TENSION AND MOBILITY OF A DNA FRAGMENT IN THE LAKES-STRAITS MODEL

We consider numerically, in the framework of the lakes-straits model, the mobility of a DNA chain under field-inversion gel-electrophoresis (FIGE). Here we investigate the role of the gel's structure on the mob ility. We consider two situations: (i) a DNA chain fragment is bounded by two straits (narrow gateways) al a fixed distance, but is otherwis e free, and (ii) the fragment is, in addition, confined within a close d volume (pore). We calculate the tension on the DNA fragment in the t wo cases. For Gaussian chains we evaluate the corresponding statistica l weights exactly, using a cellular automation algorithm. We find that the resulting tension differs drastically in the two models considere d. Nonetheless this difference influences only weakly the overall FIGE mobility.