Imaging cross-section of DNA electrophoresis in a microfabricated glass device with CLSM

In this paper, confocal laser scanning microscopy (CLSM) is used to detect and analyze DNA electrophoretic migration in a microchannel filled with in-situ polymerized cross-linked polyacrylamide. DNA distribution at the cross-section of the microchannel is observed to vary only slightly with the tested gel concentrations and the DNA sizes. However, in comparing with DNA electrophoresis using linear polymer solution (LPA), significant differences are observed in the distribution of DNA molecules on the observation plane using a cross-linked matrix (UV-polymerized polyacrylamide). Instead of a uniform signal boost upon the pass of one DNA band in linear polymer matrix, the electrophoretic process with cross-linked polyacrylamide presents a cross-section image with most DNA molecules aggregate near the vertical center of the microchannel during migration. This observation suggests an inhomogeneous nanostructure of in-situ polymerized cross-linked polyacrylamide in a microfabricated glass channel, consistent with SEM results. However, the phenomenon of DNA bands tending to focus in the vertical center along z-axis has not been previously reported. We also conclude from these observations that geometries containing fewer dead corners are desirable to minimize residual DNA in the microchannel.