NSTI Nanotech 2009

Microchip-based Investigation of the Interplay Between the Nanoporous Gel Morphology and the Onset of Entropic Trapping in DNA Gel Electrophoresis

N. Shi, V.M. Ugaz
Texas A&M University, US

Keywords: microfluidics, electrophoresis, DNA

Abstract:

Miniaturized DNA electrophoresis devices pose unique design challenges that arise from the need to exert increasingly precise and reproducible control over all aspects of the process to optimize separation performance over ultra-short distances. The properties of the sieving gel matrix are particularly important because its nanoscale pore morphology plays a key role in directing DNA migration. Here we explore this interplay in photopolymerized crosslinked polyacrylamide gels by combining a versatile microfluidic platform that allows continuous monitoring of DNA separation progress so that the size dependence of mobility and diffusion coefficients can be established with a unique combination of methods that enable both the mean pore size and pore size distribution of the gel to be quantified. This innovative approach allows us to identify how polymerization conditions (i.e., UV intensity during photopolymerization) influence the gel pore size distribution, and ultimately shape overall separation performance. Analysis of double-stranded DNA separations in the size range below 1 kb reveals that varying the rate of photopolymerization induces a corresponding change in the physical mechanism of DNA migration between reptation and entropic trapping. We then develop an interpretation of these observations based on the distribution of pore sizes and their arrangement within the gel matrix. These measurements can provide new insights that can help enable rational selection of optimal matrix materials and polymerization conditions that provide enhanced separation performance.
 
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