DNA migration and separation on surfaces with a microscale dielectrophoretic trap array.

We studied the surface migration of DNA chains driven by a dc electric field across localized dielectrophoretic traps. By adjusting the length scale of the trap array, separation of a selected band of DNA was accomplished with a scaling exponent between mobility and number of base pairs similar to that obtained in capillary electrophoresis. We then provided a model, which predicts the trapping and extension of DNA chains at a dielectrophoretic trap responsible for the surface mobility and separation.

Influence of electric field intensity, ionic strength, and migration distance on the mobility and diffusion in DNA surface electrophoresis.

In order to increase the separation rate of surface electrophoresis while preserving the resolution for large DNA chains, e.g., genomic DNA, the mobility and diffusion of Lambda DNA chains adsorbed on flat silicon substrate under an applied electric field, as a function of migration distance, ionic strength, and field intensity, were studied using laser fluorescence microscope. The mobility was found to follow a power law with the field intensity beyond a certain threshold. The detected DNA peak width was shown to be constant with migration distance, slightly smaller with stronger field intensity, but significantly decreased with higher ionic strength. The molecular dynamics simulation demonstrated that the peak width was strongly related with the conformation of DNA chains adsorbed onto surface. The results also implied that there was no diffusion of DNA during migration on surface. Therefore, the Nernst-Einstein relation is not valid in the surface electrophoresis and the separation rate could be improved without losing resolution by decreasing separation distance, increasing buffer concentration, and field intensity. The results indicate the fast separation of genomic DNA chains by surface electrophoresis is possible.

Drying of DNA droplets.

The evaporation kinetics of droplets containing DNA was studied, as a function of DNA concentration. Drops containing very low DNA concentrations dried by maintaining a constant base, whereas those with high concentration dried with a constant contact angle. To understand this phenomenon, the distribution of the DNA inside the droplet was measured using confocal microscopy. The results indicated that the DNA was condensed mostly on the surface of the droplets. In the case of high concentration droplets, it formed a shell, whereas isolated islands were found for droplets of low DNA concentrations. Rheologic results indicate the formation of a hydro gel in the low concentration drops, whereas phase separation between the self-assembled DNA structures and the water phase occurred at higher concentration.

DNA separation at a liquid-solid interface.

We demonstrate that it is possible to separate a broad band of DNA on a solid substrate without topological obstacles. The mobility was found to scale with molecular size (N) as N(-0.25), while the resolution scaled as N(0.75) indicating that diffusivity on this substrate was minimal. By varying the buffer concentration we were able to show that the mobility for a given chain length scaled with the persistent length (p) as p(1/2). This could be shown to be related to the Gaussian conformation of the chains adsorbed on the surface. A two-dimensional corrugated surface of nonporous silica beads was produced using a self-assembling process at the air/water interface. Even though the surface corrugations were comparable to persistence length we show that they do not affect the mobility, indicating that surface friction rather than topological constraints are the predominant mechanism of separation on a surface.