A technique for the detection of large DNA alterations in complex genomes

As part of our effort to understand the chromosomal organization of streptomycetes, we have developed a method for detecting large alterations in the DNA, in particular to visualize insertions, transpositions, and deletions. The method involves the labeling of the DNA of two strains with [ 3H]thymidine or [ 14C]thymidine, extraction and purification of the DNA, digestion with restriction endonucleases, and one-dimensional agarose gel electrophoresis of the two samples in the same slot. Following electrophoresis, the gel is cut into thin slices, and the 14C 3H ratio is measured in each slice. Deviations from the average standard ratio are caused by differences in the restriction site arrangement in the DNA of the two strains, which may be caused by rearrangements in the DNA. The method has a high resolution of one restriction fragment change.