaitan M, Locascio LE, Stavis SM. Quantitative Measurements of the Size Scaling of Linear and Circular DNA in Nanofluidic Slitlike Confinement. Macromolecules 2012. [DOI: 10.1021/ma202559k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elizabeth A. Strychalski
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg,
Maryland 20899-1000, United States
| | - Jon Geist
- Semiconductor and Dimensional Metrology Division, National Institute of Standards and Technology, Gaithersburg,
Maryland 20899-1000, United States
| | - Michael Gaitan
- Semiconductor and Dimensional Metrology Division, National Institute of Standards and Technology, Gaithersburg,
Maryland 20899-1000, United States
| | - Laurie E. Locascio
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg,
Maryland 20899-1000, United States
| | - Samuel M. Stavis
- Semiconductor and Dimensional Metrology Division, National Institute of Standards and Technology, Gaithersburg,
Maryland 20899-1000, United States
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Dobrindt J, Rodrigo Teixeira da Silva E, Alves C, Oliveira CLP, Nallet F, Andreoli de Oliveira E, Navailles L. Anisotropic Brownian motion in ordered phases of DNA fragments. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2012; 35:3. [PMID: 22270455 DOI: 10.1140/epje/i2012-12003-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 12/20/2011] [Indexed: 05/31/2023]
Abstract
Using Fluorescence Recovery After Photobleaching, we investigate the Brownian motion of DNA rod-like fragments in two distinct anisotropic phases with a local nematic symmetry. The height of the measurement volume ensures the averaging of the anisotropy of the in-plane diffusive motion parallel or perpendicular to the local nematic director in aligned domains. Still, as shown in using a model specifically designed to handle such a situation and predicting a non-Gaussian shape for the bleached spot as fluorescence recovery proceeds, the two distinct diffusion coefficients of the DNA particles can be retrieved from data analysis. In the first system investigated (a ternary DNA-lipid lamellar complex), the magnitude and anisotropy of the diffusion coefficient of the DNA fragments confined by the lipid bilayers are obtained for the first time. In the second, binary DNA-solvent system, the magnitude of the diffusion coefficient is found to decrease markedly as DNA concentration is increased from isotropic to cholesteric phase. In addition, the diffusion coefficient anisotropy measured within cholesteric domains in the phase coexistence region increases with concentration, and eventually reaches a high value in the cholesteric phase.
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Affiliation(s)
- J Dobrindt
- Université de Bordeaux, Centre de recherche Paul-Pascal - CNRS, 115 avenue du Docteur-Schweitzer, F-33600, Pessac, France
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Jones JJ, van der Maarel JRC, Doyle PS. Effect of nanochannel geometry on DNA structure in the presence of macromolecular crowding agent. NANO LETTERS 2011; 11:5047-53. [PMID: 21988280 DOI: 10.1021/nl203114f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We experimentally and numerically study the effects of macromolecular crowding agents on DNA structure when confined to a nanochannel. Curiously, DNA response to crowding is significantly different between bulk phase, nanoslit confinement, and nanotube confinement. Coarse grained Brownian dynamics simulations reproduce trends seen in the experiments and allow us to develop a deeper understanding of the key physics at play in these systems. It is proposed that the occupancy of free volume next to the channel wall by crowders causes an effective reduction in confining dimensions of the channel that initially swells DNA in nanoconfinement.
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Affiliation(s)
- Jeremy J Jones
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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15
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Negishi M, Ichikawa M, Nakajima M, Kojima M, Fukuda T, Yoshikawa K. Phase behavior of crowded like-charged mixed polyelectrolytes in a cell-sized sphere. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:061921. [PMID: 21797417 DOI: 10.1103/physreve.83.061921] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Indexed: 05/23/2023]
Abstract
We studied the phase behavior of a mixture of two semiflexible negatively charged polyelectrolytes, giant DNA and alginate, under crowded condition in a cell-sized sphere (5-40 μm in diameter), where the persistence length of giant DNA is 50 nm and that of alginate is 5 nm. Through microscopic observation, we found that the polymer mixture exhibits a unique phase behavior, which depends on the size of the sphere, whereas the mixture remains homogeneous and isotropic in bulk solution. When the sphere is small, DNA is completely depleted on the surface. When the sphere is medium sized, a portion of the DNA is depleted on the surface, and the remainder stays within the sphere. By introducing a curvature-dependent term for the interaction between DNA and the surface into the Flory-Huggins model, we interpret the observed characteristics of the phase behavior in terms of the relative importance of the surface-to-volume effect.
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Affiliation(s)
- Makiko Negishi
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto, Japan
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16
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Chaudhuri D, Mulder B. Size and shape of excluded volume polymers confined between parallel plates. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:031803. [PMID: 21517518 DOI: 10.1103/physreve.83.031803] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Revised: 11/01/2010] [Indexed: 05/30/2023]
Abstract
A number of recent experiments have provided detailed observations of the configurations of long DNA strands under nano-to-micrometer-sized confinement. We therefore revisit the problem of an excluded volume polymer chain confined between two parallel plates with varying plate separation. We show that the nonmonotonic behavior of the overall size of the chain as a function of plate separation, seen in computer simulations and reproduced by earlier theories, can already be predicted on the basis of scaling arguments. However, the behavior of the size in a plane parallel to the plates, a quantity observed in recent experiments, is predicted to be monotonic, in contrast to the experimental findings. We analyze this problem in depth with a mean-field approach that maps the confined polymer onto an anisotropic Gaussian chain, which allows the size of the polymer to be determined separately in the confined and unconfined directions. The theory allows the analytical construction of a smooth crossover between the small-plate-separation de Gennes regime and the large-plate-separation Flory regime. The results show good agreement with molecular dynamics simulations in the presence of a Langevin heat bath and confirm the scaling predictions.
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Affiliation(s)
- Debasish Chaudhuri
- FOM Institute AMOLF, Science Park 104, NL-1098XG Amsterdam, The Netherlands.
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17
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Tang J, Levy SL, Trahan DW, Jones JJ, Craighead HG, Doyle PS. Revisiting the Conformation and Dynamics of DNA in Slitlike Confinement. Macromolecules 2010. [DOI: 10.1021/ma101157x] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Tang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Stephen L. Levy
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853
| | - Daniel W. Trahan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jeremy J. Jones
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Harold G. Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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