I am going to fabricate a free flow electrophoresis (FFE) chamber. The chamber will contains the sample plus buffers (electrolytes). In capillary electrophoresis, IEF or gel-based electrophoresis the electrodes are in touch with buffers, because in those systems usually there is no external forces/pumps for buffer movement and electrochemical current needs to enforce the ions separation in designed direction that may not be straight.
However, in (FFE) system the buffer flow will be carried out by external pump and the electrical repulsion will be applied in perpendicular of sample flow which both are in a straight direction. So, is it also necessary in free-flow electrophoresis system that the electrodes be in touch with liquids (buffers) or not? in the other words, if the anode/cathode electrodes doesn't be in touch with buffer, the electric field/potential is still there and it could pushes the ionic particles in a straight direction towards opposite poles, is it true?
Electrodes should always be in touch with the (buffered) liquids or else there will be no current possible, hence no electrophoretic movement. You may use a filter or semipermiable device to separate the electrode conpartment from the electrophoresis buffer. Take care that the buffer in the electrode compartment is exact the same as in the adjacent separation compartment.
Check commercial equipment how your punp could be isolated.
Jos P M Wielders is right, you need to close the electrical circuit. The current flowing depends on voltage applied, conductivity of the buffer and geometry of the chamber (cross-section and distance between electrodes). This is important as the electrical power (voltage times current) is converted to heat, which has to be dissipated. That is why the salt content of your sample should be as low as possible.
If you build your own equipment, have an electrician (and your safety officer, if applicable) advise you on safety. High voltages and high conductivity buffers are not to be trifled with!
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