Confined dynamics of a single DNA molecule

Chinappi, Mauro; Angelis, E. De

doi:10.1098/rsta.2011.0096

Cited by 6 publications

(4 citation statements)

References 22 publications

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“…However, it may be possible to make progress using mesoscopic, explicit fluid algorithms for confined systems, such as Dissipative Particle Dynamics (DPD) [116–118] or Multi-Particle Collision Dynamics (MPCD) [119]. Both methods have been used for modeling confined polymers [56,120–122]. …”

Section: Discussionmentioning

confidence: 99%

Hydrodynamics of DNA confined in nanoslits and nanochannels

Dorfman

Gupta

Jain

et al. 2014

Eur. Phys. J. Spec. Top.

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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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Section: Discussionmentioning

confidence: 99%

Hydrodynamics of DNA confined in nanoslits and nanochannels

Dorfman

Gupta

Jain

et al. 2014

Eur. Phys. J. Spec. Top.

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“…Recent coarse-grained simulations studies have found good agreement with the predictions for blob-to-deflection transition and the scaling law dependences in nanochannels. , MC studies have examined the conformation and the free energy of DNA in strong confinement. ,,, In Q1D nanochannels, a transition in the chain relaxation dynamics is also found in experiments and coarse-grained simulations of DNA. ,, In Q2D nanoslits, it is less clear whether a qualitative change of chain properties occurs, as slit confinement does not inhibit long wavelength collective chain motion. Prior simulation studies have probed the chain property dependences for slit heights larger than the Kuhn length, ,− but the coarse-grained flexible polymer model for DNA prevented investigations in the H < P regime. To better understand the conformation and dynamics of confined DNA molecules in nanoslits, coarse-grained dynamics simulations are performed to study how R ∥ and t relax depend on H in nanoslits.…”

Section: Introductionmentioning

confidence: 99%

Dynamics and Conformation of Semiflexible Polymers in Strong Quasi-1D and -2D Confinement

et al. 2014

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We investigate the conformation and relaxation dynamics of single DNA molecules in strong confinement (smaller than persistence length) with coarse-grained semiflexible chain (SFC) models using overdamped Langevin dynamics simulations. DNA properties in nanochannels and nanoslits are studied in confinement with height (H) ranging from the DNA radius of gyration (R g) to smaller than the persistence length (P). Qualitatively different dependences of chain conformation and relaxation time on H in moderate (P < H < R g) and strong (H < P) confinement are observed for very stiff SFC in the nanochannel but not in the nanoslit. The chain relaxation time (t relax) exhibits strong power-law dependence in H < P nanochannels, verified with and without including hydrodynamic interactions (HI). The inclusion of hydrodynamic interactions affects chain relaxation dynamics even in strong confinement, indicating the intersegmental hydrodynamic interactions affect dominant segmental relaxation mechanisms of strongly confined polymers.

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“…Connement affects also the chain dynamic properties as chain relaxation slows down with connement. 28,31 Aware of this effect, we performed extensive simulations to attain the equilibrium properties. One of the indications of reaching equilibrium is shown in the master plot in Fig.…”

Section: Excluded Volume Regimementioning

confidence: 99%

“…[1][2][3][4][5][6][7][8] They present an efficient, nondestructive, and simple way of DNA manipulation and characterization when determining structural details in nano-and microuidic experiments. 9,10 In order to understand the structural and dynamic properties of a single chain conned in a channel and slit a great deal of theoretical, [11][12][13][14] experimental, 1,2,8,10,15 and simulation [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33] studies have been published. The studies have shown that the chain relaxation slows down upon increasing the connement.…”

Section: Introductionmentioning

confidence: 99%

Stripe to slab confinement for the linearization of macromolecules in nanochannels

2015

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We investigated the recently suggested advantageous analysis of chain linearization experiments with macromolecules confined in a stripe-like channel (Huang and Battacharya, EPL, 2014, 106, 18004) using Monte Carlo simulations. The enhanced chain extension in a stripe, which is due to the significant excluded volume interactions between the monomers in two dimensions, weakens considerably on transition to an experimentally feasible slit-like channel. Based on the chain extension-confinement strength dependence and the structure factor behavior for a chain in a stripe, we infer the excluded volume regime (de Gennes regime) typical for two-dimensional systems. On widening of the stripe in a direction perpendicular to the stripe plane, i.e. on the transition to the slab geometry, the advantageous chain extension decreases and a Gaussian regime is observed for not very long semiflexible chains. The evidence for pseudo-ideality in confined chains is based on four indicators: the extension curves, variation of the extension with the persistence length P, estimated limits for the regimes in the investigated systems, and the structure factor behavior. The slab behavior can be observed when the two-dimensional stripe (originally of a one-monomer thickness) reaches a reduced thickness D larger than approximately D/P ≈ 0.2 in the third dimension. This maximum height of a slab at which the advantage of a stripe is retained is very low and has implications for DNA linearization experiments.

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Confined dynamics of a single DNA molecule

Cited by 6 publications

References 22 publications

Hydrodynamics of DNA confined in nanoslits and nanochannels

Hydrodynamics of DNA confined in nanoslits and nanochannels

Dynamics and Conformation of Semiflexible Polymers in Strong Quasi-1D and -2D Confinement

Stripe to slab confinement for the linearization of macromolecules in nanochannels

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