Tube leakage during electrophoresis retards reptating DNA in unmodified and hydroxyethylated agarose gels

The resistance towards DNA-loop formation is considerably higher in 2% hydroxyethylated agarose gels (average pore radius PE=380 {}) than in 1% ordinary agarose gel (PE=1000 {}) [B. {}kerman, preceding paper, Phys. Rev. E 54, 6685 (1996)]. This is exploited here to study how DNA-loop formation affects the electrophoretic migration of native $T2$-DNA in agarose gels between 0.5 and 25 V/cm. Linear dichroism (LD) spectroscopy shows that the migration is cyclic in nature in both gels, but the period time is 30% longer in the hydroxyethylated gel at high fields, indicating a 30% higher tube friction coefficient than in unmodified agarose. Together with an observed reduced tube orientation, as expected from the smaller pores according to reptation theory, this explains why the electrophoretic mobility is lower than in unmodified agarose at all fields. Analysis of the field-free decay of the LD shows that in both gels the degree of electrophoretic stretching of the molecules along the path in the gel increases and saturates with increasing field in parallel with the mobility. However, the field enhancement of the mobility occurs for lower fields in the hydroxyethylated agarose because there are fewer loops to be consumed by the stretching in this gel. This observation supports that the loops contribute to the resistance towards migration at intermediate fields.