Analysis of the breaking sites in the physical degradation of DNA

The 3'-termini of procaryotic and eucaryotic DNA fragments obtained by shearing, sonication and irradiation have been analyzed. Analysis of the 3'-ends of DNA fragments was done by 32-P-labeling with terminal transferase, hydrolysis of products by spleen DNAase and spleen exonuclease and separation of labeled 3'-terminal nucleotides on polyethyleneimine plates. In the case of sonication the deviation from DNA base composition of 3'-terminal nucleotides is very close to random for Escherichia coli and Haemophilius influenzae DNA, whereas for calf thymus, mouse and yeast mitochondrial DNAs a significant increase in dA and decrease in dC was observed. Shearing at high salt released random 3'-termini in E. coli DNA and 3'-termini with 4 to 6% deviation from base composition in calf thymus DNA. In the case of gamma-irradiation no real differences have been found between E. coli and calf thymus DNA and 3'-terminal nucleotide composition is very close to random. Mechanical breakage of eucaryotic DNA seems to release 3'-termini having a composition which differs slightly but significantly from the average base composition of the DNA.