The experimental procedure first requires a sample of purified plasmid DNA for each digest to be run. Digestion is then performed with each enzyme(s) chosen. The resulting samples are subsequently run on an electrophoresis gel, typically on agarose gel.
The first step following the completion of electrophoresis is to add up the sizes of the fragments in each lane. The sum of the individual fragments should equal the size of the original fragment, and each digest's fragments should also sum up to be the same size as each other. If fragment sizes do not properly add up, there are two likely problems. In one case, some of the smaller fragments may have run off the end of the gel. This frequently occurs if the gel is run too long.   A second possible source of error is that the gel was not dense enough and therefore was unable to resolve fragments close in size.  This leads to a lack of separation of fragments which were close in size. If all of the digests produce fragments that add up one may infer the position of the REN (restriction endonuclease) sites by placing them in spots on the original DNA fragment that would satisfy the fragment sizes produced by all three digests