The comet assay is frequently used to measure DNA damage in individual cells. In 
order to better understand the mechanisms behind the technique, we have studied 
the behaviour of DNA under different electrophoresis conditions in mammalian 
cells exposed to gamma radiation. The comet tails obtained after neutral 
electrophoresis seem to consist of DNA loops which are attached to structures in 
the nucleus, since the DNA cannot move in the second direction after 
two-dimensional electrophoresis. When the DNA is labelled by a short pulse, 
microautoradiography reveals that all label appear in the head of the comets 
when neutral electrophoresis is applied. After chase incubation, the label moves 
out into the tails. This gives further support to the view that the DNA loops 
are fixed to some structure in the nucleus where also the DNA synthesis takes 
place. Under alkaline electrophoresis conditions, however, the entire comet 
tails move in the new electrophoresis direction. Thus, it appears that the 
alkaline comet tails consist of free DNA fragments. Further, the effects of 
alkaline concentration and sodium chloride during unwinding and electrophoresis 
are discussed. Throughout the study, a protocol for drying and fixation of the 
comets has been used.