DNA gyrase can cleave short DNA fragments in the presence of quinolone drugs

We have analysed the DNA cleavage reaction of DNA gyrase using oligonucleotides annealed to a singlestranded M13 derivative containing a preferred gyrase cleavage site. We find that gyrase can cleave duplexes down to ∼20 bp in size in the presence of the quinolone drugs ciprofloxacin and oxolinic acid. Ciprofloxacin shows a variation in its site specificity with an apparent preference for G bases adjacent to the cleavage sites, whereas oxolinic acid stimulates cleavage predominantly at the previously determined site. With either drug, cleavage will not occur within 6 bases from the end of a DNA duplex or a nick. We suggest that cleavage site specificity with short DNA duplexes is determined by drug-DNA interactions whereas with longer fragments the positioning effect of the DNA wrap around gyrase prescribes the site of cleavage.