A novel method was used to characterize the long range susceptibility of Schizosaccharomyces pombe chromosomal DNA to endogenous endonuclease cleavage. Analyses of pulsed field gel experiments revealed two periodicities in the distribution of endogenous endonuclease hypersensitive sites. Endonuclease cleavage sites occurred, roughly at 30-509 kilobase pairs (kb) intervals under physiological conditions (25 mM KCl). At higher salt concentrations (250 mM KCl or 0.2 M and 0.9 M NaCl), endonuclease hypersensitive sites occurred at 200-300 kb intervals. Endonuclease hypersensitive sites in different chromosomal regions were monitored during different stages of the cell cycle. DNA sequencing around the endonuclease hypersensitive sites revealed the presence of clusters of A+T-rich motifs, autonomously replicating sequences (ARSs) in sequences (a characteristic of the scaffold-associated regions (SARs) and the presence of a CTG trinucleotide at most sites.