A microfluidic study of mechanisms in the electrophoresis of supercoiled DNA

Abstract

In this work, microfluidic chips were used to study the electrophoresis of supercoiled DNA (SC DNA) in agarose. This system allowed us to study the electrophoretic and trapping behaviours of SC DNA of various lengths, at various fields and separation distances. Near a critical electric field the DNA is trapped such that the concentration falls exponentially with distance. The trapping of such circular DNA has been explained in terms of the 'lobster trap' or 'impalement' model where shorter fibres become trapping sites at higher fields, leading to an ongoing (and gradual) increase in trapping with increasing field. By contrast, the present study suggests that under some circumstances the traps have a barrier such that only when the DNA has sufficient energy (at high enough fields) can it become trapped, leading to a sudden transition in behaviours at the critical field. We propose an 'activated impalement' mechanism of trapping in which only at sufficiently high fields is the SC DNA impaled and trapped for long times. The critical electric field appears to be inversely proportional to the length of the DNA molecule, suggesting that the force required to impale the SC DNA is constant.