Entropic depletion of DNA in triangular nanochannels

Reinhart, Wesley F.; Tree, Douglas R.; Dorfman, Kevin D.

doi:10.1063/1.4794371

Cited by 25 publications

(26 citation statements)

References 27 publications

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“…This suggests that f should increase by roughly this factor as well, in contrast to the measured invariance of f with respect to r. Thus, this approach fails to account for the trends observed in the present case, in contrast with the case in Ref. 33. This may arise from the fact that we consider much larger P/D ratios in the present study that were used in Ref.…”

Section: Resultscontrasting

confidence: 81%

“…This is a somewhat surprising result for triangular channels, where the effects of entropic depletion near the corners have been shown previously to be appreciable relative to the case of rectangular channels. 31,33 As noted earlier, entropic depletion leads to a reduction in the effective cross-sectional area of the channel, which in turn should effectively increase the channel dimension D. Reinhart et al developed a measure of the effective area that uses the monomer probability distribution in the transverse plane of the channel. 33 They took the effective channel width to be the geometric average of the full width at half-maximum of the projections of the distributions onto the two axes defined by the eigenvectors of the 2D distribution.…”

Section: Resultsmentioning

confidence: 99%

“…31,33 As noted earlier, entropic depletion leads to a reduction in the effective cross-sectional area of the channel, which in turn should effectively increase the channel dimension D. Reinhart et al developed a measure of the effective area that uses the monomer probability distribution in the transverse plane of the channel. 33 They took the effective channel width to be the geometric average of the full width at half-maximum of the projections of the distributions onto the two axes defined by the eigenvectors of the 2D distribution. We have calculated the same quantity, which we call D eff , as a function of apex angle θ ap for channels of a given dimension D and for polymers of a given P .…”

Section: Resultsmentioning

confidence: 99%

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Free Energy of a Folded Semiflexible Polymer Confined to a Nanochannel of Various Geometries

Polson

2018

Macromolecules

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Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the polymer, and from these functions we extract the free energy of the hairpin fold, as well as the entropic force arising from interactions between the portions of the polymer that overlap along the channel. We consider the scaling of the free energies with respect to varying the persistence length of the polymer, as well as the channel dimensions for confinement in cylindrical, rectangular and triangular channels. We focus on polymer behaviour in both the classic Odijk and backfolded Odijk regimes. We find the scaling of the entropic force to be close to that predicted from a scaling argument that treats interactions between deflection segments at the second virial level. In addition, the measured hairpin fold free energy is consistent with that obtained directly from a recent theoretical calculation for cylindrical channels. It is also consistent with values determined from measurements of the global persistence length of a polymer in the backfolded Odijk regime in recent simulation studies.

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Section: Resultscontrasting

confidence: 81%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Free Energy of a Folded Semiflexible Polymer Confined to a Nanochannel of Various Geometries

Polson

2018

Macromolecules

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“…Such simulations for circular confinement are driven more by curiosity, since fabrication of transparent circular nanochannels suitable for fluorescence microscopy is challenging but possible [125]. In contrast, triangular channels are easily fabricated [123,124] and provide a stronger extension than a square channel for a given cross-sectional area [126,127]. Moreover, hydrodynamic interactions may play a crucial role for the strong stretching found in “normally closed” triangular nanochannels [124].…”

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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“…The probability density distributions in Figure C suggest that the DNA molecule has a lower probability to locate near the sharp corners of the triangular nanochannel, since it is energetically unfavorable for DNA to bend to fit into the corners. Compared with the equivalent square nanochannel, the triangular nanochannel is effectively more confining, due to the entropic depletion in the corners . The backfolding is suppressed in the triangular nanochannel and thus the DNA extension is enhanced.…”

Section: Resultsmentioning

confidence: 99%

Tunable Confinement for Bridging Single‐Cell Manipulation and Single‐Molecule DNA Linearization

Hou

Song

et al. 2018

Small

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DNA linearization by nanoconfinement has offered a new avenue toward large-scale genome mapping. The ability to smoothly interface the widely different length scales from cell manipulation to DNA linearization is critical to the development of single-cell genomic mapping or sequencing technologies. Conventional nanochannel technologies for DNA analysis suffer from complex fabrication procedures, DNA stacking at the nanochannel entrance, and inefficient solution exchange. In this work, a dynamic and tunable confinement strategy is developed to manipulate and linearize genomic-length DNA molecules from a single cell. By leveraging pneumatic microvalve control and elastomeric collapse, an array of nanochannels with confining dimension down to 20 nm and length up to sub-millimeter is created and can be dynamically tuned in size. The curved edges of the microvalve form gradual transitions from microscale to nanoscale confinement, smoothly facilitating DNA entry into the nanochannels. A unified micro/nanofluidic device that integrates single-cell trapping and lysis, DNA extraction, purification, labeling, and linearization is developed based on dynamically controllable nanochannels. Mbp-long DNA molecules are extracted directly from a single cell and in situ linearized in the nanochannels. The device provides a facile and promising platform to achieve the ultimate goal of single-cell, single-genome analysis.

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Entropic depletion of DNA in triangular nanochannels

Cited by 25 publications

References 27 publications

Free Energy of a Folded Semiflexible Polymer Confined to a Nanochannel of Various Geometries

Free Energy of a Folded Semiflexible Polymer Confined to a Nanochannel of Various Geometries

Hydrodynamics of DNA confined in nanoslits and nanochannels

Tunable Confinement for Bridging Single‐Cell Manipulation and Single‐Molecule DNA Linearization

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