DNA electrophoresis in microfluidic post arrays under moderate electric fields

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Abstract

The dynamics of long DNA moving through microfluidic arrays of micron-sized posts under a moderate electric field are modeled by a Scher-Lax continuous-time random walk. The microscale model consists of a repetitive sequence of three steps: (i) collision with the post and extension into two arms, (ii) electric-field-driven unhooking from the post, and (iii) uniform translation until the next collision. The model features two random variables: the initial offset between the two arms of the polymer during a given collision and the distance traveled between collisions. For experimentally realistic values of the electric field strength and DNA molecular weight, scaling laws indicate that the chain will generally be in a stem-flower conformation when unhooking from the post. Compared to a taut-chain model at the same field strength, the stem-flower conformation reduces the time engaged with the post and increases the collision frequency. Analytical expressions for the mean velocity and dispersivity are derived as a function of the post density, post spacing, free-solution mobility, Kuhn length, and sequence length. The incomplete extension of the chain does not strongly affect the mean velocity, but tends to increase the dispersivity relative to a taut chain. As a result, the separation resolution decreases as the field decreases for a moderate field, in agreement with experiments. The quantitative agreement between the model and experimental data is satisfactory, especially considering that the model contains no adjustable parameters.

Original languageEnglish (US)
Article number061922
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume73
Issue number6
DOIs
StatePublished - Jul 10 2006

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