Hydrodynamics of DNA confined in nanoslits and nanochannels

Dorfman, Kevin D.; Gupta, Damini; Jain, Aashish; Muralidhar, Abhiram; Tree, Douglas R.

doi:10.1140/epjst/e2014-02326-4

Cited by 28 publications

(25 citation statements)

References 123 publications

(217 reference statements)

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“…We adopt the Kirkwood preaveraging approximation 25,33,36 to estimate the effect of HI on the diffusivity of confined molecules. In this approximation, the center of mass mobility of a chain of N b beads is 39 …”

Section: Methodsmentioning

confidence: 99%

“…25 Often, bead-spring models have been used to simulate the dynamics of such polymers in confinement via Brownian Dynamics (BD) simulations, both with 7,26,27 and without hydrodynamic interactions (HI). 28 The coarse-grained nature of these models allows simulation of experimentally relevant molecular weights with a small number of beads for a sufficiently long time.…”

Section: Introductionmentioning

confidence: 99%

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Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Muralidhar

Dorfman

2015

Macromolecules

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We compute the axial diffusivity of asymptotically long semiflexible polymers confined in square channels. Our calculations employ the Kirkwood approximation of the mobility tensor by combining computational fluid dynamics (CFD) calculations of the hydrodynamic tensor in channel confinement with pruned-enriched Rosenbluth method (PERM) simulations of a discrete wormlike chain model. Three key results emerge from our study. First, for the classic de Gennes regime, we confirm that Brochard and de Gennes’ blob theory correctly predicts the scaling of the axial diffusivity, contrary to the conclusions of previous analyses. Second, for the extended de Gennes regime, we show that a modified blob theory, which has been used to incorporate the effect of local stiffness on DNA diffusion in nanoslits, explains the deviation from the prediction of classic blob theory for diffusion in nanochannels. Third, we provide a calculation similar to the modified blob theory to explain the relative insensitivity of the diffusivity to channel size for channels between the extended de Gennes regime and the Odijk regime, which is the most relevant regime for experiments and technological applications of DNA confinement in nanochannels. Our results are not only relevant to the dynamics of confined semiflexible polymers such as DNA, but also reveal interesting analogies between confinement in channels and slits.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Muralidhar

Dorfman

2015

Macromolecules

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“…We computed X ij following the approach by Jendrejack et al, 10 which is also described in detail elsewhere. 35,36 In the original implementation by Jendrejack et al, 10 the wall correction to HI was calculated using the finite-element method. We have used the finite-difference method instead.…”

Section: A Dna Modelmentioning

confidence: 99%

Evaluation of the Kirkwood approximation for the diffusivity of channel-confined DNA chains in the de Gennes regime

Jain

Dorfman

2015

Biomicrofluidics

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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. V C 2015 AIP Publishing LLC. [http://dx

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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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Hydrodynamics of DNA confined in nanoslits and nanochannels

Cited by 28 publications

References 123 publications

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Evaluation of the Kirkwood approximation for the diffusivity of channel-confined DNA chains in the de Gennes regime

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

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