Low Field DNA Electrophoresis


Principal Investigator

P M Saville

Research School of Chemistry

Electrophoresis is a process used to size separatecharged polymer chains, such as proteins and
DNA, by interactions of the chain with the fibres of a gel. Chains get hooked on the gel fibres and are stretched by the electric field, until one side of the hooked chain slips off the fibre. An array of posts can be used to replace the fibres of an electrophoretic gel, with the added advantage of being able to separate large chains by spacing the posts far enough apart to allow downfield passage. Post and chain dimensions, impact point, electric field strength and random noise are key factors which determine the mobility of polyelectrolyte chains interacting with a post. By understanding the influence of these factors it will be possible to optimize post-arrays for size separation.
The purpose of this research was to simulate chain-post interactions and investigate the effect of electric field strength, especially in low fields where motion due to random noise becomes comparable to that due to the electric field.


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The simulation of two different length polyelectrolyte chains, colliding with posts, in fields ranging from strong to weak, been completed. The primary effect of field strength is to define the mobility of the unimpeded polyelectrolyte chains. As field strength, E, decreases chain-post collision times increase (Figure 1) and chains which get hooked about a post are not stretched to the same extent. This continues until NE=1 (N is the degree of polymerization) where the chains are no longer stretched. At these field strengths, headon impacts still result in longer collision times than an unimpeded chain, but the distribution in the collision distance is reduced to that of non-interacting chains (ie. the large change in chain mobility due to a collision is lost and so electrophoresis at these field strengths becomes less effective).

This work forms a part of a study looking at the effect of post size, field strength and random noise on the collision time of chains with a post. Future work is directed towards the consequences of chains passing between two closely spaced posts, or through a pore which acts as a bottleneck to chain mobility.

Appendix A -




Figure 1

Figure 2        
- Appendix A



What computational techniques are used?

The polyelectrolyte is modelled as a freely draining chain consisting of a two-dimensional random walk of N freely jointed beads connected by springs with bond lengths picked randomly from a gaussian distribution about a mean length a. There is an effective charge per unit length of l and the solution viscosity is h. The post is modelled as a hard core of radius hr surrounded by a soft repulsive region from hr to rr (Figure 2). The force in this repulsive region falls linearly to zero at rr. The center of mass of the chain is sited at a lateral distance, b (impact parameter), from the center of the post. An electric field of strength E is applied in the z-direction (with the y-direction perpendicular to the field). Bead motion is then in response to the sum of spring, random, repulsive and electric field forces. Chain-post interactions are characterised by the collision distance (the displacement in the z-direction of the center of mass when the first monomer reaches the -rr plane and when the last monomer crosses the hr plane) and the collision time measured over this distance.

Appendix A -