Transverse imaging and simulation of dsDNA electrophoresis in microfabricated glass channels

We have observed the non-uniform distribution of DNA molecules during PAGE in a microfabricated system. Confocal laser scanning microscopy was used to visualize fluorescently labeled DNA during electrophoretic migration. The distribution of double-stranded DNA larger than 100 bp is observed to transition from a center-biased motion on the transverse plane 1 cm downstream from injection to an edge-biased motion 2 cm downstream. Although this distribution increased with increasing dsDNA size in a cross-linked gel, no similar distribution was found with the same dsDNA molecules in a linear polyacrylamide solution (6%). Simulations of DNA distribution in gels suggest that DNA distribution non-uniformities may be caused by biased electrophoretic migration resulting from motion in an inhomogeneous gel system.