Effect of netropsin, distamycin A and chromomycin A3 on the binding and cleavage reaction of DNA gyrase

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Abstract
The influence of netropsin (Nt), distamycin A (Dst‐3) and chromomycin A3 (CHR) on the binding of gyrase from Streptomyces noursei to an 162 bp‐fragment of pBR 322 containing a strong gyrase cleavage site and on the gyrase mediated cleavage of this fragment was analyzed. Binding of the enzyme to the fragment is effectively inhibited by the GC‐specific drug CHR, but poorly influenced by Dst‐3, while Nt is ineffective. Cleavage of the fragment catalysed by the enzyme is inhibited by all three ligands but to different extent. Dst‐3 and Nt inhibit the enzyme cleavage reaction at 20‐ or 250‐fold higher concentration than that required for CHR. The inhibitory mechanism of CHR on gyrase‐DNA binding and cleavage may be related to a competitive interaction of the ligand to GC sequences located at and around the gyrase cleavage site. The fact that AT‐specific minor groove binders Dst‐3 and Nt poorly inhibit the binding of gyrase to the fragment due to the low amount of the AT basepair sequences contained in the fragment and their inhibitory influence on the cleavage step underlines the role of the DNA minor groove during enzyme action.