Barriers against DNA-loop formation in a porous matrix

The resistance towards DNA bending imposed by a porous matrix has been investigated by studying the rate of helix-loop penetration through agarose gel pores as driven by electric fields between 1.1 and 6.7 V/cm. YOYO-stained DNA molecules (680 kilo-base-pairs) were prepared in a well-defined globally oriented state by an electrophoretic procedure (YOYO denotes dimer of oxazole-yellow). Loop initiation by a field perpendicular to the global orientation was detected by linear dichroism (LD) spectroscopy in terms of an initial net helix orientation perpendicular to the applied held direction, reflecting the stretching of the chain between the loopholes by the initial growth of the comparatively weakly oriented loop heads. The rate of loop nucleation exhibits a strong field dependence in agreement with a model based on the entropy cost of loop formation. The effect of increasing the average pore radius from 0.7 to 3 P, where P is the persistence length of DNA (500 Angstrom), is significantly weaker than predicted from the model, however. After initially being perpendicular, the net helix orientation is eventually along the field direction, and during this phase the LD exhibits several oscillations before reaching a steady state. By comparison with fluorescence microscopy observations on individual molecules under identical conditions the LD oscillations are identified in terms of loop growth and competition. The spectroscopically measured average rates of these later loop processes exhibit considerably weaker held dependence than loop nucleation, and with power-law dependencies (E(1.2-2)) in agreement with the DNA coils being stretched by electrophoretic transport of the polymer ends.