Stretching DNA by electric field and flow field in microfluidic devices: An experimental validation to the devices designed with computer simulations

Abstract

We examined the performance of three microfluidic devices for stretching DNA. The first device is a microchannel with a contraction, and the remaining two are the modifications to the first. The modified designs were made with the help of computer simulations [C. C. Hsieh and T. H. Lin, Biomicrofluidics 5(4), 044106 (2011) and C. C. Hsieh, T. H. Lin, and C. D. Huang, Biomicrofluidics 6, 044105 (2012)] and they were optimized for operating with electric field. In our experiments, we first used DC electric field to stretch DNA. However, the experimental results were not even in qualitative agreement with our simulations. More detailed investigation revealed that DNA molecules adopt a globular conformation in high DC field and therefore become more difficult to stretch. Owing to the similarity between flow field and electric field, we turned to use flow field to stretch DNA with the same devices. The evolution patterns of DNA conformation in flow field were found qualitatively the same as our prediction based on electric field. We analyzed the maximum values, the evolution and the distributions of DNA extension at different Deborah number in each device. We found that the shear and the hydrodynamic interaction have significant influence on the performance of the devices. V C 2013 American Institute of Physics.

Collapse of DNA under alternating electric fields

“…13–17 Collapse can be brought about both by a.c. and d.c. electric fields. Furthermore, a series of prior observations is consistent with the notion that polyelectrolytes should collapse beyond a certain critical electric field strength.…”

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface

“…Dynamic stretching utilizes the dynamic field or field gradient to unravel the DNA molecule in free solution and polymer-enhanced or porous medium. The field could be electric (DC and AC), 3-10 hydrodynamic, 2,[11][12][13][14] or combination of both. 15 DNA anchoring stretches tethered DNA by using external forces.…”

Polyelectrolyte in Electric Field: Disparate Conformational Behavior along an Aminopolysaccharide Chain

“…A more recent study using single-molecule fluorescence microscopy, however, showed that the bacterial phage T4 DNA becomes significantly more compact under a DC electric field and becomes a globule at a field strength of 250 V/cm or 2.5 × 10 –2 mV/nm . Similar observation was made in microfluidic experiments . The collapse of λ-DNA was also observed under AC electric fields at sufficiently high strength using fluorescence microscopy, , and the authors suggested that the earlier observation of DNA stretching was due to an artifact of video microscopy.…”

“…Comparison to Experiments and Theories of PE Chain Conformations in Electric Field. Single-molecule fluorescence microscopy 26 and microfluidic experiments 27 demonstrated that DNAs become compact under large electric fields. The backbone bending showed by our simulations of the 5-mer and 20-mer chitosan chains is consistent with these experiments.…”

“…26 Similar observation was made in microfluidic experiments. 27 The collapse of λ-DNA was also observed under AC electric fields at sufficiently high strength using fluorescence microscopy, 28,29 and the authors suggested that the earlier observation of DNA stretching was due to an artifact of video microscopy. However, the authors also noted that when the field strength was further increased above 1220 V/cm or 0.122 mV/nm, the DNA appeared to elongate in the direction of electric field.…”