DNA molecule dynamics in converging–diverging microchannels

Abstract

The conformation and dynamics of double-stranded DNA molecules in a pressure-driven flow-through sharp/gradual converging (contraction half)-diverging (expansion half) square microchannels with a contraction/expansion ratio of 4:1/1:4 were examined using fluorescently labelled lambda-phage DNA at 2.2< or =De< or =30.7 (De is Deborah number, a dimensionless number used in rheology to characterize how fluid a material is). Both the diffusion and stretching of individual DNA molecules and their local flow velocity were visualized, recorded and measured with using MPIV (microparticle image velocimetry) and CLSM (confocal laser-scanning microscopy). The onset of the coil-stretch transition in DNA molecules and their time-dependent velocity in the elongational flow were determined at the micro scale. Velocity distribution was measured via MPIV through orange fluorescent particles and carboylate-modified microspheres of 1 mum diameter. The channel geometry effect in terms of the channel contraction/expansion angle, the mass flow rate and the solution viscosity on the conformation and diffusion were also studied and discussed.

DNA stretching on the wall surfaces in curved microchannels with different radii

“…Comparisons were also made, as shown in Figure 7, with those related studies for the viscosities of 40 and 80 cP. The present data are consistently higher than those of previous studies [2,10] with regard to both the percentage of the stretched DNA molecules and their stretch ratio. In fact, about 10% of DNA molecule stretch can reach the ratio of 0.52, and about 7% of DNA molecules can reach 0.63.…”

DNA molecule stretching through thermo-electrophoresis and thermal convection in a heated converging-diverging microchannel

“…The size and dimensions of the heating foil were chosen and designed so that the temperature distribution on the xz plane (at y = 0) of the test section remained uniform upon heating. The microfabrication process followed that of [3], except for slight modifications in the channel size and converging-diverging ratio. The relevant geometric size and dimensions are listed in Table 1.…”

“…The flow cell was mounted onto an epifluorescent microscope (IX71/FV300, Olympus, Tokyo, Japan) equipped with a ×40 magnification, NA 0.85 air immersion objective lens, following that described by [3]. The EOF was driven by a high-voltage power supply (PS 350, Stanford Research System, Sunnyvale, CA, USA) to drive the flow, with a slight modification for the flow cell and the flow circulation loop.…”

“…Reservoirs (4 × 4 mm) were cut at each end of the curved PDMS microchannel with a scalpel, and the channels were soaked for 12 h at 45°C in 1× TBE (1× TBE contains, in 1 l, 108 g of Tris base, 55 g of boric acid, and 40 ml of 0.5 M EDTA, pH 8.3) to eliminate permeation-driven flow [3]. …”

“…Both approaches have their own advantages/disadvantages which depend on the particular application. For the former, with fluorescently labeled DNA molecules, it is possible to visualize the change in the conformation of a single DNA molecule under an optical microscope [2,3]. …”