After lysis of the cells (typically 1 to 2 hours at 4 °C) the slides are washed in distilled water to remove all salts and immersed in a second solution – an electrophoresis solution. Again this solution can have its pH adjusted depending upon the type of damage that is being investigated.
The slides are left for ~20 minutes in the electrophoresis solution prior to an electric field being applied. In alkaline conditions the DNA double helix is denatured and the nucleoid becomes single stranded.
An electric field is applied (typically 1 V/cm) for ~20 minutes. The slides are then neutralised to pH 7, stained with a DNA-specific fluorescent stain and analysed using a microscope with an attached CCD (charge-coupled device – essentially a digital camera) that is connected to a computer with image analysis software.