Reducing the variance in the translocation times by prestretching the polymer

We investigate the dynamics of driving a polyelectrolyte such as DNA through a nanopore and into a cross-linked gel. Placing the gel on the trans-side of the nanopore can increase the translocation time while not negatively affecting the capture rates. Thus, this setup combines the mechanics of gel electrophoresis with nanopore translocation. However, contrary to typical gel electrophoresis scenarios, the effect of the field is localized in the immediate vicinity of the nanopore and becomes negligible inside the gel matrix. Thus, we investigate the process by which a semiflexible polymer can be pushed into a gel matrix via a localized field and we describe how the dynamics of gel penetration depends upon the field intensity, polymer stiffness, and gel pore size. Our simulation results show that a semiflexible polymer enters the gel region with two distinct mechanisms depending upon the ratio between the bending length scale and the gel pore size. In both regimes, the gel fibers cause a net increase in the mean translocation time. Interestingly, the translocation rate is found to be constant (a potentially useful feature for many applications) during the predominant part of the translocation process when the polymer is stiff over a length scale comparable to the gel pore size.

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“…Similar to other coarse‐grained translocation simulations, we used LD to integrate a generic bead spring polymer model of

N = 100

beads with excluded volume interactions . The Weeks–Chandler–Andersen (WCA) potential is used to model excluded volume interactions .…”

Section: Methodsmentioning

confidence: 99%

Langevin dynamcis simulations of driven polymer translocation into a cross‐linked gel

Sibrac

Slater

2017

Electrophoresis

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“…Previous studies have shown that polymers stretched prior to translocation display reduced conformational entropy (and σ/τ values) due to their more elongated conformations [67,72,73].…”

Section: Modulation Of Translocation Time Statisticsmentioning

confidence: 99%

Elucidating the Dynamics of Polymer Transport through Nanopores using Asymmetric Salt Concentrations

Charron

Philipp

et al. 2022

Preprint

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While notable progress has been made in recent years both experimentally and theoretically in understanding the highly complex dynamics of polymer capture and transport through nanopores, there remains significant disagreement between experimental observation and theoretical prediction that needs to be resolved. Asymmetric salt concentrations, where the concentrations of ions on each side of the membrane are different, can be used to enhance capture rates and prolong translocation times of electrophoretically driven polymers translocating through a nanopore from the low salt concentration reservoir, which are both attractive features for single-molecule analysis. However, since asymmetric salt concentrations affect the electrophoretic pull inside and outside the pore differently, it also offers a useful control parameter to elucidate the otherwise inseparable physics of the capture and translocation process. In this work, we attempt to paint a complete picture of the dynamics of polymer capture and translocation in both symmetric and asymmetric salt concentration conditions by reporting the dependence of multiple translocation metrics on voltage, polymer length, and salt concentration gradient. Using asymmetric salt concentration conditions, we experimentally observe the predictions of tension propagation theory, and infer the significant impact of the electric field outside the pore in capturing polymers and in altering polymer conformations prior to translocation.

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“…Previous studies have shown that polymers stretched prior to translocation display reduced conformational entropy (and σ/τ values) due to their more elongated conformations. 57,63,64 Interpreting σ/τ values as being inversely correlated with the average conformation elongation, Figure 5c should therefore show a non-monotonic relationship between elongation and salt concentration ratio Ctrans/Ccis: For a fixed Ccis and varying Ctrans, capture-opposing ASC conditions (Ctrans/Ccis < 1) result in less elongated polymer conformations than SSC conditions (Ctrans/Ccis = 1), which in turn result in more elongated conformations than capture-promoting ASC conditions (Ctrans/Ccis > 1), with the maximal elongation occurring near Ctrans/Ccis = 1 (see Figure 5d). To further validate the increase of σ/τ in capture-promoting ASC conditions and support the proposed elongation interpretation, the dependence of σ and σ/τ on polymer length is shown in Figure S9.…”

Section: Modulation Of Translocation Time Statisticsmentioning

confidence: 99%

Elucidating the Dynamics of Polymer Transport through Nanopores using Asymmetric Salt Concentrations

Charron

Philipp

et al. 2021

Preprint

View full text Add to dashboard Cite

While notable progress has been made in recent years both experimentally and theoretically in understanding the highly complex dynamics of polymer capture and transport through nanopores, there remains significant disagreement between experimental observation and theoretical prediction that needs to be resolved. Asymmetric salt concentrations, where the concentrations of ions on each side of the membrane are different, can be used to enhance capture rates and prolong translocation times of polymers translocating through a nanopore from the low salt concentration reservoir, which are both attractive features for single-molecule analysis. However, since asymmetric salt concentrations affect the electrophoretic pull inside and outside the pore differently, it also offers a useful control parameter to elucidate the otherwise inseparable physics of the capture and translocation process. In this work, we attempt to paint a complete picture of the dynamics of polymer capture and translocation in both symmetric and asymmetric salt concentration conditions by reporting the dependence of multiple translocation metrics on voltage, polymer length, and salt concentration gradient. Using asymmetric salt concentration conditions, we experimentally observe the predictions of tension propagation theory and verify the significant impact of the electric field gradient on pre-stretching polymers on approach to the pore.

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Reducing the variance in the translocation times by prestretching the polymer

Cited by 11 publications

References 50 publications

Langevin dynamcis simulations of driven polymer translocation into a cross‐linked gel

Langevin dynamcis simulations of driven polymer translocation into a cross‐linked gel

Elucidating the Dynamics of Polymer Transport through Nanopores using Asymmetric Salt Concentrations

Elucidating the Dynamics of Polymer Transport through Nanopores using Asymmetric Salt Concentrations

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