Numerical Study of Linear and Circular Model DNA Chains Confined in a Slit: Metric and Topological Properties

Micheletti, Cristian; Orlandini, Enzo

doi:10.1021/ma202503k

Cited by 72 publications

(125 citation statements)

References 71 publications

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“…It should be mentioned, that in [49] the profiles of critical forces which are necessary to apply in order to overcome this entropically induced repulsion were obtained in the framework of a new numerical approach which was the implementation of the generalized atmospheric sampling (GAS) algorithm for lattice knots proposed by Rensburg and Rechnitzer in [50]. Recently advanced MC simulation techniques [51] have been used in order to study the effect of nanoslit confinement on topological properties of circular model DNA, which was modeled as a semiflexible polymer chain. They have shown that the knotting probability has strong slit width dependence.…”

Section: The European Physical Journal Special Topicsmentioning

confidence: 99%

Linear and ring polymers in confined geometries

Usatenko

Kuterba

Chamati

et al. 2017

Eur. Phys. J. Spec. Top.

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Abstract. A short overview of the theoretical and experimental works on the polymer-colloid mixtures is given. The behaviour of a dilute solution of linear and ring polymers in confined geometries like slit of two parallel walls or in the solution of mesoscopic colloidal particles of big size with different adsorbing or repelling properties in respect to polymers is discussed. Besides, we consider the massive field theory approach in fixed space dimensions d = 3 for the investigation of the interaction between long flexible polymers and mesoscopic colloidal particles of big size and for the calculation of the correspondent depletion interaction potentials and the depletion forces between confining walls. The presented results indicate the interesting and nontrivial behavior of linear and ring polymers in confined geometries and give possibility better to understand the complexity of physical effects arising from confinement and chain topology which plays a significant role in the shaping of individual chromosomes and in the process of their segregation, especially in the case of elongated bacterial cells. The possibility of using linear and ring polymers for production of new types of nano-and micro-electromechanical devices is analyzed.

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Section: The European Physical Journal Special Topicsmentioning

confidence: 99%

Linear and ring polymers in confined geometries

Usatenko

Kuterba

Chamati

et al. 2017

Eur. Phys. J. Spec. Top.

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“…Consequently, there have been many recent theoretical and experimental studies of this phenomenon. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] In particular, it has been possible for two decades to image individual fluorescently labeled dsDNA under conditions of nanoscale confinement in nanofluidic devices with slit-like geometries. In this way, the in-plane radius of gyration of dsDNA as a function of slit height has been recently measured.…”

mentioning

confidence: 99%

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

et al. 2015

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There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency.Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations.An understanding of the many factors influencing the size of dsDNA under nanoscale confinement is highly relevant to rationally designing measurement technologies for genomic sequencing and medical sensing and for accurately describing crowding effects on dsDNA organization in living systems. Consequently, there have been many recent theoretical and experimental studies of this phenomenon. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] In particular, it has been possible for two decades to image individual fluorescently labeled dsDNA under conditions of nanoscale confinement in nanofluidic devices with slit-like geometries. In this way, the in-plane radius of gyration of dsDNA as a function of slit height has been recently measured. Fig. 1 summarizes the results of these experimental measurements, which exhibit a puzzling scatter under nominally similar experimental conditions. Scaling arguments and continuum chain models have dominated the majority of the recent theoretical treatments of this problem, which generally ignore polymer-surface interactions and hav...

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“…Even DNA fragments shorter than b k can be simulated as single slender-bodies [57] [58]. Michelleti further modified this model by incorporating the bending energy between connecting rods to study linear and circular DNA chains in slit confinement structures [59].…”

Section: Other Polymer Modelsmentioning

confidence: 99%

Computational Studies of DNA Separations in Micro-Fabricated Devices: Review of General Approaches and Recent Applications

Monjezi¹,

Behdani²,

Palaniappan³

et al. 2017

ACES

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DNA separation techniques have drawn attention because of their uses in applications such as gene analysis and manipulation. There have been many studies utilizing micro-fabricated devices for faster and more efficient separations than traditional methods using gel electrophoresis. Although many experimental studies have presented various new devices and methods, computational studies have played a pivotal role in this development by identifying separation mechanisms and by finding optimal designs for efficient separation conditions. The simulation of DNA separation methods in micro-fabricated devices requires the correct capture of the dynamics and the structure of a single polymer molecule that is being affected by an applied flow field or an electric field in complex geometries. In this work, we summarize the polymer models (the bead-spring model, the bead-rod model, the slender-body model, and the touching-bead model) and the methods, focusing on Brownian dynamics simulation, used to calculate inhomogeneous fields taking into consideration complex boundaries (the finite element method, the boundary element method, the lattice-Boltzmann method, and the dissipative particle dynamics simulation). The worm-like chain model (adapted from the bead-spring model) combined with the finite element method has been most commonly used but other models have shown more efficient and accurate results. We also review the applications of these simulation approaches in various separation methods and devices: gel electrophoresis, post arrays, capillary electrophoresis, microchannel flows, entropic traps, nanopores, and rotational flows. As more complicated geometries are involved in new devices, more rigorous models (such as incorporating the hydrodynamic interactions of DNA with solid boundaries) that can correctly capture the dynamic behaviors of DNA in such devices are needed.

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Numerical Study of Linear and Circular Model DNA Chains Confined in a Slit: Metric and Topological Properties

Cited by 72 publications

References 71 publications

Linear and ring polymers in confined geometries

Linear and ring polymers in confined geometries

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

Computational Studies of DNA Separations in Micro-Fabricated Devices: Review of General Approaches and Recent Applications

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