In the presence of subunit A inhibitors DNA gyrase cleaves DNA fragments as short as 20 bp at specific sites

Nucleic Acids Res. 1997 Feb 1;25(3):604-11. doi: 10.1093/nar/25.3.604.


A key step in the supercoiling reaction is the DNA gyrase-mediated cleavage and religation step of double-stranded DNA. Footprinting studies suggest that the DNA gyrase binding site is 100-150 bp long and that the DNA is wrapped around the enzyme with the cleavage site located near the center of the fragment. Subunit A inhibitors interrupt this cleavage and resealing cycle and result in cleavage occurring at preferred sites. We have been able to show that even a 30 bp DNA fragment containing a 20 bp preferred cleavage sequence from the pBR322 plasmid was a substrate for the DNA gyrase-mediated cleavage reaction in the presence of inhibitors. This DNA fragment was cleaved, although with reduced efficiency, at the same sites as a 122 bp DNA fragment. A 20 bp DNA fragment was cleaved with low efficiency at one of these sites and a 10 bp DNA fragment was no longer a substrate. We therefore propose that subunit A inhibitors interact with DNA at inhibitor-specific positions, thus determining cleavage sites by forming ternary complexes between DNA, inhibitors and DNA gyrase.

MeSH terms

  • Benzimidazoles / chemistry
  • Benzimidazoles / pharmacology
  • Binding Sites
  • Calcium / pharmacology
  • Ciprofloxacin / chemistry
  • Ciprofloxacin / pharmacology
  • Fleroxacin / chemistry
  • Fleroxacin / pharmacology
  • Magnesium / pharmacology
  • Molecular Structure
  • Plasmids / metabolism*
  • Pyrimidines / chemistry
  • Pyrimidines / pharmacology
  • Topoisomerase II Inhibitors*


  • Benzimidazoles
  • Pyrimidines
  • Topoisomerase II Inhibitors
  • Ro 47-3359
  • Ciprofloxacin
  • Magnesium
  • Fleroxacin
  • Calcium