Onset of channeling during DNA electrophoresis in a sparse ordered post array.

Biomicrofluidics
Jia OuKevin D Dorfman

Abstract

The "channeling hypothesis" of DNA electrophoresis in sparse, ordered arrays of posts predicts that the DNA will move through the array relatively unhindered if (i) the spacing between the posts is larger than the DNA coil and (ii) the electric field lines are straight. We tested this hypothesis by studying the electrophoretic separation of a small plasmid DNA (pUC19, 2686 base pairs) and a large, linear DNA (lambda-DNA, 48 500 base pairs) in a hexagonal array of 1 mum diameter posts with a pitch of 7 mum. At low electric field strengths, these DNAs are separated due to the long-lived, rope-over-pulley collisions of lambda-DNA with the posts. The resolution is lost as the electric field increases due to the onset of channeling by the lambda-DNA. Using a diffusive model, we show that channeling arises at low electric fields due to the finite size of the array. This channeling is not intrinsic to the system and is attenuated by increasing the size of the array. Higher electric fields lead to intrinsic channeling, which is attributed to the disparate time scales for a rope-over-pulley collision and transverse diffusion between collisions. The onset of channeling is a gradual process, in agreement with extant Brownian dynamics simu...Continue Reading

References

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Aug 8, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Jia OuKevin D Dorfman

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Citations

Nov 8, 2014·Biomicrofluidics·Joel D P Thomas, Kevin D Dorfman
Nov 8, 2014·Biomicrofluidics·Lingling Wu, Stephen Levy
Mar 6, 2012·Lab on a Chip·Sung-Gyu ParkKevin D Dorfman
Jul 31, 2013·Lab on a Chip·Joel D P ThomasKevin D Dorfman
Jul 24, 2010·Journal of Chromatography. a·Jaeseol Cho, Kevin D Dorfman
Feb 23, 2018·Lab on a Chip·Pranav AgrawalKevin D Dorfman
Oct 5, 2017·Electrophoresis·Matthew C VandeSandeHendrick W de Haan
Jul 23, 2013·Electrophoresis·Zhen Chen, Kevin D Dorfman
Dec 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Daniel W Olson, Kevin D Dorfman

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Methods Mentioned

BETA
electrophoresis
chip
scanning electron microscopy
chips

Software Mentioned

LABVIEW

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