Use about 150 ml of a mid-log culture, depending on the number of plugs required. If a CHEF apparatus is used then a 3 day run is sufficient. Ethidium bromide is used to stain the gels after running. Cla I site which would not normally be cut. Different restriction enzymes have differing abilities to restrict genomic DNA, which tends to be more aggregated and contain more protein.
Partial digestion can then become a problem.
Complete digestion of the DNA will produce a banding pattern characteristic of the restriction enzyme being used, due to multiple copies of the mitochondrial rRNA genes. This means that it is difficult to strip off the probe, so if rehybridisation is anticipated it may be better to use GeneScreen. Photograph the gel alongside a ruler, at the usual UV wavelength. Place the membrane on top of the gel, followed by the two pieces of 3MM paper which have been cut to the same size. Finally add the paper towels on top to make a stack and weigh down with approximately 500 g. Leave overnight to transfer.