(266b) Dynamics of Single DNA Molecules During Electrophoresis in a Microfabricated Post Array

Using epifluorescence video microscopy, we studied the dynamics of single molecules of lambda-DNA during electrophoresis in a regular hexagonal array of 1 micron diameter oxidized silicon posts. We used custom software to track the two-dimensional projection of the molecule, the center of mass, and the total intensity of the molecule in each video frame as it travels through the array. Using the output of our tracking program, we can automatically identify DNA-post collisions and thus study a relatively large ensemble of events. We found that the distance between collisions follows a log-normal distribution, in contrast to existing models of DNA transport in post arrays. For each collision, we measured the collision hold-up time, defined as the delay of the translation of the center of mass of the molecule. The distribution of hold-up times in our system is similar to what is found in BD simulations and experiments in magnetic post arrays. Using the latter data sets, we also confirmed the common assumption that collision events are independent from one another by showing that the holdup times and distance between consecutive collisions are uncorrelated. From the distribution of velocities of the molecules we are also able to calculate a dispersion coefficient for the ensemble of molecules. We find that dispersion in the post array has three sources: (i) molecular diffusion, (ii) rope-over pulley collisions and unhooking, and (iii) fluctuations in the in-array velocity caused by the geometry of the post array.