Dynamic Compression of Single Nanochannel Confined DNA via a Nanodozer Assay

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Dynamic Compression of Single Nanochannel Confined DNA via a Nanodozer Assay

Ahmed Khorshid, Philip Zimny, David Tétreault-La Roche, Geremia Massarelli, Takahiro Sakaue, and Walter Reisner

Phys. Rev. Lett. 113, 268104 – Published 30 December 2014

Abstract

We show that a single DNA molecule confined and extended in a nanochannel can be dynamically compressed by sliding a permeable gasket at a fixed velocity relative to the stationary polymer. The gasket is realized experimentally by optically trapping a nanosphere inside a nanochannel. The trapped bead acts like a “nanodozer,” directly applying compressive forces to the molecule without requirement of chemical attachment. Remarkably, these strongly nonequilibrium measurements can be quantified via a simple nonlinear convective-diffusion formalism and yield insights into the local blob statistics, allowing us to conclude that the compressed nanochannel-confined chain exhibits mean-field behavior.

Received 13 August 2014

DOI:https://doi.org/10.1103/PhysRevLett.113.268104

Authors & Affiliations

Ahmed Khorshid¹, Philip Zimny¹, David Tétreault-La Roche¹, Geremia Massarelli¹, Takahiro Sakaue^2,*, and Walter Reisner^1,†

¹Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
²Department of Physics, Kyushu University 33, Fukuoka 812-8581, Japan

^*Corresponding author. reisner@physics.mcgill.ca
^†Corresponding author. sakaue@phys.kyushu-u.ac.jp

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Vol. 113, Iss. 26 — 31 December 2014

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Images

Figure 1
(a) A 3D graphic of a bead gasket initiating compression of a nanochannel-confined polymer molecule. (b) The device geometry: an array of nanochannels spans the gap between two $U$ -shaped microchannels. The microchannels, used to load DNA and beads into the nanochannels, are coupled to four reservoirs that contain sandblasted loading ports. (c) An SEM of the $300 \times 310 nm$ nanochannels used in the study ( $2 μ m$ scale bar). (d)–(g) A graphical compression event, shown in the frame comoving with the bead.
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Figure 2
(a),(b) and (c),(d) and (e),(f) and (g),(h), respectively, show kymographs and corresponding steady-state ramp profiles with linear ramp fits for compression events with $V = 0.1 μ m / s$ [(a),(b)], $0.25 μ m / s$ [(c),(d)], $1 μ m / s$ [(e),(f)], and $10 μ m / s$ [(g),(h)]. The vertical scale bar is $10 μ m$ ; the horizontal bar gives a time scale of 2 s capturing compression events progressing from left to right. (a),(b) is a compression event at a very low $V$ where the molecule is slightly compressed and translocating close to its equilibrium state. Note that profiles (a),(b) and (c),(d) exist in regime II. The boxes on (e) snapshot (1) bead intensity, (2) transient dynamics, and (3) steady-state regime. The inset in (f) shows the intensity profile prior to bead subtraction.
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Figure 3
(a) The slope function $f_{slope}$ versus sliding speed with a linear least-squares fit. The best-fit slope $A_{slope} = 0.17 \pm 0.01 s / μ m^{2}$ . (b) Histogrammed values of the $χ^{2}$ ratio for fits to the experimental intensity profiles with $α = 1$ and $α = 4 / 3$ . The mean value of the $χ^{2}$ ratio is $0.74 \pm 0.03$ , strong evidence that $α = 1$ is correct. (c) The steady-state extension $r_{\min} / r_{0}$ as a function of sliding speed with a least-squares fit (the bold line) to the combined blob model prediction for regime II and III, yielding $β = 0.48 \pm 0.2$ and a self-consistently determined $V_{c} = 1.4 \pm 0.5 μ m / s$ . The prediction for $β = 4 / 7$ ( $ν = 3 / 5$ ) is shown for comparison (the dashed curve). (d) The steady-state edge intensity: the edge intensity is consistent with unity (the dashed line) for $V < V_{c}$ and then rises monotonically. A power-law fit (the bold line) to the high- $V$ points ( $V > 2 μ m / s$ ) yields $γ = 0.44 \pm 0.15$ .
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Figure 4
(a) A graphic and (b) a schematic of the steady-state concentration profile $c_{s} (x)$ for sliding speeds $V < V^{⋆}$ (regime I): in this regime the polymer translates with the bead. (c) A graphic and (d) a schematic of $c_{s} (x)$ for sliding speeds $V^{⋆} < V < V^{⋆ ⋆}$ (regime II): in this regime the polymer is partially compressed. (e) A graphic and (f) a schematic of $c_{s} (x)$ for $V > V^{⋆ ⋆}$ (regime III): in this regime the polymer is entirely compressed.
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